segmentation fault during consensus #266
Description
Hi,
I am using verkko 2.1 (bioconda verkko bioconda 2.1) in a local machine with 208 threads and 2 TB RAM, running CentOS7. I am assembling the Y chromosome of HG002 using subsets of the HiFi and ONT UL reads, and I am repeatedly getting a segmentation fault error during the consensus step. The HiFi and ONT reads were obtained as follows. I used minimap2 and seqtk to get the Y-linked reads from HiFi and ONT reads, and assembled them with verkko. Several variations worked well, but one paticular read dataset (HiFi + ONT) is always causing a fatal error (I uploaded these reads to https://drive.google.com/drive/folders/1kp4zPwQ27rNNzvXeM-3MdUT5slNXiLUH?usp=sharing). 2024-06-20T113029.669398.snakemake.log The command line I am using is:
conda activate verkko
nohup verkko -d Y_asm2 --local-memory 1000 --hifi HiFi35x_Yreads_clean.fastq.gz --nano ONT60x_Yreads_clean.fastq.gz --threads 100 > nohup_Y_asm2.txt &
I attached the snakemake log file.
The error message follows:
Consensus did not finish successfully, exit code \$?.
69 of 72 steps (96%) done
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-06-17T214529.496147.snakemake.log
Digging a bit more, I found no error message in ./7-consensus/buildPackages.err , but there is a detailed report in 7-consensus/packages/part005.err , as follows in the end of this message.
I obtained the reads twice (using seqtk)), with the same error result. So now I am stuck. Any suggestions?
thanks,
Bernardo
# -- Opening output FASTA file '../7-consensus/packages/part005.fasta.WORKING'.
# --
# -- Computing consensus for b=0 to e=4294967295 with errorRate 0.0500 (max 0.2000) and minimum overlap 3000
# --
# alignEdLib()-- WARNING: tigbgn 533523 > tigend 531512 - tiglen 531512 utgpos 533773-549246 padding 250
# alignEdLib()-- WARNING: updated tigbgn 0 > tigend 549246 - tiglen 531512 utgpos 533773-549246 padding 250
# alignEdLib()-- WARNING: tigbgn 534370 > tigend 531512 - tiglen 531512 utgpos 534620-554990 padding 250
# alignEdLib()-- WARNING: updated tigbgn 0 > tigend 554990 - tiglen 531512 utgpos 534620-554990 padding 250
# alignEdLib()-- WARNING: tigbgn 536266 > tigend 531512 - tiglen 531512 utgpos 536516-549917 padding 250
# alignEdLib()-- WARNING: updated tigbgn 0 > tigend 549917 - tiglen 531512 utgpos 536516-549917 padding 250
# alignEdLib()-- WARNING: tigbgn 536530 > tigend 531512 - tiglen 531512 utgpos 536780-548120 padding 250
# alignEdLib()-- WARNING: updated tigbgn 0 > tigend 548120 - tiglen 531512 utgpos 536780-548120 padding 250
# ERROR: alignment from 535366 to 546625, but tiglen is only 531512
# utgcns: utgcns/unitigConsensus.C:869: bool alignEdLib(dagAlignment&, tgPosition&, char*, uint32, char*, uint32, double, bool): Assertion `aln.end <= tiglen' failed.
# ----------CONTAINED READS---------- -DOVETAIL READS-
# tigID length reads used coverage ignored coverage used coverage
# ------- --------- ------- -------- -------- -------- -------- -------- --------
# 6 14740 4 2 1.19x 0 0.00x 2 1.68x
# 11 1572918 2107 1419 8.93x 0 0.00x 688 5.87x
# 18 469157 535 345 7.86x 0 0.00x 190 5.75x
# 30 453951 181 175 8.88x 0 0.00x 6 2.39x
# Failed with 'Aborted'; backtrace (libbacktrace):
# Failed with 'Segmentation fault'; backtrace (libbacktrace):
# ./packages/part005.sh: line 18: 293115 Segmentation fault (core dumped) /home6/tools/miniconda3/envs/verkko/lib/verkko/bin/utgcns -threads 8 -import ../7-consensus/packages/part005.cnspack -A ../7-consensus/packages/part005.fasta.WORKING -C 2 -norealign -maxcoverage 50 -e 0.05 -em 0.20 -EM 0 -l 3000 -edlib
# Consensus did not finish successfully, exit code 0.
# Files in current directory:
# total 8896
# -rwxr-xr-x 1 bernardo tools 1215 Jun 20 10:08 extractONT.sh
# -rw-r--r-- 1 bernardo tools 48 Jun 20 10:08 extractONT.err
# -rw-r--r-- 1 bernardo tools 3848 Jun 20 10:08 ont_subset.id
# -rw-r--r-- 1 bernardo tools 4853742 Jun 20 10:08 ont_subset.fasta.gz
# -rw-r--r-- 1 bernardo tools 86 Jun 20 10:08 ont_subset.extract
# -rwxr-xr-x 1 bernardo tools 447 Jun 20 10:08 buildPackages.sh
# -rw-r--r-- 1 bernardo tools 4199297 Jun 20 10:08 packages.readName_to_ID.map
# -rw-r--r-- 1 bernardo tools 18024 Jun 20 10:09 buildPackages.err
# -rw-r--r-- 1 bernardo tools 870 Jun 20 10:09 packages.tigName_to_ID.map
# -rw-r--r-- 1 bernardo tools 2855 Jun 20 10:09 packages.report
# -rw-r--r-- 1 bernardo tools 0 Jun 20 10:09 packages.finished
# drwxr-xr-x 2 bernardo tools 4096 Jun 20 10:11 packages
# Files in packages/:
# total 311764
# -rw-r--r-- 1 bernardo tools 159536904 Jun 20 10:09 part001.cnspack
# -rw-r--r-- 1 bernardo tools 12873952 Jun 20 10:09 part005.cnspack
# -rw-r--r-- 1 bernardo tools 12977304 Jun 20 10:09 part004.cnspack
# -rw-r--r-- 1 bernardo tools 13103980 Jun 20 10:09 part003.cnspack
# -rw-r--r-- 1 bernardo tools 61223936 Jun 20 10:09 part002.cnspack
# -rw-r--r-- 1 bernardo tools 11476064 Jun 20 10:09 part007.cnspack
# -rw-r--r-- 1 bernardo tools 11586852 Jun 20 10:09 part006.cnspack
# -rw-r--r-- 1 bernardo tools 6079000 Jun 20 10:09 part008.cnspack
# -rwxr-xr-x 1 bernardo tools 605 Jun 20 10:09 part006.sh
# -rwxr-xr-x 1 bernardo tools 605 Jun 20 10:09 part007.sh
# -rwxr-xr-x 1 bernardo tools 605 Jun 20 10:09 part005.sh
# -rwxr-xr-x 1 bernardo tools 605 Jun 20 10:09 part004.sh
# -rwxr-xr-x 1 bernardo tools 605 Jun 20 10:09 part003.sh
# -rwxr-xr-x 1 bernardo tools 605 Jun 20 10:09 part001.sh
# -rw-r--r-- 1 bernardo tools 0 Jun 20 10:09 part001.fasta.WORKING
# -rw-r--r-- 1 bernardo tools 191 Jun 20 10:09 part001.err
# -rwxr-xr-x 1 bernardo tools 605 Jun 20 10:09 part002.sh
# -rwxr-xr-x 1 bernardo tools 605 Jun 20 10:09 part008.sh
# -rw-r--r-- 1 bernardo tools 191 Jun 20 10:09 part008.err
# -rw-r--r-- 1 bernardo tools 1032192 Jun 20 10:09 part008.fasta.WORKING
# -rw-r--r-- 1 bernardo tools 771 Jun 20 10:09 part006.err
# -rw-r--r-- 1 bernardo tools 2669120 Jun 20 10:09 part006.fasta
# -rw-r--r-- 1 bernardo tools 853 Jun 20 10:09 part007.err
# -rw-r--r-- 1 bernardo tools 2727324 Jun 20 10:09 part007.fasta
# -rw-r--r-- 1 bernardo tools 525 Jun 20 10:09 part003.err
# -rw-r--r-- 1 bernardo tools 3338554 Jun 20 10:09 part003.fasta
# -rw-r--r-- 1 bernardo tools 525 Jun 20 10:09 part004.err
# -rw-r--r-- 1 bernardo tools 3051813 Jun 20 10:09 part004.fasta
# -rw-r--r-- 1 bernardo tools 525 Jun 20 10:11 part002.err
# -rw-r--r-- 1 bernardo tools 14652343 Jun 20 10:11 part002.fasta
# -rw-r--r-- 1 bernardo tools 2817683 Jun 20 10:12 part005.fasta.WORKING
# -rw-r--r-- 1 bernardo tools 3174 Jun 20 10:12 part005.err