Error "No such file or directory) Error parsing loci file line" when run ascat.pl

[yufanzhouonline]

Hi keiranmraine,

When run ascat.pl on Docker, I found an error.

Then I change SNP corrections files of chromosome 1, 2, 3 ... to chr1, chr2, chr3 to make chromosome labels same as bam file.

But the error is still there in "Sanger_CGP_Ascat_Implement_allele_count.1.err"

I only test chromosome 19 with command line:

ascat.pl -t /share/a3b4nqo/gatk/mousechr19/CD_4NQO_178_tumor_S26.rg.dup.sort.realn.chr19.bam -n /share/a3b4nqo/gatk/mousechr19/CD_4NQO_178_tail_S25.rg.dup.sort.realn.chr19.bam -r /share/a3b4nqo/gatk/mousechr19/CD_4NQO_178_ascat/mm10_selected.fa -sg /share/a3b4nqo/gatk/mousechr19/CD_4NQO_178_ascat/SnpGcCorrectionsYZnew.tsv -pr WGS -g XY -gc Y -o /share/a3b4nqo/gatk/mousechr19/CD_4NQO_178_ascat/changexy/ 2>&1 | tee runascat.log

The following is Sanger_CGP_Ascat_Implement_allele_count.1.err:

• cut -f 2,3 /share/a3b4nqo/gatk/mousechr19/CD_4NQO_178_ascat/SnpGcCorrectionsYZnew.tsv
• grep -vP '^Chr\tPosition'
• grep -P '^61331239 '
• /opt/wtsi-cgp/bin/alleleCounter -b /share/a3b4nqo/gatk/mousechr19/CD_4NQO_178_tumor_S26.rg.dup.sort.realn.chr19.bam -o /share/a3b4nqo/gatk/mousechr19/CD_4NQO_178_ascat/changexy/tmpAscat/allele_count/CD_4NQO_178_tumor_S26.61331239.allct -l /share/a3b4nqo/gatk/mousechr19/CD_4NQO_178_ascat/changexy/tmpAscat/allele_count/loci_files/CD_4NQO_178_tumor_S26.61331239 -c 61331239 -r /share/a3b4nqo/gatk/mousechr19/CD_4NQO_178_ascat/mm10_selected.fa -d -m 20
  Reading locis
  [ERROR] (./src/alleleCounter.c: get_position_info_from_file:288 errno: No such file or directory) Error parsing loci file line number 0 as a string match: '61331239 .
  '.
  [ERROR] (./src/alleleCounter.c: read_locis_from_file:359 errno: None) Error trying to fetch position from file at line 0.
  Done reading locis
  [ERROR] (./src/alleleCounter.c: main:411 errno: None) Error reading loci_stats from file.
  /share/a3b4nqo/gatk/mousechr19/CD_4NQO_178_ascat/changexy/tmpAscat/logs/Sanger_CGP_Ascat_Implement_allele_count.1.sh: line 4: 230 Aborted (core dumped) /opt/wtsi-cgp/bin/alleleCounter -b /share/a3b4nqo/gatk/mousechr19/CD_4NQO_178_tumor_S26.rg.dup.sort.realn.chr19.bam -o /share/a3b4nqo/gatk/mousechr19/CD_4NQO_178_ascat/changexy/tmpAscat/allele_count/CD_4NQO_178_tumor_S26.61331239.allct -l /share/a3b4nqo/gatk/mousechr19/CD_4NQO_178_ascat/changexy/tmpAscat/allele_count/loci_files/CD_4NQO_178_tumor_S26.61331239 -c 61331239 -r /share/a3b4nqo/gatk/mousechr19/CD_4NQO_178_ascat/mm10_selected.fa -d -m 20
  Command exited with non-zero status 134
  87.33user 18.37system 1:18.40elapsed 134%CPU (0avgtext+0avgdata 1624maxresident)k
  3184inputs+32outputs (15major+2590minor)pagefaults 0swaps

Would you please let me know how I fix this issue?

Thank you so much