Thanks a lot for the reply. I found out a mistake in the path in the bam list but the same error shows up. After running the command independently this is what I get
dell@ubuntu:~$ calcRoiCovg /media/dell/NEW/ACTREC-12.rmdup.bam /media/dell/NEW/ACTREC-4.rmdup.bam /home/dell/Downloads/rois.tsv /home/dell/Downloads/hg19from2bit.fa /home/dell/Downloads/output/roicovgs/120418I812FCD0VLLACXXL5HUMpxiXAABAAAPEI-54.covg 6 8 20
[bamheaderread] EOF marker is absent.
Badly formatted ROI: chr1 16007988 16008107
ROI file should be a tab-delimited list of [chrom, start, stop, annotation]
where start and stop are both 1-based chromosomal loci
For example:
20 44429404 44429608 ELMO2
MT 5903 7445 MT-CO1
NOTE: ROI file must be sorted by chromosome/contig names
gmt music bmr calc-covg-helper --normal-tumor-bam-pair "120418I812FCD0VLLACXXL5HUMpxiXAABAAAPEI-54/media/dell/NEW/ACTREC-12.rmdup.bam/media/dell/NEW/ACTREC-4.rmdup.bam" --roi-file "/home/dell/Downloads/rois.tsv" --reference-sequence "/home/dell/Downloads/hg19from2bit.fa" --output-file "/home/dell/Downloads/output/roicovgs/120418I812FCD0VLLACXXL5HUMpxiXAABAAAPEI-54.covg"
*Use of uninitialized value $normalbam in -s at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm line 143.
Use of uninitialized value $normalbam in concatenation (.) or string at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm line 143.
Normal BAM file not found or is empty:
Use of uninitialized value $tumorbam in -s at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm line 144.
Use of uninitialized value $tumorbam in concatenation (.) or string at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm line 144.
Tumor BAM file not found or is empty:
Use of uninitialized value $normal_bam in -s at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm line 145.
ERROR: Please see 'gmt music bmr calc-covg-helper --help' for more information.
About the EOF marker can it be added to the file separately by script? And I also tried the by removing the chr prefix from chromosomes of ROI file but it Skipped all the ROIs of chr 1 and rest is not taken in both cases and no output is getting generated. I have used joinx comand to sort my ROI file.
My ROI file looks like this:
chr1 14643 14762 LOC376475
chr1 14763 14882 LOC376475
chr1 14944 15063 FAM39B
bamlist
120418I812FCD0VLLACXXL5HUMpxiXAABAAAPEI-54 /media/dell/NEW/ACTREC-12.rmdup.bam /media/dell/NEW/ACTREC-4.rmdup.bam
120418I812FCD0VLLACXXL5HUMpxiXAABAAAPEI-54 /media/dell/NEW/ACTREC-12.rmdup.bam /media/dell/NEW/ACTREC-4.rmdup.bam
120418I812FCD0VLLACXXL5_HUMpxiXAABAAAPEI-54 /media/dell/NEW/ACTREC-12.rmdup.bam /media/dell/NEW/ACTREC-4.rmdup.bam
other than this I am also getting the following error:
dell@ubuntu:~$ genome music bmr calc-covg \
--bam-list /home/dell/Downloads/bam_list \
--output-dir /home/dell/Downloads/output/ \
--reference-sequence /home/dell/Downloads/hg19_from_2bit.fa \
--roi-file /home/dell/Downloads/roi_s.tsv
[bamheaderread] EOF marker is absent.
Badly formatted ROI: chr1 16007988 16008107
ROI file should be a tab-delimited list of [chrom, start, stop, annotation]
where start and stop are both 1-based chromosomal loci
For example:
20 44429404 44429608 ELMO2
MT 5903 7445 MT-CO1
NOTE: ROI file must be sorted by chromosome/contig names
Failed to execute: calcRoiCovg /media/dell/NEW/ACTREC-12.rmdup.bam /media/dell/NEW/ACTREC-4.rmdup.bam /home/dell/Downloads/rois.tsv /home/dell/Downloads/hg19from2bit.fa /home/dell/Downloads/output/roicovgs/120418I812FCD0VLLACXXL5HUMpxiXAABAAAPEI-54.covg 6 8 20
Failed to execute: 'gmt music bmr calc-covg-helper --normal-tumor-bam-pair "120418I812FCD0VLLACXXL5HUMpxiXAABAAAPEI-54 /media/dell/NEW/ACTREC-12.rmdup.bam /media/dell/NEW/ACTREC-4.rmdup.bam" --roi-file "/home/dell/Downloads/rois.tsv" --reference-sequence "/home/dell/Downloads/hg19from2bit.fa" --output-file "/home/dell/Downloads/output/roicovgs/120418I812FCD0VLLACXXL5HUMpxiXAABAAAPEI-54.covg"'
120418I812FCD0VLLACXXL5HUMpxiXAABAAAPEI-54.covg found in /home/dell/Downloads/output/roicovgs. Skipping re-calculation.
Use of uninitialized value $totcovd in concatenation (.) or string at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcCovg.pm line 353.
Use of uninitialized value $totatcovd in concatenation (.) or string at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcCovg.pm line 353.
Use of uninitialized value $totcgcovg in concatenation (.) or string at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcCovg.pm line 353.
Use of uninitialized value $totcpgcovd in concatenation (.) or string at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcCovg.pm line 353.
I know this is very long but I am very new to this. Your help would be greatly appreciated. Thank You.
Hello,
I'm trying to run bmr calc-covg and got an warning message:
[fai_fetch] Warning - Reference 1 not found in FASTA file, returning empty sequence Failed to execute: calcRoiCovg ..,
I checked my ROI file to make sure the format is fine. ROI file looks like this:
1 10003486 10045556 NMNAT1 1 100111431 100160097 PALMD 1 100174259 100231349 FRRS1 1 10027439 10027516 MIR5697 ...
I also changed the fasta file so that the sequence header match the chr name in ROI
What could be the reason for the error?
Thanks!