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slurm-2556293.out

slurm-2556293.out 23 KB
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  1. WARNING: While bind mounting '/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15:/mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15': 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/part15 --region chr17:1-28642702 --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/part15/logs
    6. 

  6. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp
    7. 

  7. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/split_beds
    8. 

  8. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/candidates
    9. 

  9. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/pileup_tensor_can
    10. 

  10. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/fa_tensor_can
    11. 

  11. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/vcf_output
    12. 

  12. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/tmp_vcf_output
    13. 

  13. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/logs/clair3_log
    14. 

  14. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/phased_output
    15. 

  15. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/vcf
    16. 

  16. [INFO] --include_all_ctgs enabled
    17. 

  17. [INFO] Call variants in contigs: chr17
    18. 

  18. [INFO] Number of chunks for each contig: 17
    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/part15
    27. 

  27. [INFO] OUTPUT VCF PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/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/part15/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: chr17:1-28642702
    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/part15/tmp/clair3_output/clair3_normal_output --ctg_name=chr17 --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/part15/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/part15/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: chr17
    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/part15/tmp/clair3_output/clair3_normal_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr17 --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/part15/tmp/clair3_output/clair3_normal_output/log
    109. 

  109. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/pileup_output
    110. 

  110. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/merge_output
    111. 

  111. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/phase_output
    112. 

  112. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/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/part15/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/part15/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/part15/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/part15/tmp/clair3_output/clair3_normal_output/tmp/full_alignment_output/candidate_bed
    117. 

  117. [INFO] Call variant in contigs: chr17
    118. 

  118. [INFO] Chunk number for each contig: 17
    119. 

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

  120. Calling variants ...
    121. 

  121. Total processed positions in chr17 (chunk 6/17) : 38596
    122. 

  122. Total time elapsed: 95.29 s
    123. 

  123. Calling variants ...
    124. 

  124. Total processed positions in chr17 (chunk 5/17) : 61627
    125. 

  125. Total time elapsed: 143.16 s
    126. 

  126. Calling variants ...
    127. 

  127. Total processed positions in chr17 (chunk 13/17) : 78825
    128. 

  128. Total time elapsed: 173.07 s
    129. 

  129. Calling variants ...
    130. 

  130. Total processed positions in chr17 (chunk 3/17) : 85876
    131. 

  131. Total time elapsed: 181.43 s
    132. 

  132. Calling variants ...
    133. 

  133. Total processed positions in chr17 (chunk 4/17) : 84539
    134. 

  134. Total time elapsed: 181.84 s
    135. 

  135. Calling variants ...
    136. 

  136. Total processed positions in chr17 (chunk 14/17) : 81181
    137. 

  137. Total time elapsed: 181.83 s
    138. 

  138. Calling variants ...
    139. 

  139. Total processed positions in chr17 (chunk 15/17) : 81543
    140. 

  140. Total time elapsed: 182.32 s
    141. 

  141. Calling variants ...
    142. 

  142. Total processed positions in chr17 (chunk 10/17) : 83514
    143. 

  143. Total time elapsed: 183.69 s
    144. 

  144. Calling variants ...
    145. 

  145. Total processed positions in chr17 (chunk 12/17) : 83512
    146. 

  146. Total time elapsed: 187.00 s
    147. 

  147. Calling variants ...
    148. 

  148. Total processed positions in chr17 (chunk 8/17) : 83634
    149. 

  149. Total time elapsed: 188.40 s
    150. 

  150. Calling variants ...
    151. 

  151. Total processed positions in chr17 (chunk 11/17) : 83228
    152. 

  152. Total time elapsed: 188.88 s
    153. 

  153. Calling variants ...
    154. 

  154. Total processed positions in chr17 (chunk 16/17) : 93033
    155. 

  155. Total time elapsed: 191.89 s
    156. 

  156. Calling variants ...
    157. 

  157. Total processed positions in chr17 (chunk 7/17) : 82191
    158. 

  158. Total time elapsed: 194.59 s
    159. 

  159. Calling variants ...
    160. 

  160. Total processed positions in chr17 (chunk 9/17) : 92357
    161. 

  161. Total time elapsed: 198.54 s
    162. 

  162. Calling variants ...
    163. 

  163. Total processed positions in chr17 (chunk 1/17) : 90481
    164. 

  164. Total time elapsed: 201.20 s
    165. 

  165. Calling variants ...
    166. 

  166. Total processed positions in chr17 (chunk 2/17) : 89155
    167. 

  167. Total time elapsed: 202.31 s
    168. 

  168. Calling variants ...
    169. 

  169. Total processed positions in chr17 (chunk 17/17) : 98267
    170. 

  170. Total time elapsed: 214.09 s
    171. 

  171. 

  172. real	3m44.304s
    173. 

  173. user	50m1.430s
    174. 

  174. sys	2m26.943s
    175. 

  175. 

  176. [INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging
    177. 

  177. [INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 15
    178. 

  178. [INFO] Total heterozygous SNP positions selected: chr17: 53664
    179. 

  179. 

  180. real	0m2.855s
    181. 

  181. user	0m2.653s
    182. 

  182. sys	0m0.172s
    183. 

  183. 

  184. [INFO] 3/7 Phase VCF file using LongPhase
    185. 

  185. LongPhase Ver 1.7
    186. 

  186. 

  187. --- File Parameter --- 
    188. 

  188. SNP File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/chr17.vcf
    189. 

  189. SV  File      : 
    190. 

  190. MOD File      : 
    191. 

  191. REF File      : /home/t_steimle/ref/hs1/chm13v2.0.fa
    192. 

  192. Output Prefix : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/tmp/phase_output/phase_vcf/phased_chr17
    193. 

  193. Generate Dot  : False
    194. 

  194. BAM File      : /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/norm/CHAHA_norm_hs1.bam 
    195. 

  195. 

  196. --- Phasing Parameter --- 
    197. 

  197. Seq Platform       : ONT
    198. 

  198. Phase Indel        : False
    199. 

  199. Distance Threshold : 300000
    200. 

  200. Connect Adjacent   : 20
    201. 

  201. Edge Threshold     : 0.7
    202. 

  202. Mapping Quality    : 1
    203. 

  203. Variant Confidence : 0.75
    204. 

  204. ReadTag Confidence : 0.65
    205. 

  205. 

  206. parsing VCF ... 0s
    207. 

  207. parsing SV VCF ... 0s
    208. 

  208. parsing Meth VCF ... 0s
    209. 

  209. reading reference ... 1s
    210. 

  210. (chr17,6s)
    211. 

  211. parsing total:  6s
    212. 

  212. merge results ... 0s
    213. 

  213. writeResult SNP ... 1s
    214. 

  214. 

  215. total process: 8s
    216. 

  216. 

  217. real	0m8.006s
    218. 

  218. user	0m26.299s
    219. 

  219. sys	0m1.603s
    220. 

  220. 

  221. [INFO] 5/7 Select candidates for full-alignment calling
    222. 

  222. [INFO] Set variants quality cutoff 19.0
    223. 

  223. [INFO] Set reference calls quality cutoff 13.0
    224. 

  224. [INFO] Low quality reference calls to be processed in chr17: 123647
    225. 

  225. [INFO] Low quality variants to be processed in chr17: 107365
    226. 

  226. 

  227. real	0m3.208s
    228. 

  228. user	0m2.830s
    229. 

  229. sys	0m0.319s
    230. 

  230. 

  231. [INFO] 6/7 Call low-quality variants using full-alignment model
    232. 

  232. Calling variants ...
    233. 

  233. Total processed positions in chr17 (chunk 24/24) : 1012
    234. 

  234. Total time elapsed: 15.71 s
    235. 

  235. Calling variants ...
    236. 

  236. Total processed positions in chr17 (chunk 16/24) : 10000
    237. 

  237. Total time elapsed: 119.10 s
    238. 

  238. Calling variants ...
    239. 

  239. Total processed positions in chr17 (chunk 14/24) : 10000
    240. 

  240. Total time elapsed: 121.61 s
    241. 

  241. Calling variants ...
    242. 

  242. Total processed positions in chr17 (chunk 19/24) : 10000
    243. 

  243. Total time elapsed: 121.63 s
    244. 

  244. Calling variants ...
    245. 

  245. Total processed positions in chr17 (chunk 18/24) : 10000
    246. 

  246. Total time elapsed: 121.65 s
    247. 

  247. Calling variants ...
    248. 

  248. Total processed positions in chr17 (chunk 6/24) : 10000
    249. 

  249. Total time elapsed: 122.69 s
    250. 

  250. Calling variants ...
    251. 

  251. Total processed positions in chr17 (chunk 22/24) : 10000
    252. 

  252. Total time elapsed: 123.51 s
    253. 

  253. Calling variants ...
    254. 

  254. Total processed positions in chr17 (chunk 21/24) : 10000
    255. 

  255. Total time elapsed: 124.82 s
    256. 

  256. Calling variants ...
    257. 

  257. Total processed positions in chr17 (chunk 9/24) : 10000
    258. 

  258. Total time elapsed: 125.01 s
    259. 

  259. Calling variants ...
    260. 

  260. Total processed positions in chr17 (chunk 4/24) : 10000
    261. 

  261. Total time elapsed: 125.55 s
    262. 

  262. Calling variants ...
    263. 

  263. Total processed positions in chr17 (chunk 3/24) : 10000
    264. 

  264. Total time elapsed: 126.30 s
    265. 

  265. Calling variants ...
    266. 

  266. Total processed positions in chr17 (chunk 12/24) : 10000
    267. 

  267. Total time elapsed: 127.36 s
    268. 

  268. Calling variants ...
    269. 

  269. Total processed positions in chr17 (chunk 5/24) : 10000
    270. 

  270. Total time elapsed: 127.54 s
    271. 

  271. Calling variants ...
    272. 

  272. Total processed positions in chr17 (chunk 10/24) : 10000
    273. 

  273. Total time elapsed: 127.68 s
    274. 

  274. Calling variants ...
    275. 

  275. Total processed positions in chr17 (chunk 15/24) : 10000
    276. 

  276. Total time elapsed: 128.53 s
    277. 

  277. Calling variants ...
    278. 

  278. Total processed positions in chr17 (chunk 20/24) : 10000
    279. 

  279. Total time elapsed: 128.48 s
    280. 

  280. Calling variants ...
    281. 

  281. Total processed positions in chr17 (chunk 13/24) : 10000
    282. 

  282. Total time elapsed: 130.01 s
    283. 

  283. Calling variants ...
    284. 

  284. Total processed positions in chr17 (chunk 11/24) : 10000
    285. 

  285. Total time elapsed: 130.35 s
    286. 

  286. Calling variants ...
    287. 

  287. Total processed positions in chr17 (chunk 17/24) : 10000
    288. 

  288. Total time elapsed: 129.08 s
    289. 

  289. Calling variants ...
    290. 

  290. Total processed positions in chr17 (chunk 2/24) : 10000
    291. 

  291. Total time elapsed: 130.48 s
    292. 

  292. Calling variants ...
    293. 

  293. Total processed positions in chr17 (chunk 23/24) : 10000
    294. 

  294. Total time elapsed: 131.76 s
    295. 

  295. Calling variants ...
    296. 

  296. Total processed positions in chr17 (chunk 7/24) : 10000
    297. 

  297. Total time elapsed: 132.22 s
    298. 

  298. Calling variants ...
    299. 

  299. Total processed positions in chr17 (chunk 1/24) : 10000
    300. 

  300. Total time elapsed: 133.61 s
    301. 

  301. Calling variants ...
    302. 

  302. Total processed positions in chr17 (chunk 8/24) : 10000
    303. 

  303. Total time elapsed: 135.06 s
    304. 

  304. 

  305. real	2m19.593s
    306. 

  306. user	47m42.523s
    307. 

  307. sys	2m20.775s
    308. 

  308. 

  309. [INFO] 7/7 Merge pileup VCF and full-alignment VCF
    310. 

  310. [INFO] Pileup variants processed in chr17: 46074
    311. 

  311. [INFO] Full-alignment variants processed in chr17: 113883
    312. 

  312. 

  313. real	0m3.762s
    314. 

  314. user	0m4.756s
    315. 

  315. sys	0m0.345s
    316. 

  316. 

  317. [INFO] Finish calling, output file: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_normal_output/merge_output.vcf.gz
    318. 

  318. 

  319. real	6m41.397s
    320. 

  320. user	98m39.308s
    321. 

  321. sys	4m52.491s
    322. 

  322. 

  323. [INFO] Call Germline Variant in Tumor BAM using Clair3
    324. 

  324. [INFO] RUN THE FOLLOWING COMMAND:
    325. 

  325. ( /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/part15/tmp/clair3_output/clair3_tumor_output --ctg_name=chr17 --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/part15/logs/clair3_log/2_CLAIR3_TUMOR.log
    326. 

  326. 

  327. [INFO] CLAIR3 VERSION: v1.0.8
    328. 

  328. [INFO] BAM FILE PATH: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/CHAHA_diag_hs1.bam
    329. 

  329. [INFO] REFERENCE FILE PATH: /home/t_steimle/ref/hs1/chm13v2.0.fa
    330. 

  330. [INFO] MODEL PATH: /opt/conda/envs/clairs/bin/clairs_models/clair3_models/r1041_e82_400bps_sup_v420
    331. 

  331. [INFO] OUTPUT FOLDER: /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output
    332. 

  332. [INFO] PLATFORM: ont
    333. 

  333. [INFO] THREADS: 40
    334. 

  334. [INFO] BED FILE PATH: EMPTY
    335. 

  335. [INFO] VCF FILE PATH: EMPTY
    336. 

  336. [INFO] CONTIGS: chr17
    337. 

  337. [INFO] CONDA PREFIX: 
    338. 

  338. [INFO] SAMTOOLS PATH: samtools
    339. 

  339. [INFO] PYTHON PATH: python3
    340. 

  340. [INFO] PYPY PATH: pypy3
    341. 

  341. [INFO] PARALLEL PATH: parallel
    342. 

  342. [INFO] WHATSHAP PATH: whatshap
    343. 

  343. [INFO] LONGPHASE PATH: /opt/conda/envs/clairs/bin/longphase
    344. 

  344. [INFO] CHUNK SIZE: 5000000
    345. 

  345. [INFO] FULL ALIGN PROPORTION: 0.7
    346. 

  346. [INFO] FULL ALIGN REFERENCE PROPORTION: 0.1
    347. 

  347. [INFO] PHASING PROPORTION: 0.7
    348. 

  348. [INFO] MINIMUM MQ: 5
    349. 

  349. [INFO] MINIMUM COVERAGE: 4
    350. 

  350. [INFO] SNP AF THRESHOLD: 0.08
    351. 

  351. [INFO] INDEL AF THRESHOLD: 0.15
    352. 

  352. [INFO] BASE ERROR IN GVCF: 0.001
    353. 

  353. [INFO] GQ BIN SIZE IN GVCF: 5
    354. 

  354. [INFO] ENABLE FILEUP ONLY CALLING: False
    355. 

  355. [INFO] ENABLE FAST MODE CALLING: False
    356. 

  356. [INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
    357. 

  357. [INFO] ENABLE PRINTING REFERENCE CALLS: False
    358. 

  358. [INFO] ENABLE OUTPUT GVCF: False
    359. 

  359. [INFO] ENABLE HAPLOID PRECISE MODE: False
    360. 

  360. [INFO] ENABLE HAPLOID SENSITIVE MODE: False
    361. 

  361. [INFO] ENABLE INCLUDE ALL CTGS CALLING: False
    362. 

  362. [INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False
    363. 

  363. [INFO] ENABLE REMOVING INTERMEDIATE FILES: False
    364. 

  364. [INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: True
    365. 

  365. [INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
    366. 

  366. [INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
    367. 

  367. [INFO] ENABLE HAPLOTAGGING FINAL BAM: False
    368. 

  368. [INFO] ENABLE LONG INDEL CALLING: False
    369. 

  369. [INFO] ENABLE C_IMPLEMENT: True
    370. 

  370. 

  371. + /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/part15/tmp/clair3_output/clair3_tumor_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=chr17 --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
    372. 

  372. 

  373. [INFO] Check environment variables
    374. 

  374. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/log
    375. 

  375. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/pileup_output
    376. 

  376. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/merge_output
    377. 

  377. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/phase_output
    378. 

  378. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/gvcf_tmp_output
    379. 

  379. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output
    380. 

  380. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_vcf
    381. 

  381. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/phase_output/phase_bam
    382. 

  382. [INFO] Create folder /mnt/beegfs02/scratch/t_steimle/data/wgs/CHAHA/diag/ClairS/part15/tmp/clair3_output/clair3_tumor_output/tmp/full_alignment_output/candidate_bed
    383. 

  383. [INFO] Call variant in contigs: chr17
    384. 

  384. [INFO] Chunk number for each contig: 17
    385. 

  385. [INFO] 1/7 Call variants using pileup model
    386. 

  386. Calling variants ...
    387. 

  387. Total processed positions in chr17 (chunk 15/17) : 11069
    388. 

  388. Total time elapsed: 73.46 s
    389. 

  389. Calling variants ...
    390. 

  390. Total processed positions in chr17 (chunk 11/17) : 10550
    391. 

  391. Total time elapsed: 73.77 s
    392. 

  392. Calling variants ...
    393. 

  393. Total processed positions in chr17 (chunk 12/17) : 10782
    394. 

  394. Total time elapsed: 74.56 s
    395. 

  395. Calling variants ...
    396. 

  396. Total processed positions in chr17 (chunk 10/17) : 11845
    397. 

  397. Total time elapsed: 75.71 s
    398. 

  398. Calling variants ...
    399. 

  399. Total processed positions in chr17 (chunk 14/17) : 11398
    400. 

  400. Total time elapsed: 75.65 s
    401. 

  401. Calling variants ...
    402. 

  402. Total processed positions in chr17 (chunk 7/17) : 12155
    403. 

  403. Total time elapsed: 78.00 s
    404. 

  404. Calling variants ...
    405. 

  405. Total processed positions in chr17 (chunk 3/17) : 12437
    406. 

  406. Total time elapsed: 78.22 s
    407. 

  407. Calling variants ...
    408. 

  408. Total processed positions in chr17 (chunk 2/17) : 13822
    409. 

  409. Total time elapsed: 78.40 s
    410. 

  410. Calling variants ...
    411. 

  411. Total processed positions in chr17 (chunk 6/17) : 13099
    412. 

  412. Total time elapsed: 78.92 s
    413. 

  413. Calling variants ...
    414. 

  414. Total processed positions in chr17 (chunk 8/17) : 13984
    415. 

  415. Total time elapsed: 79.86 s
    416. 

  416. Calling variants ...
    417. 

  417. Total processed positions in chr17 (chunk 16/17) : 15105
    418. 

  418. Total time elapsed: 81.61 s
    419. 

  419. Calling variants ...
    420. 

  420. Total processed positions in chr17 (chunk 4/17) : 13833
    421. 

  421. Total time elapsed: 82.04 s
    422. 

  422. Calling variants ...
    423. 

  423. Total processed positions in chr17 (chunk 17/17) : 16957
    424. 

  424. Total time elapsed: 82.85 s
    425. 

  425. Calling variants ...
    426. 

  426. Total processed positions in chr17 (chunk 1/17) : 18647
    427. 

  427. Total time elapsed: 90.68 s
    428. 

  428. Calling variants ...
    429. 

  429. Total processed positions in chr17 (chunk 5/17) : 23171
    430. 

  430. Total time elapsed: 93.07 s
    431. 

  431. slurmstepd: error: *** JOB 2556293 ON n12 CANCELLED AT 2025-12-08T16:49:54 ***
    432. 

  432. slurmstepd: error: Detected 2 oom_kill events in StepId=2556293.batch. Some of the step tasks have been OOM Killed.
    433. 

  433. 

  434. ----------------------------------------------
    435. 

  435. |                SLURM EPILOG                |
    436. 

  436. ----------------------------------------------
    437. 

  437. Job ID: 2556293
    438. 

  438. Cluster: flamingo
    439. 

  439. User/Group: t_steimle/gs_hpc_biopath
    440. 

  440. Nodelist: n12
    441. 

  441. Nodes: 1
    442. 

  442. Cores per node: 40
    443. 

  443. Job started at: 2025-12-08 16:41:15
    444. 

  444. Job ended at:   2025-12-08 16:49:54
    445. 

  445. Job Wall-clock time: 00:08:39
    446. 

  446. CPU Utilized: 02:04:09
    447. 

  447. CPU Efficiency: 35.88% of 05:46:00 core-walltime
    448. 

  448. Memory Utilized: 34.06 GB
    449. 

  449. Memory Efficiency: 85.15% of 40.00 GB
    450.