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slurm-2557978.out

slurm-2557978.out 38 KB
Cronologia Originale

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  1. WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40': destination is already in the mount point list
    2. 

  2. 

  3. [COMMAND] /opt/bin/run_clairs --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --platform ont_r10_dorado_sup_5khz_ssrs --output_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40 --region chr9:55624206-150617247 --sample_name CHAHA_diag --include_all_ctgs --print_germline_calls --enable_indel_calling --enable_clair3_germline_output --use_longphase_for_intermediate_haplotagging True 
    4. 

  4. 

  5. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs
    6. 

  6. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp
    7. 

  7. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/split_beds
    8. 

  8. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/candidates
    9. 

  9. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/pileup_tensor_can
    10. 

  10. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/fa_tensor_can
    11. 

  11. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/vcf_output
    12. 

  12. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/tmp_vcf_output
    13. 

  13. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log
    14. 

  14. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output
    15. 

  15. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/vcf
    16. 

  16. [INFO] --include_all_ctgs enabled
    17. 

  17. [INFO] Call variants in contigs: chr9
    18. 

  18. [INFO] Number of chunks for each contig: 31
    19. 

  19. 

  20. [INFO] CALLER VERSION: 0.4.4
    21. 

  21. [INFO] NORMAL BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
    22. 

  22. [INFO] TUMOR BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
    23. 

  23. [INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
    24. 

  24. [INFO] PLATFORM: ont_r10_dorado_sup_5khz_ssrs
    25. 

  25. [INFO] THREADS: 40
    26. 

  26. [INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40
    27. 

  27. [INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/output.vcf.gz
    28. 

  28. [INFO] PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/pileup.pkl
    29. 

  29. [INFO] FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/full_alignment.pkl
    30. 

  30. [INFO] BED FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/region.bed
    31. 

  31. [INFO] GENOTYPING MODE VCF FILE PATH: None
    32. 

  32. [INFO] HYBRID MODE VCF FILE PATH: None
    33. 

  33. [INFO] REGION FOR CALLING: chr9:55624206-150617247
    34. 

  34. [INFO] CONTIGS FOR CALLING: None
    35. 

  35. [INFO] CONDA BINARY PREFIX: /opt/conda/envs/clairs
    36. 

  36. [INFO] SAMTOOLS BINARY PATH: samtools
    37. 

  37. [INFO] PYTHON BINARY PATH: python3
    38. 

  38. [INFO] PYPY BINARY PATH: pypy3
    39. 

  39. [INFO] PARALLEL BINARY PATH: parallel
    40. 

  40. [INFO] LONGPHASE BINARY PATH: /opt/conda/envs/clairs/bin/longphase
    41. 

  41. [INFO] CHUNK SIZE: 5000000
    42. 

  42. [INFO] SNV MINIMUM AF: 0.05
    43. 

  43. [INFO] SNV MINIMUM QUAL: 8
    44. 

  44. [INFO] INDEL MINIMUM AF: 0.1
    45. 

  45. [INFO] INDEL PILEUP MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/pileup.pkl
    46. 

  46. [INFO] INDEL FULL-ALIGNMENT MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/ont_r10_dorado_sup_5khz_ssrs/indel/full_alignment.pkl
    47. 

  47. [INFO] INDEL MINIMUM QUAL: 8
    48. 

  48. [INFO] NORMAL VCF FILE PATH: None
    49. 

  49. [INFO] DISABLE PHASING: False
    50. 

  50. [INFO] ENABLE DRY RUN: False
    51. 

  51. [INFO] ENABLE INDEL CALLING: True
    52. 

  52. [INFO] ENABLE PRINTING REFERENCE CALLS: False
    53. 

  53. [INFO] ENABLE PRINTING GERMLINE CALLS: True
    54. 

  54. [INFO] ENABLE INCLUDING ALL CTGS FOR CALLING: True
    55. 

  55. [INFO] ENABLE REMOVING INTERMEDIATE FILES: False
    56. 

  56. 

  57. [INFO] Call Germline Variants in Normal BAM using Clair3
    58. 

  58. [INFO] RUN THE FOLLOWING COMMAND:
    59. 

  59. ( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output --ctg_name=chr9 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log/1_CLAIR3_NORMAL.log
    60. 

  60. 

  61. [INFO] CLAIR3 VERSION: v1.0.8
    62. 

  62. [INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam
    63. 

  63. [INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
    64. 

  64. [INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
    65. 

  65. [INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output
    66. 

  66. [INFO] PLATFORM: ont
    67. 

  67. [INFO] THREADS: 40
    68. 

  68. [INFO] BED FILE PATH: EMPTY
    69. 

  69. [INFO] VCF FILE PATH: EMPTY
    70. 

  70. [INFO] CONTIGS: chr9
    71. 

  71. [INFO] CONDA PREFIX: 
    72. 

  72. [INFO] SAMTOOLS PATH: samtools
    73. 

  73. [INFO] PYTHON PATH: python3
    74. 

  74. [INFO] PYPY PATH: pypy3
    75. 

  75. [INFO] PARALLEL PATH: parallel
    76. 

  76. [INFO] WHATSHAP PATH: whatshap
    77. 

  77. [INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
    78. 

  78. [INFO] CHUNK SIZE: 5000000
    79. 

  79. [INFO] FULL ALIGN PROPORTION: 0.7
    80. 

  80. [INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
    81. 

  81. [INFO] PHASING PROPORTION: 0.7
    82. 

  82. [INFO] MINIMUM MQ: 5
    83. 

  83. [INFO] MINIMUM COVERAGE: 4
    84. 

  84. [INFO] SNP AF THRESHOLD: 0.08
    85. 

  85. [INFO] INDEL AF THRESHOLD: 0.15
    86. 

  86. [INFO] BASE ERROR IN GVCF: 0.001
    87. 

  87. [INFO] GQ BIN SIZE IN GVCF: 5
    88. 

  88. [INFO] ENABLE FILEUP ONLY CALLING: False
    89. 

  89. [INFO] ENABLE FAST MODE CALLING: False
    90. 

  90. [INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
    91. 

  91. [INFO] ENABLE PRINTING REFERENCE CALLS: False
    92. 

  92. [INFO] ENABLE OUTPUT GVCF: False
    93. 

  93. [INFO] ENABLE HAPLOID PRECISE MODE: False
    94. 

  94. [INFO] ENABLE HAPLOID SENSITIVE MODE: False
    95. 

  95. [INFO] ENABLE INCLUDE ALL CTGS CALLING: False
    96. 

  96. [INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
    97. 

  97. [INFO] ENABLE REMOVING INTERMEDIATE FILES: False
    98. 

  98. [INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
    99. 

  99. [INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
    100. 

  100. [INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
    101. 

  101. [INFO] ENABLE HAPLOTAGGING FINAL BAM: False
    102. 

  102. [INFO] ENABLE LONG INDEL CALLING: False
    103. 

  103. [INFO] ENABLE C_IMPLEMENT: True
    104. 

  104. 

  105. + /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr9 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
    106. 

  106. 

  107. [INFO] Check environment variables
    108. 

  108. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/log
    109. 

  109. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
    110. 

  110. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/merge_output
    111. 

  111. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/phase_output
    112. 

  112. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/gvcf_tmp_output
    113. 

  113. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output
    114. 

  114. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf
    115. 

  115. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_bam
    116. 

  116. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
    117. 

  117. [INFO] Call variant in contigs: chr9
    118. 

  118. [INFO] Chunk number for each contig: 31
    119. 

  119. [INFO] 1/7 Call variants using pileup model
    120. 

  120. Calling variants ...
    121. 

  121. Total processed positions in chr9 (chunk 12/31) : 1257
    122. 

  122. Total time elapsed: 17.96 s
    123. 

  123. Calling variants ...
    124. 

  124. Total processed positions in chr9 (chunk 13/31) : 2641
    125. 

  125. Total time elapsed: 20.38 s
    126. 

  126. Calling variants ...
    127. 

  127. Total processed positions in chr9 (chunk 15/31) : 17476
    128. 

  128. Total time elapsed: 48.85 s
    129. 

  129. Calling variants ...
    130. 

  130. Total processed positions in chr9 (chunk 14/31) : 21538
    131. 

  131. Total time elapsed: 53.60 s
    132. 

  132. Calling variants ...
    133. 

  133. Total processed positions in chr9 (chunk 10/31) : 33522
    134. 

  134. Total time elapsed: 78.54 s
    135. 

  135. Calling variants ...
    136. 

  136. Total processed positions in chr9 (chunk 11/31) : 37053
    137. 

  137. Total time elapsed: 86.05 s
    138. 

  138. Calling variants ...
    139. 

  139. Total processed positions in chr9 (chunk 16/31) : 56455
    140. 

  140. Total time elapsed: 119.76 s
    141. 

  141. Calling variants ...
    142. 

  142. Total processed positions in chr9 (chunk 17/31) : 62283
    143. 

  143. Total time elapsed: 127.62 s
    144. 

  144. Calling variants ...
    145. 

  145. Total processed positions in chr9 (chunk 9/31) : 63514
    146. 

  146. Total time elapsed: 131.78 s
    147. 

  147. Calling variants ...
    148. 

  148. Total processed positions in chr9 (chunk 3/31) : 71362
    149. 

  149. Total time elapsed: 135.99 s
    150. 

  150. Calling variants ...
    151. 

  151. Total processed positions in chr9 (chunk 5/31) : 74395
    152. 

  152. Total time elapsed: 139.66 s
    153. 

  153. Calling variants ...
    154. 

  154. Total processed positions in chr9 (chunk 24/31) : 79394
    155. 

  155. Total time elapsed: 141.54 s
    156. 

  156. Calling variants ...
    157. 

  157. Total processed positions in chr9 (chunk 29/31) : 78305
    158. 

  158. Total time elapsed: 142.68 s
    159. 

  159. Calling variants ...
    160. 

  160. Total processed positions in chr9 (chunk 7/31) : 76859
    161. 

  161. Total time elapsed: 143.38 s
    162. 

  162. Calling variants ...
    163. 

  163. Total processed positions in chr9 (chunk 8/31) : 79476
    164. 

  164. Total time elapsed: 144.97 s
    165. 

  165. Calling variants ...
    166. 

  166. Total processed positions in chr9 (chunk 25/31) : 76301
    167. 

  167. Total time elapsed: 145.07 s
    168. 

  168. Calling variants ...
    169. 

  169. Total processed positions in chr9 (chunk 6/31) : 72961
    170. 

  170. Total time elapsed: 146.47 s
    171. 

  171. Calling variants ...
    172. 

  172. Total processed positions in chr9 (chunk 26/31) : 82443
    173. 

  173. Total time elapsed: 148.27 s
    174. 

  174. Calling variants ...
    175. 

  175. Total processed positions in chr9 (chunk 20/31) : 75744
    176. 

  176. Total time elapsed: 148.83 s
    177. 

  177. Calling variants ...
    178. 

  178. Total processed positions in chr9 (chunk 23/31) : 81576
    179. 

  179. Total time elapsed: 150.46 s
    180. 

  180. Calling variants ...
    181. 

  181. Total processed positions in chr9 (chunk 2/31) : 77468
    182. 

  182. Total time elapsed: 151.04 s
    183. 

  183. Calling variants ...
    184. 

  184. Total processed positions in chr9 (chunk 4/31) : 76648
    185. 

  185. Total time elapsed: 151.73 s
    186. 

  186. Calling variants ...
    187. 

  187. Total processed positions in chr9 (chunk 22/31) : 81615
    188. 

  188. Total time elapsed: 154.06 s
    189. 

  189. Calling variants ...
    190. 

  190. Total processed positions in chr9 (chunk 19/31) : 78752
    191. 

  191. Total time elapsed: 154.05 s
    192. 

  192. Calling variants ...
    193. 

  193. Total processed positions in chr9 (chunk 28/31) : 79687
    194. 

  194. Total time elapsed: 155.51 s
    195. 

  195. Calling variants ...
    196. 

  196. Total processed positions in chr9 (chunk 18/31) : 77860
    197. 

  197. Total time elapsed: 155.64 s
    198. 

  198. Calling variants ...
    199. 

  199. Total processed positions in chr9 (chunk 27/31) : 81764
    200. 

  200. Total time elapsed: 157.11 s
    201. 

  201. Calling variants ...
    202. 

  202. Total processed positions in chr9 (chunk 1/31) : 85324
    203. 

  203. Total time elapsed: 159.15 s
    204. 

  204. Calling variants ...
    205. 

  205. Total processed positions in chr9 (chunk 30/31) : 88072
    206. 

  206. Total time elapsed: 162.12 s
    207. 

  207. Calling variants ...
    208. 

  208. Total processed positions in chr9 (chunk 21/31) : 89341
    209. 

  209. Total time elapsed: 152.60 s
    210. 

  210. Calling variants ...
    211. 

  211. Total processed positions in chr9 (chunk 31/31) : 95505
    212. 

  212. Total time elapsed: 155.05 s
    213. 

  213. 

  214. real	3m4.784s
    215. 

  215. user	62m4.077s
    216. 

  216. sys	3m33.310s
    217. 

  217. 

  218. [INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
    219. 

  219. [INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 14
    220. 

  220. [INFO] Total heterozygous SNP positions selected: chr9: 77784
    221. 

  221. 

  222. real	0m4.754s
    223. 

  223. user	0m4.489s
    224. 

  224. sys	0m0.192s
    225. 

  225. 

  226. [INFO] 3/7 Phase VCF file using LongPhase
    227. 

  227. LongPhase Ver 1.7
    228. 

  228. 

  229. --- File Parameter --- 
    230. 

  230. SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr9.vcf
    231. 

  231. SV  File      : 
    232. 

  232. MOD File      : 
    233. 

  233. REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
    234. 

  234. Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr9
    235. 

  235. Generate Dot  : False
    236. 

  236. BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
    237. 

  237. 

  238. --- Phasing Parameter --- 
    239. 

  239. Seq Platform       : ONT
    240. 

  240. Phase Indel        : False
    241. 

  241. Distance Threshold : 300000
    242. 

  242. Connect Adjacent   : 20
    243. 

  243. Edge Threshold     : 0.7
    244. 

  244. Mapping Quality    : 1
    245. 

  245. Variant Confidence : 0.75
    246. 

  246. ReadTag Confidence : 0.65
    247. 

  247. 

  248. parsing VCF ... 0s
    249. 

  249. parsing SV VCF ... 0s
    250. 

  250. parsing Meth VCF ... 0s
    251. 

  251. reading reference ... 2s
    252. 

  252. (chr9,10s)
    253. 

  253. parsing total:  10s
    254. 

  254. merge results ... 0s
    255. 

  255. writeResult SNP ... 0s
    256. 

  256. 

  257. total process: 12s
    258. 

  258. 

  259. real	0m12.323s
    260. 

  260. user	0m23.247s
    261. 

  261. sys	0m1.686s
    262. 

  262. 

  263. [INFO] 5/7 Select candidates for full-alignment calling
    264. 

  264. [INFO] Set variants quality cutoff 19.0
    265. 

  265. [INFO] Set reference calls quality cutoff 13.0
    266. 

  266. [INFO] Low quality reference calls to be processed in chr9: 181543
    267. 

  267. [INFO] Low quality variants to be processed in chr9: 165238
    268. 

  268. 

  269. real	0m5.203s
    270. 

  270. user	0m4.807s
    271. 

  271. sys	0m0.313s
    272. 

  272. 

  273. [INFO] 6/7 Call low-quality variants using full-alignment model
    274. 

  274. Calling variants ...
    275. 

  275. Total processed positions in chr9 (chunk 19/35) : 10000
    276. 

  276. Total time elapsed: 92.62 s
    277. 

  277. Calling variants ...
    278. 

  278. Total processed positions in chr9 (chunk 17/35) : 10000
    279. 

  279. Total time elapsed: 96.32 s
    280. 

  280. Calling variants ...
    281. 

  281. Total processed positions in chr9 (chunk 29/35) : 10000
    282. 

  282. Total time elapsed: 96.61 s
    283. 

  283. Calling variants ...
    284. 

  284. Total processed positions in chr9 (chunk 2/35) : 10000
    285. 

  285. Total time elapsed: 96.49 s
    286. 

  286. Calling variants ...
    287. 

  287. Total processed positions in chr9 (chunk 26/35) : 10000
    288. 

  288. Total time elapsed: 98.14 s
    289. 

  289. Calling variants ...
    290. 

  290. Total processed positions in chr9 (chunk 10/35) : 10000
    291. 

  291. Total time elapsed: 98.23 s
    292. 

  292. Calling variants ...
    293. 

  293. Total processed positions in chr9 (chunk 7/35) : 10000
    294. 

  294. Total time elapsed: 98.31 s
    295. 

  295. Calling variants ...
    296. 

  296. Total processed positions in chr9 (chunk 1/35) : 10000
    297. 

  297. Total time elapsed: 102.22 s
    298. 

  298. Calling variants ...
    299. 

  299. Total processed positions in chr9 (chunk 30/35) : 10000
    300. 

  300. Total time elapsed: 102.47 s
    301. 

  301. Calling variants ...
    302. 

  302. Total processed positions in chr9 (chunk 25/35) : 10000
    303. 

  303. Total time elapsed: 102.89 s
    304. 

  304. Calling variants ...
    305. 

  305. Total processed positions in chr9 (chunk 4/35) : 10000
    306. 

  306. Total time elapsed: 103.42 s
    307. 

  307. Calling variants ...
    308. 

  308. Total processed positions in chr9 (chunk 23/35) : 10000
    309. 

  309. Total time elapsed: 103.94 s
    310. 

  310. Calling variants ...
    311. 

  311. Total processed positions in chr9 (chunk 28/35) : 10000
    312. 

  312. Total time elapsed: 104.38 s
    313. 

  313. Calling variants ...
    314. 

  314. Total processed positions in chr9 (chunk 6/35) : 10000
    315. 

  315. Total time elapsed: 104.32 s
    316. 

  316. Calling variants ...
    317. 

  317. Total processed positions in chr9 (chunk 3/35) : 10000
    318. 

  318. Total time elapsed: 104.69 s
    319. 

  319. Calling variants ...
    320. 

  320. Total processed positions in chr9 (chunk 20/35) : 10000
    321. 

  321. Total time elapsed: 104.80 s
    322. 

  322. Calling variants ...
    323. 

  323. Total processed positions in chr9 (chunk 15/35) : 10000
    324. 

  324. Total time elapsed: 105.81 s
    325. 

  325. Calling variants ...
    326. 

  326. Total processed positions in chr9 (chunk 24/35) : 10000
    327. 

  327. Total time elapsed: 106.00 s
    328. 

  328. Calling variants ...
    329. 

  329. Total processed positions in chr9 (chunk 12/35) : 10000
    330. 

  330. Total time elapsed: 106.02 s
    331. 

  331. Calling variants ...
    332. 

  332. Total processed positions in chr9 (chunk 18/35) : 10000
    333. 

  333. Total time elapsed: 106.35 s
    334. 

  334. Calling variants ...
    335. 

  335. Total processed positions in chr9 (chunk 16/35) : 10000
    336. 

  336. Total time elapsed: 106.68 s
    337. 

  337. Calling variants ...
    338. 

  338. Total processed positions in chr9 (chunk 8/35) : 10000
    339. 

  339. Total time elapsed: 106.87 s
    340. 

  340. Calling variants ...
    341. 

  341. Total processed positions in chr9 (chunk 9/35) : 10000
    342. 

  342. Total time elapsed: 106.89 s
    343. 

  343. Calling variants ...
    344. 

  344. Total processed positions in chr9 (chunk 27/35) : 10000
    345. 

  345. Total time elapsed: 107.09 s
    346. 

  346. Calling variants ...
    347. 

  347. Total processed positions in chr9 (chunk 21/35) : 10000
    348. 

  348. Total time elapsed: 107.27 s
    349. 

  349. Calling variants ...
    350. 

  350. Total processed positions in chr9 (chunk 14/35) : 10000
    351. 

  351. Total time elapsed: 107.48 s
    352. 

  352. Calling variants ...
    353. 

  353. Total processed positions in chr9 (chunk 13/35) : 10000
    354. 

  354. Total time elapsed: 107.50 s
    355. 

  355. Calling variants ...
    356. 

  356. Total processed positions in chr9 (chunk 11/35) : 10000
    357. 

  357. Total time elapsed: 107.78 s
    358. 

  358. Calling variants ...
    359. 

  359. Total processed positions in chr9 (chunk 5/35) : 10000
    360. 

  360. Total time elapsed: 107.99 s
    361. 

  361. Calling variants ...
    362. 

  362. Total processed positions in chr9 (chunk 22/35) : 10000
    363. 

  363. Total time elapsed: 108.92 s
    364. 

  364. Calling variants ...
    365. 

  365. Total processed positions in chr9 (chunk 35/35) : 6781
    366. 

  366. Total time elapsed: 55.49 s
    367. 

  367. Calling variants ...
    368. 

  368. Total processed positions in chr9 (chunk 32/35) : 10000
    369. 

  369. Total time elapsed: 69.14 s
    370. 

  370. Calling variants ...
    371. 

  371. Total processed positions in chr9 (chunk 31/35) : 10000
    372. 

  372. Total time elapsed: 74.70 s
    373. 

  373. Calling variants ...
    374. 

  374. Total processed positions in chr9 (chunk 34/35) : 10000
    375. 

  375. Total time elapsed: 78.02 s
    376. 

  376. Calling variants ...
    377. 

  377. Total processed positions in chr9 (chunk 33/35) : 10000
    378. 

  378. Total time elapsed: 81.45 s
    379. 

  379. 

  380. real	3m4.889s
    381. 

  381. user	55m57.941s
    382. 

  382. sys	3m16.335s
    383. 

  383. 

  384. [INFO] 7/7 Merge pileup VCF and full-alignment VCF
    385. 

  385. [INFO] Pileup variants processed in chr9: 70909
    386. 

  386. [INFO] Full-alignment variants processed in chr9: 180962
    387. 

  387. 

  388. real	0m6.255s
    389. 

  389. user	0m6.847s
    390. 

  390. sys	0m0.266s
    391. 

  391. 

  392. [INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
    393. 

  393. 

  394. real	7m3.909s
    395. 

  395. user	119m5.300s
    396. 

  396. sys	6m54.136s
    397. 

  397. 

  398. [INFO] Call Germline Variant in Tumor BAM using Clair3
    399. 

  399. [INFO] RUN THE FOLLOWING COMMAND:
    400. 

  400. ( /opt/conda/envs/clairs/bin/run_clair3.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --threads 40 --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output --ctg_name=chr9 --samtools=samtools --pypy=pypy3 --python=python3 --min_coverage=4 --snp_min_af=0.08 --indel_min_af=0.15 --longphase_for_phasing  ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log/2_CLAIR3_TUMOR.log
    401. 

  401. 

  402. [INFO] CLAIR3 VERSION: v1.0.8
    403. 

  403. [INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
    404. 

  404. [INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
    405. 

  405. [INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
    406. 

  406. [INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output
    407. 

  407. [INFO] PLATFORM: ont
    408. 

  408. [INFO] THREADS: 40
    409. 

  409. [INFO] BED FILE PATH: EMPTY
    410. 

  410. [INFO] VCF FILE PATH: EMPTY
    411. 

  411. [INFO] CONTIGS: chr9
    412. 

  412. [INFO] CONDA PREFIX: 
    413. 

  413. [INFO] SAMTOOLS PATH: samtools
    414. 

  414. [INFO] PYTHON PATH: python3
    415. 

  415. [INFO] PYPY PATH: pypy3
    416. 

  416. [INFO] PARALLEL PATH: parallel
    417. 

  417. [INFO] WHATSHAP PATH: whatshap
    418. 

  418. [INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
    419. 

  419. [INFO] CHUNK SIZE: 5000000
    420. 

  420. [INFO] FULL ALIGN PROPORTION: 0.7
    421. 

  421. [INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
    422. 

  422. [INFO] PHASING PROPORTION: 0.7
    423. 

  423. [INFO] MINIMUM MQ: 5
    424. 

  424. [INFO] MINIMUM COVERAGE: 4
    425. 

  425. [INFO] SNP AF THRESHOLD: 0.08
    426. 

  426. [INFO] INDEL AF THRESHOLD: 0.15
    427. 

  427. [INFO] BASE ERROR IN GVCF: 0.001
    428. 

  428. [INFO] GQ BIN SIZE IN GVCF: 5
    429. 

  429. [INFO] ENABLE FILEUP ONLY CALLING: False
    430. 

  430. [INFO] ENABLE FAST MODE CALLING: False
    431. 

  431. [INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
    432. 

  432. [INFO] ENABLE PRINTING REFERENCE CALLS: False
    433. 

  433. [INFO] ENABLE OUTPUT GVCF: False
    434. 

  434. [INFO] ENABLE HAPLOID PRECISE MODE: False
    435. 

  435. [INFO] ENABLE HAPLOID SENSITIVE MODE: False
    436. 

  436. [INFO] ENABLE INCLUDE ALL CTGS CALLING: False
    437. 

  437. [INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
    438. 

  438. [INFO] ENABLE REMOVING INTERMEDIATE FILES: False
    439. 

  439. [INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
    440. 

  440. [INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
    441. 

  441. [INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
    442. 

  442. [INFO] ENABLE HAPLOTAGGING FINAL BAM: False
    443. 

  443. [INFO] ENABLE LONG INDEL CALLING: False
    444. 

  444. [INFO] ENABLE C_IMPLEMENT: True
    445. 

  445. 

  446. + /opt/conda/envs/clairs/bin/scripts/clair3_c_impl.sh --bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --threads 40 --model_path /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420 --platform ont --output /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr9 --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=4 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=True --longphase=/opt/conda/envs/clairs/bin/longphase --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=True --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False
    447. 

  447. 

  448. [INFO] Check environment variables
    449. 

  449. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/log
    450. 

  450. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
    451. 

  451. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
    452. 

  452. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
    453. 

  453. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
    454. 

  454. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
    455. 

  455. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
    456. 

  456. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
    457. 

  457. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
    458. 

  458. [INFO] Call variant in contigs: chr9
    459. 

  459. [INFO] Chunk number for each contig: 31
    460. 

  460. [INFO] 1/7 Call variants using pileup model
    461. 

  461. Calling variants ...
    462. 

  462. Total processed positions in chr9 (chunk 12/31) : 3313
    463. 

  463. Total time elapsed: 63.75 s
    464. 

  464. Calling variants ...
    465. 

  465. Total processed positions in chr9 (chunk 13/31) : 9677
    466. 

  466. Total time elapsed: 75.54 s
    467. 

  467. Calling variants ...
    468. 

  468. Total processed positions in chr9 (chunk 8/31) : 8048
    469. 

  469. Total time elapsed: 76.99 s
    470. 

  470. Calling variants ...
    471. 

  471. Total processed positions in chr9 (chunk 5/31) : 8157
    472. 

  472. Total time elapsed: 78.17 s
    473. 

  473. Calling variants ...
    474. 

  474. Total processed positions in chr9 (chunk 18/31) : 8449
    475. 

  475. Total time elapsed: 78.96 s
    476. 

  476. Calling variants ...
    477. 

  477. Total processed positions in chr9 (chunk 23/31) : 9152
    478. 

  478. Total time elapsed: 80.13 s
    479. 

  479. Calling variants ...
    480. 

  480. Total processed positions in chr9 (chunk 27/31) : 10222
    481. 

  481. Total time elapsed: 80.37 s
    482. 

  482. Calling variants ...
    483. 

  483. Total processed positions in chr9 (chunk 9/31) : 7557
    484. 

  484. Total time elapsed: 81.04 s
    485. 

  485. Calling variants ...
    486. 

  486. Total processed positions in chr9 (chunk 19/31) : 11050
    487. 

  487. Total time elapsed: 81.73 s
    488. 

  488. Calling variants ...
    489. 

  489. Total processed positions in chr9 (chunk 4/31) : 11173
    490. 

  490. Total time elapsed: 81.98 s
    491. 

  491. Calling variants ...
    492. 

  492. Total processed positions in chr9 (chunk 6/31) : 10501
    493. 

  493. Total time elapsed: 82.23 s
    494. 

  494. Calling variants ...
    495. 

  495. Total processed positions in chr9 (chunk 20/31) : 11420
    496. 

  496. Total time elapsed: 83.61 s
    497. 

  497. Calling variants ...
    498. 

  498. Total processed positions in chr9 (chunk 24/31) : 11713
    499. 

  499. Total time elapsed: 84.00 s
    500. 

  500. Calling variants ...
    501. 

  501. Total processed positions in chr9 (chunk 26/31) : 12517
    502. 

  502. Total time elapsed: 84.11 s
    503. 

  503. Calling variants ...
    504. 

  504. Total processed positions in chr9 (chunk 2/31) : 13146
    505. 

  505. Total time elapsed: 86.25 s
    506. 

  506. Calling variants ...
    507. 

  507. Total processed positions in chr9 (chunk 17/31) : 11841
    508. 

  508. Total time elapsed: 87.22 s
    509. 

  509. Calling variants ...
    510. 

  510. Total processed positions in chr9 (chunk 1/31) : 15967
    511. 

  511. Total time elapsed: 89.50 s
    512. 

  512. Calling variants ...
    513. 

  513. Total processed positions in chr9 (chunk 15/31) : 22912
    514. 

  514. Total time elapsed: 93.68 s
    515. 

  515. Calling variants ...
    516. 

  516. Total processed positions in chr9 (chunk 28/31) : 6980
    517. 

  517. Total time elapsed: 47.43 s
    518. 

  518. Calling variants ...
    519. 

  519. Total processed positions in chr9 (chunk 7/31) : 10077
    520. 

  520. Total time elapsed: 48.37 s
    521. 

  521. Calling variants ...
    522. 

  522. Total processed positions in chr9 (chunk 29/31) : 8642
    523. 

  523. Total time elapsed: 49.57 s
    524. 

  524. Calling variants ...
    525. 

  525. Total processed positions in chr9 (chunk 3/31) : 9920
    526. 

  526. Total time elapsed: 49.92 s
    527. 

  527. Calling variants ...
    528. 

  528. Total processed positions in chr9 (chunk 25/31) : 9578
    529. 

  529. Total time elapsed: 50.63 s
    530. 

  530. Calling variants ...
    531. 

  531. Total processed positions in chr9 (chunk 22/31) : 12435
    532. 

  532. Total time elapsed: 51.57 s
    533. 

  533. Calling variants ...
    534. 

  534. Total processed positions in chr9 (chunk 11/31) : 40307
    535. 

  535. Total time elapsed: 115.89 s
    536. 

  536. Calling variants ...
    537. 

  537. Total processed positions in chr9 (chunk 30/31) : 12175
    538. 

  538. Total time elapsed: 53.41 s
    539. 

  539. Calling variants ...
    540. 

  540. Total processed positions in chr9 (chunk 21/31) : 11701
    541. 

  541. Total time elapsed: 54.40 s
    542. 

  542. Calling variants ...
    543. 

  543. Total processed positions in chr9 (chunk 10/31) : 17506
    544. 

  544. Total time elapsed: 58.44 s
    545. 

  545. Calling variants ...
    546. 

  546. Total processed positions in chr9 (chunk 31/31) : 16000
    547. 

  547. Total time elapsed: 55.65 s
    548. 

  548. Calling variants ...
    549. 

  549. Total processed positions in chr9 (chunk 14/31) : 27421
    550. 

  550. Total time elapsed: 65.13 s
    551. 

  551. Calling variants ...
    552. 

  552. Total processed positions in chr9 (chunk 16/31) : 56368
    553. 

  553. Total time elapsed: 141.70 s
    554. 

  554. 

  555. real	2m25.563s
    556. 

  556. user	26m45.350s
    557. 

  557. sys	3m12.482s
    558. 

  558. 

  559. [INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
    560. 

  560. [INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 19
    561. 

  561. [INFO] Total heterozygous SNP positions selected: chr9: 77791
    562. 

  562. 

  563. real	0m1.682s
    564. 

  564. user	0m1.459s
    565. 

  565. sys	0m0.151s
    566. 

  566. 

  567. [INFO] 3/7 Phase VCF file using LongPhase
    568. 

  568. LongPhase Ver 1.7
    569. 

  569. 

  570. --- File Parameter --- 
    571. 

  571. SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/chr9.vcf
    572. 

  572. SV  File      : 
    573. 

  573. MOD File      : 
    574. 

  574. REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
    575. 

  575. Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf/phased_chr9
    576. 

  576. Generate Dot  : False
    577. 

  577. BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
    578. 

  578. 

  579. --- Phasing Parameter --- 
    580. 

  580. Seq Platform       : ONT
    581. 

  581. Phase Indel        : False
    582. 

  582. Distance Threshold : 300000
    583. 

  583. Connect Adjacent   : 20
    584. 

  584. Edge Threshold     : 0.7
    585. 

  585. Mapping Quality    : 1
    586. 

  586. Variant Confidence : 0.75
    587. 

  587. ReadTag Confidence : 0.65
    588. 

  588. 

  589. parsing VCF ... 1s
    590. 

  590. parsing SV VCF ... 0s
    591. 

  591. parsing Meth VCF ... 0s
    592. 

  592. reading reference ... 1s
    593. 

  593. (chr9,45s)
    594. 

  594. parsing total:  45s
    595. 

  595. merge results ... 0s
    596. 

  596. writeResult SNP ... 1s
    597. 

  597. 

  598. total process: 48s
    599. 

  599. 

  600. real	0m47.622s
    601. 

  601. user	1m39.107s
    602. 

  602. sys	0m6.712s
    603. 

  603. 

  604. [INFO] 5/7 Select candidates for full-alignment calling
    605. 

  605. [INFO] Set variants quality cutoff 22.0
    606. 

  606. [INFO] Set reference calls quality cutoff 8.0
    607. 

  607. [INFO] Low quality reference calls to be processed in chr9: 19049
    608. 

  608. [INFO] Low quality variants to be processed in chr9: 171149
    609. 

  609. 

  610. real	0m1.655s
    611. 

  611. user	0m1.429s
    612. 

  612. sys	0m0.187s
    613. 

  613. 

  614. [INFO] 6/7 Call low-quality variants using full-alignment model
    615. 

  615. Calling variants ...
    616. 

  616. Total processed positions in chr9 (chunk 20/20) : 198
    617. 

  617. Total time elapsed: 5.14 s
    618. 

  618. Calling variants ...
    619. 

  619. Total processed positions in chr9 (chunk 9/20) : 10000
    620. 

  620. Total time elapsed: 103.97 s
    621. 

  621. Calling variants ...
    622. 

  622. Total processed positions in chr9 (chunk 6/20) : 10000
    623. 

  623. Total time elapsed: 106.05 s
    624. 

  624. Calling variants ...
    625. 

  625. Total processed positions in chr9 (chunk 1/20) : 10000
    626. 

  626. Total time elapsed: 108.09 s
    627. 

  627. Calling variants ...
    628. 

  628. Total processed positions in chr9 (chunk 8/20) : 10000
    629. 

  629. Total time elapsed: 109.62 s
    630. 

  630. Calling variants ...
    631. 

  631. Total processed positions in chr9 (chunk 2/20) : 10000
    632. 

  632. Total time elapsed: 112.64 s
    633. 

  633. Calling variants ...
    634. 

  634. Total processed positions in chr9 (chunk 3/20) : 10000
    635. 

  635. Total time elapsed: 115.34 s
    636. 

  636. Calling variants ...
    637. 

  637. Total processed positions in chr9 (chunk 19/20) : 10000
    638. 

  638. Total time elapsed: 118.04 s
    639. 

  639. Calling variants ...
    640. 

  640. Total processed positions in chr9 (chunk 13/20) : 10000
    641. 

  641. Total time elapsed: 118.74 s
    642. 

  642. Calling variants ...
    643. 

  643. Total processed positions in chr9 (chunk 17/20) : 10000
    644. 

  644. Total time elapsed: 119.76 s
    645. 

  645. Calling variants ...
    646. 

  646. Total processed positions in chr9 (chunk 10/20) : 10000
    647. 

  647. Total time elapsed: 119.63 s
    648. 

  648. Calling variants ...
    649. 

  649. Total processed positions in chr9 (chunk 14/20) : 10000
    650. 

  650. Total time elapsed: 120.51 s
    651. 

  651. Calling variants ...
    652. 

  652. Total processed positions in chr9 (chunk 7/20) : 10000
    653. 

  653. Total time elapsed: 121.34 s
    654. 

  654. Calling variants ...
    655. 

  655. Total processed positions in chr9 (chunk 15/20) : 10000
    656. 

  656. Total time elapsed: 123.04 s
    657. 

  657. Calling variants ...
    658. 

  658. Total processed positions in chr9 (chunk 18/20) : 10000
    659. 

  659. Total time elapsed: 123.50 s
    660. 

  660. Calling variants ...
    661. 

  661. Total processed positions in chr9 (chunk 4/20) : 10000
    662. 

  662. Total time elapsed: 125.47 s
    663. 

  663. Calling variants ...
    664. 

  664. Total processed positions in chr9 (chunk 12/20) : 10000
    665. 

  665. Total time elapsed: 131.99 s
    666. 

  666. Calling variants ...
    667. 

  667. Total processed positions in chr9 (chunk 16/20) : 10000
    668. 

  668. Total time elapsed: 134.56 s
    669. 

  669. Calling variants ...
    670. 

  670. Total processed positions in chr9 (chunk 11/20) : 10000
    671. 

  671. Total time elapsed: 139.32 s
    672. 

  672. Calling variants ...
    673. 

  673. Total processed positions in chr9 (chunk 5/20) : 10000
    674. 

  674. Total time elapsed: 155.07 s
    675. 

  675. 

  676. real	2m38.507s
    677. 

  677. user	35m49.457s
    678. 

  678. sys	1m53.587s
    679. 

  679. 

  680. [INFO] 7/7 Merge pileup VCF and full-alignment VCF
    681. 

  681. [INFO] Pileup variants processed in chr9: 73865
    682. 

  682. [INFO] Full-alignment variants processed in chr9: 160201
    683. 

  683. 

  684. real	0m2.867s
    685. 

  685. user	0m2.939s
    686. 

  686. sys	0m0.181s
    687. 

  687. 

  688. [INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz
    689. 

  689. 

  690. real	6m8.256s
    691. 

  691. user	64m28.253s
    692. 

  692. sys	5m14.468s
    693. 

  693. 

  694. [INFO] Select Heterozygous SNP for Phasing
    695. 

  695. [INFO] RUN THE FOLLOWING COMMAND:
    696. 

  696. ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log/parallel_1_select_hetero_snp_for_phasing.log -j 40 pypy3 /opt/bin/clairs.py select_hetero_snp_for_phasing --tumor_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_tumor_output/merge_output.vcf.gz --normal_vcf_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz --output_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/vcf --ctg_name {1} --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing True :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log/1_select_hetero_snp_for_phasing.log
    697. 

  697. 

  698. [INFO] Total HET SNP calls selected: chr9: 107191, not found:2348, not match:108, low_qual_count:0. Total normal:119728 Total tumor:109647, pro: 0.9776
    699. 

  699. 

  700. [INFO] Phase the Tumor BAM
    701. 

  701. [INFO] RUN THE FOLLOWING COMMAND:
    702. 

  702. ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log/parallel_4_phase_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase phase  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/vcf/{1}.vcf -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam -r /home/t_steimle/ref/hs1/chm13v2.0.fa -t 40 -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_phased_{1} --ont :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/CONTIGS && parallel -j 40 bgzip -f /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log/4_phase_tumor.log && parallel -j 40 tabix -f -p vcf /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/CONTIGS
    703. 

  703. 

  704. LongPhase Ver 1.7
    705. 

  705. 

  706. --- File Parameter --- 
    707. 

  707. SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/vcf/chr9.vcf
    708. 

  708. SV  File      : 
    709. 

  709. MOD File      : 
    710. 

  710. REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
    711. 

  711. Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_phased_chr9
    712. 

  712. Generate Dot  : False
    713. 

  713. BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam 
    714. 

  714. 

  715. --- Phasing Parameter --- 
    716. 

  716. Seq Platform       : ONT
    717. 

  717. Phase Indel        : False
    718. 

  718. Distance Threshold : 300000
    719. 

  719. Connect Adjacent   : 20
    720. 

  720. Edge Threshold     : 0.7
    721. 

  721. Mapping Quality    : 1
    722. 

  722. Variant Confidence : 0.75
    723. 

  723. ReadTag Confidence : 0.65
    724. 

  724. 

  725. parsing VCF ... 1s
    726. 

  726. parsing SV VCF ... 0s
    727. 

  727. parsing Meth VCF ... 0s
    728. 

  728. reading reference ... 1s
    729. 

  729. (chr9,49s)
    730. 

  730. parsing total:  49s
    731. 

  731. merge results ... 0s
    732. 

  732. writeResult SNP ... 1s
    733. 

  733. 

  734. total process: 52s
    735. 

  735. 

  736. [INFO] Haplotag the Tumor BAM
    737. 

  737. [INFO] RUN THE FOLLOWING COMMAND:
    738. 

  738. ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log/parallel_5_haplotag_tumor.log -j 40 /opt/conda/envs/clairs/bin/longphase haplotag -o /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_{1} --reference /home/t_steimle/ref/hs1/chm13v2.0.fa --region {1}  -s /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_phased_{1}.vcf.gz -b /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/CONTIGS ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/clair3_log/5_tumor_haplotag.log && parallel -j 40 samtools index  -@40 /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_{1}.bam :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/CONTIGS
    739. 

  739. 

  740. phased SNP file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_phased_chr9.vcf.gz
    741. 

  741. phased SV file:    
    742. 

  742. phased MOD file:   
    743. 

  743. input bam file:    /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
    744. 

  744. input ref file:    /home/t_steimle/ref/hs1/chm13v2.0.fa
    745. 

  745. output bam file:   /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/clair3_output/phased_output/tumor_chr9.bam
    746. 

  746. number of threads: 1
    747. 

  747. write log file:    false
    748. 

  748. log file:          
    749. 

  749. -------------------------------------------
    750. 

  750. tag region:                    chr9
    751. 

  751. filter mapping quality below:  1
    752. 

  752. percentage threshold:          0.6
    753. 

  753. tag supplementary:             false
    754. 

  754. -------------------------------------------
    755. 

  755. parsing SNP VCF ... 1s
    756. 

  756. tag read start ...
    757. 

  757. chr: chr9 ... 1322s
    758. 

  758. tag read 1325s
    759. 

  759. -------------------------------------------
    760. 

  760. total process time:  1326s
    761. 

  761. total alignment:     1870680
    762. 

  762. total supplementary: 62722
    763. 

  763. total secondary:     0
    764. 

  764. total unmapped:      0
    765. 

  765. total tag alignment: 709540
    766. 

  766. total untagged:      1161140
    767. 

  767. 

  768. [INFO] STEP 1: Extract Variant Candidates from Tumor and Normal BAMs
    769. 

  769. [INFO] RUN THE FOLLOWING COMMAND:
    770. 

  770. ( parallel --joblog /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/parallel_1_extract_tumor_candidates.log -C " " -j 40 pypy3 /opt/bin/clairs.py extract_pair_candidates --tumor_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam --normal_bam_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam --ref_fn /home/t_steimle/ref/hs1/chm13v2.0.fa --samtools samtools --snv_min_af 0.05 --indel_min_af 0.1 --chunk_id {2}  --chunk_num {3}  --ctg_name {1}  --platform ont --min_coverage 4 --bed_fn /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/split_beds/{1} --candidates_folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/candidates --output_depth True  --select_indel_candidates True --hybrid_mode_vcf_fn None --genotyping_mode_vcf_fn None :::: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/CHUNK_LIST ) 2>&1 | tee /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/logs/1_EC.log && pypy3 /opt/bin/clairs.py concat_files --input_dir /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part40/tmp/candidates --input_prefix CANDIDATES_FILE_ --output_fn CANDIDATES_FILES 
    771. 

  771. 

  772. [INFO] chr9 chunk 0/31: Total snv candidates found: 74, total indel candidates found: 46
    773. 

  773. [INFO] chr9 chunk 1/31: Total snv candidates found: 1194, total indel candidates found: 371
    774. 

  774. [INFO] chr9 chunk 4/31: Total snv candidates found: 656, total indel candidates found: 215
    775.