Stuck halfway

[shaka-emperor]

Hi, I used following command to process 24 chromosome simultaneously:

cat 1.txt | parallel /home/IFNgroup/yejianyu/IMSindel/bin/imsindel --thread 1 --chr {} --bam /home/IFNgroup/yejianyu/Whloe_Genome_sequence/202201_WGS/data_process/P1_NORM_GRCh38_HBV.sort.bam --outd P1_Norm --indelsize 10000 --reffa /home/IFNgroup/yejianyu/ref/bwa_build_index/GRCh38.fa (40 threads, 128 GB ram)

head 1.txt chr1 chr2 chr3 chr4 chr5

While it gave me back 18 chromosomes output, there still had nothing for the rest 6 chromosomes. And here is the last running message from IMSindel, I am not sure whether it is a warning message or not, but It stuck here for a week.

2. collecting unmapped reads...done
3. considering support reads...

   backward clip with support reads: 1684

   forward clip with support reads: 1575

   non_clips with suport reads: 4616

4. considering support reads...done
5. making consensus seqs from support reads... v7.490 (2021/Oct/30) mafft stderr: outputhat23=16 treein = 0 compacttree = 0 stacksize: 8192 kb generating a scoring matrix for nucleotide (dist=200) ... done All-to-all alignment. /home/yejianyu/anaconda3/bin/mafft: line 2756: 42213 Killed "$prefix/tbfast" -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -O $LGOP -E $LEXP -N $usenaivepairscore $focusarg -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>> "$progressfile"

   <Thread:0x000055c92855a360@/home/IFNgroup/yejianyu/IMSindel/lib/ims_indel/consensus.rb:84 run> terminated with exception (report_on_exception is true):

   /home/IFNgroup/yejianyu/IMSindel/lib/ims_indel/consensus_util.rb:17:in trim_consensus': undefined methodinclude?' for nil:NilClass (NoMethodError) from /home/IFNgroup/yejianyu/IMSindel/lib/ims_indel/consensus.rb:102:in block in make_consensus' from /home/IFNgroup/yejianyu/IMSindel/lib/ims_indel/consensus.rb:100:ineach' from /home/IFNgroup/yejianyu/IMSindel/lib/ims_indel/consensus.rb:100:in with_index' from /home/IFNgroup/yejianyu/IMSindel/lib/ims_indel/consensus.rb:100:inmake_consensus' from /home/IFNgroup/yejianyu/IMSindel/lib/ims_indel/consensus.rb:85:in block (2 levels) in make_consensus_with_threads' /home/IFNgroup/yejianyu/IMSindel/lib/ims_indel/consensus_util.rb:17:intrim_consensus': undefined method include?' for nil:NilClass (NoMethodError) from /home/IFNgroup/yejianyu/IMSindel/lib/ims_indel/consensus.rb:102:inblock in make_consensus' from /home/IFNgroup/yejianyu/IMSindel/lib/ims_indel/consensus.rb:100:in each' from /home/IFNgroup/yejianyu/IMSindel/lib/ims_indel/consensus.rb:100:inwith_index' from /home/IFNgroup/yejianyu/IMSindel/lib/ims_indel/consensus.rb:100:in make_consensus' from /home/IFNgroup/yejianyu/IMSindel/lib/ims_indel/consensus.rb:85:inblock (2 levels) in make_consensus_with_threads'

[holrock]

It seems that mafft has terminated with an error. IMSindel is failing to catch the error. programs has stopped.