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molgenis / vip

Variant Interpretation Pipeline
https://molgenis.github.io/vip/
GNU Lesser General Public License v3.0
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`clair3_call` can fail with 'Chromosome blocks not continuous' error #431

Closed dennishendriksen closed 1 year ago

dennishendriksen commented 1 year ago

The fastq_illumina_pairedend_trio consistently fails with

  [W::hts_itr_multi_cram] No index entry for region 130:0-1040
  [W::hts_itr_multi_cram] No index entry for region 131:0-1368
  [W::hts_itr_multi_cram] No index entry for region 133:0-1048
  [W::hts_itr_multi_cram] No index entry for region 134:0-1428
  [W::hts_itr_multi_cram] No index entry for region 135:0-1428
  [W::hts_itr_multi_cram] No index entry for region 136:0-1026
  [W::hts_itr_multi_cram] No index entry for region 138:0-1803
  [W::hts_itr_multi_cram] No index entry for region 139:0-2855
  [W::hts_itr_multi_cram] No index entry for region 140:0-3530
  [W::hts_itr_multi_cram] No index entry for region 141:0-8320
  [W::hts_itr_multi_cram] No index entry for region 142:0-1048
  [W::hts_itr_multi_cram] No index entry for region 143:0-1045
  [W::hts_itr_multi_cram] No index entry for region 144:0-1298
  [W::hts_itr_multi_cram] No index entry for region 145:0-2387
  [W::hts_itr_multi_cram] No index entry for region 146:0-1537
  [W::hts_itr_multi_cram] No index entry for region 147:0-1143
  [W::hts_itr_multi_cram] No index entry for region 148:0-1880
  [W::hts_itr_multi_cram] No index entry for region 149:0-1216
  [W::hts_itr_multi_cram] No index entry for region 150:0-970
  [W::hts_itr_multi_cram] No index entry for region 151:0-1788
  [W::hts_itr_multi_cram] No index entry for region 152:0-1484
  [W::hts_itr_multi_cram] No index entry for region 153:0-1750
  [W::hts_itr_multi_cram] No index entry for region 154:0-1308
  [W::hts_itr_multi_cram] No index entry for region 155:0-1658
  [W::hts_itr_multi_cram] No index entry for region 156:0-971
  [W::hts_itr_multi_cram] No index entry for region 157:0-1930
  [W::hts_itr_multi_cram] No index entry for region 158:0-990
  [W::hts_itr_multi_cram] No index entry for region 159:0-4215
  [W::hts_itr_multi_cram] No index entry for region 160:0-1136
  [W::hts_itr_multi_cram] No index entry for region 161:0-2656
  [W::hts_itr_multi_cram] No index entry for region 162:0-1650
  [W::hts_itr_multi_cram] No index entry for region 163:0-1451
  [W::hts_itr_multi_cram] No index entry for region 164:0-2378
  [W::hts_itr_multi_cram] No index entry for region 166:0-7992
  [W::hts_itr_multi_cram] No index entry for region 167:0-7642
  [W::hts_itr_multi_cram] No index entry for region 173:0-15008
  [W::hts_itr_multi_cram] No index entry for region 174:0-164239
  [W::hts_itr_multi_cram] No index entry for region 175:0-210658
  [W::hts_itr_multi_cram] No index entry for region 177:0-41891
  [W::hts_itr_multi_cram] No index entry for region 178:0-66486
  [W::hts_itr_multi_cram] No index entry for region 179:0-198735
  [W::hts_itr_multi_cram] No index entry for region 180:0-93321
  [W::hts_itr_multi_cram] No index entry for region 181:0-158759
  [W::hts_itr_multi_cram] No index entry for region 183:0-150742
  [W::hts_itr_multi_cram] No index entry for region 184:0-27745
  [W::hts_itr_multi_cram] No index entry for region 186:0-40191
  [W::hts_itr_multi_cram] No index entry for region 187:0-36723
  [E::hts_idx_push] Chromosome blocks not continuous
  [E::sam_index] Read 'A00744:46:HV3C3DSXX:2:1521:3179:31266' with ref_name='chrX', ref_length=156040895, flags=83, pos=113453652 cannot be indexed
  samtools index: failed to create index for "vip_AshkenazimTrio_HG003.cram.bam"

on gearshift, but consistently passes on fender compute cluster.

Workaround it to run the cram-to-bam convert-and-slice with 1 thread.