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wwood / dirseq

Work out whether RNAseq reads in general agree with the direction of the gene predicted
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Chromosome undefined #7

Open uqmwu opened 2 years ago

uqmwu commented 2 years ago

Hi Ben， Now I have installed dirseq and tried with the example you provided, no issue. But when I use it for my data, I have got the following error:

INFO dirseq 24/06 12:08:52: Running command: sed '/^##FASTA$/,$d' "/scratch/project/alkane/C3_anammox/C3_anammox_BINNING/prokka_anotate/prokka_out/bin.0/bin.0.gff" > /scratch/user/uqmwu4/tmp/dirseq20220624-16987-cnw3os.gff3 INFO dirseq 24/06 12:08:52: Command finished with exitstatus 0 INFO dirseq 24/06 12:08:52: Listing contigs in sorted order .. INFO dirseq 24/06 12:08:52: Running command: samtools idxstats "/scratch/project/alkane/C3_anammox/bam_filter/bin.0.bam" |cut -f1,2 |grep -v '^*' >"/scratch/user/uqmwu4/tmp/bam_contigs20220624-16987-1othn1o" INFO dirseq 24/06 12:08:52: Command finished with exitstatus 0 INFO dirseq 24/06 12:08:52: Finding featureless contigs INFO dirseq 24/06 12:08:52: Running command: grep -v '^#' "/scratch/user/uqmwu4/tmp/dirseq20220624-16987-cnw3os.gff3" |cut -f1 |sort |uniq |grep -vFw -f /dev/stdin "/scratch/user/uqmwu4/tmp/bam_contigs20220624-16987-1othn1o" |cut -f1 INFO dirseq 24/06 12:08:52: Command finished with exitstatus 0 INFO dirseq 24/06 12:08:52: Found 596 featureless contigs INFO dirseq 24/06 12:08:52: Running bedtools sort INFO dirseq 24/06 12:08:52: Running command: cat /scratch/user/uqmwu4/tmp/extra_features20220624-16987-cz5y3.gff "/scratch/user/uqmwu4/tmp/dirseq20220624-16987-cnw3os.gff3" |bedtools sort -i /dev/stdin -faidx "/scratch/user/uqmwu4/tmp/bam_contigs20220624-16987-1othn1o" >"/scratch/user/uqmwu4/tmp/sorted_gff20220624-16987-ayr8yn.gff3" INFO dirseq 24/06 12:08:52: Command finished with exitstatus 1 /home/uqmwu4/.gem/ruby/gems/bio-commandeer-0.4.0/lib/bio-commandeer/commandeer.rb:62:in `raise_if_failed': Command returned non-zero exit status (1), likely indicating failure. Command run was cat /scratch/user/uqmwu4/tmp/extra_features20220624-16987-cz5y3.gff "/scratch/user/uqmwu4/tmp/dirseq20220624-16987-cnw3os.gff3" |bedtools sort -i /dev/stdin -faidx "/scratch/user/uqmwu4/tmp/bam_contigs20220624-16987-1othn1o" >"/scratch/user/uqmwu4/tmp/sorted_gff20220624-16987-ayr8yn.gff3" and the STDERR was: (Bio::CommandFailedException) Chromosome "k141_100310_length_12288" undefined in /scratch/user/uqmwu4/tmp/bam_contigs20220624-16987-1othn1o

The bam file was generated using coverM make and then filtered using coverM filter. So what is the issue here? Thanks!

wwood commented 2 years ago

Hi,

This looks to me as if the BAM files where not made by mapping to the same set of contigs that went into the bin itself. So they have different names, does that sound plausible?

wwood commented 1 year ago

Hmm, would you mind sending the data to me somehow and the command line that you used? E.g. via cloudstor to my QUT email account, please? Hard to know from that log.

-------------- Ben Woodcroft Group leader, Centre for Microbiome Research, QUT

From: uqmwu @.> Sent: Friday, June 24, 2022 2:52:20 PM To: wwood/dirseq @.> Cc: Subscribed @.***> Subject: [wwood/dirseq] Chromosome undefined (Issue #7)

Hi Ben， Now I have installed dirseq and tried with the example you provided, no issue. But when I use it for my data, I have got the following error:

INFO dirseq 24/06 12:08:52: Running command: sed '/^##FASTA$/,$d' "/scratch/project/alkane/C3_anammox/C3_anammox_BINNING/prokka_anotate/prokka_out/bin.0/bin.0.gff" > /scratch/user/uqmwu4/tmp/dirseq20220624-16987-cnw3os.gff3 INFO dirseq 24/06 12:08:52: Command finished with exitstatus 0 INFO dirseq 24/06 12:08:52: Listing contigs in sorted order .. INFO dirseq 24/06 12:08:52: Running command: samtools idxstats "/scratch/project/alkane/C3_anammox/bam_filter/bin.0.bam" |cut -f1,2 |grep -v '^*' >"/scratch/user/uqmwu4/tmp/bam_contigs20220624-16987-1othn1o" INFO dirseq 24/06 12:08:52: Command finished with exitstatus 0 INFO dirseq 24/06 12:08:52: Finding featureless contigs INFO dirseq 24/06 12:08:52: Running command: grep -v '^#' "/scratch/user/uqmwu4/tmp/dirseq20220624-16987-cnw3os.gff3" |cut -f1 |sort |uniq |grep -vFw -f /dev/stdin "/scratch/user/uqmwu4/tmp/bam_contigs20220624-16987-1othn1o" |cut -f1 INFO dirseq 24/06 12:08:52: Command finished with exitstatus 0 INFO dirseq 24/06 12:08:52: Found 596 featureless contigs INFO dirseq 24/06 12:08:52: Running bedtools sort INFO dirseq 24/06 12:08:52: Running command: cat /scratch/user/uqmwu4/tmp/extra_features20220624-16987-cz5y3.gff "/scratch/user/uqmwu4/tmp/dirseq20220624-16987-cnw3os.gff3" |bedtools sort -i /dev/stdin -faidx "/scratch/user/uqmwu4/tmp/bam_contigs20220624-16987-1othn1o" >"/scratch/user/uqmwu4/tmp/sorted_gff20220624-16987-ayr8yn.gff3" INFO dirseq 24/06 12:08:52: Command finished with exitstatus 1 /home/uqmwu4/.gem/ruby/gems/bio-commandeer-0.4.0/lib/bio-commandeer/commandeer.rb:62:in `raise_if_failed': Command returned non-zero exit status (1), likely indicating failure. Command run was cat /scratch/user/uqmwu4/tmp/extra_features20220624-16987-cz5y3.gff "/scratch/user/uqmwu4/tmp/dirseq20220624-16987-cnw3os.gff3" |bedtools sort -i /dev/stdin -faidx "/scratch/user/uqmwu4/tmp/bam_contigs20220624-16987-1othn1o" >"/scratch/user/uqmwu4/tmp/sorted_gff20220624-16987-ayr8yn.gff3" and the STDERR was: (Bio::CommandFailedException) Chromosome "k141_100310_length_12288" undefined in /scratch/user/uqmwu4/tmp/bam_contigs20220624-16987-1othn1o

The bam file was generated using coverM make and then filtered using coverM filter. So what is the issue here? Thanks!

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