Stampy software error with PairSorter

megnat · 11-26-2020, 04:04 AM

Hi all,
I am trying to map reads (Paired End) from a sample to a reference assembly that is somewhat divergenct (~3%). So I used the bam file after bwa mapping and tried to run that through stampy again as follows:
${STAMPY} -t30 -g athCun1_ens -h athCun1_ens --bamkeepgoodreads --bwamark --substitutionrate=0.03 --output=JO1.adaptersmarked.aligned.merged.ensembl.stampy-div3.sam -M JO1.adaptersmarked.aligned.merged.ensembl.bam
It created multiple bam and one sam file (I had listed sam as the output type, by extension). The output error file had an error in it (see below) but also the numbers of aligned reads (I think).
stampy: (PairSorter) 'samtools sort -o -n -m200000000 - JO1.adaptersmarked.aligned.merged.ensembl.stampy-div3.samec7b5a5b-5bec-4c39-9ab4-ce6e1f320c23' returned messages on stderr:
stampy: (PairSorter) (samtools ERROR) [bam_header_read] EOF marker is absent. The input is probably truncated.
stampy: (PairSorter) 'samtools view -h -' returned messages on stderr:
stampy: (PairSorter) (samtools ERROR) [bam_header_read] EOF marker is absent. The input is probably truncated.
stampy: # Nucleotides (all/1/2): 52813084200 26406542100 26406542100
stampy: # Variants: 3212191560 1458708466 1753483094
stampy: # Fraction: 0.0608 0.0552 0.0664
stampy: Done
However, when I checked the output sam file with samtools flagstat, it showed almost the same number (and percentage) of reads getting mapped. However, the proportion of properly paired reads went down a bit.
Would you know (a) what the error means and how to fix that? (b) Why I might be getting mapping where the proportion of paired reads decreases?
Thank you in advance!

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
SUBJECT: Stampy software error with PairSorter	megnat	Bioinformatics	0	11-26-2020 01:11 AM
Unknown error with Stampy	vivi7	Bioinformatics	2	08-16-2016 12:46 AM
stampy install error	bossy	Bioinformatics	2	02-11-2014 08:36 AM
stampy error with bwa	pankajsvats	Bioinformatics	6	01-11-2012 06:39 AM

11-26-2020, 04:04 AM	#1
megnat Junior Member Location: India Join Date: Nov 2020 Posts: 2	Stampy software error with PairSorter Hi all, I am trying to map reads (Paired End) from a sample to a reference assembly that is somewhat divergenct (~3%). So I used the bam file after bwa mapping and tried to run that through stampy again as follows: ${STAMPY} -t30 -g athCun1_ens -h athCun1_ens --bamkeepgoodreads --bwamark --substitutionrate=0.03 --output=JO1.adaptersmarked.aligned.merged.ensembl.stampy-div3.sam -M JO1.adaptersmarked.aligned.merged.ensembl.bam It created multiple bam and one sam file (I had listed sam as the output type, by extension). The output error file had an error in it (see below) but also the numbers of aligned reads (I think). stampy: (PairSorter) 'samtools sort -o -n -m200000000 - JO1.adaptersmarked.aligned.merged.ensembl.stampy-div3.samec7b5a5b-5bec-4c39-9ab4-ce6e1f320c23' returned messages on stderr: stampy: (PairSorter) (samtools ERROR) [bam_header_read] EOF marker is absent. The input is probably truncated. stampy: (PairSorter) 'samtools view -h -' returned messages on stderr: stampy: (PairSorter) (samtools ERROR) [bam_header_read] EOF marker is absent. The input is probably truncated. stampy: # Nucleotides (all/1/2): 52813084200 26406542100 26406542100 stampy: # Variants: 3212191560 1458708466 1753483094 stampy: # Fraction: 0.0608 0.0552 0.0664 stampy: Done However, when I checked the output sam file with samtools flagstat, it showed almost the same number (and percentage) of reads getting mapped. However, the proportion of properly paired reads went down a bit. Would you know (a) what the error means and how to fix that? (b) Why I might be getting mapping where the proportion of paired reads decreases? Thank you in advance!