samtools-1.9 might break host filtering step
As part of the effort to enable conda-based installation, it occured that samtools-1.9 was installed, despite that 0.1.19 should be installed (iris had newer version for an as-of-yet unknown reason, i.e., all.yaml specified samtools==0.1.19 and was identical between iris and litcrit).
It is speculated that this lead to the host filtering step failing on iris:
rule mt_filtering:
input: Preprocessing/mt.r1.trimmed.rna_filtered.fq, Preprocessing/mt.r2.trimmed.rna_filtered.fq, Preprocessing/mt.se.trimmed.rna_filtered.fq,
/home/users/claczny/projects/imp-devel/dbs/hg38-db/filtering/hg38.fa, /home/users/claczny/projects/imp-devel/dbs/hg38-db/filtering/hg38.fa, /home/
users/claczny/projects/imp-devel/dbs/hg38-db/filtering/hg38.fa.amb, /home/users/claczny/projects/imp-devel/dbs/hg38-db/filtering/hg38.fa.ann, /hom
e/users/claczny/projects/imp-devel/dbs/hg38-db/filtering/hg38.fa.bwt, /home/users/claczny/projects/imp-devel/dbs/hg38-db/filtering/hg38.fa.pac, /h
ome/users/claczny/projects/imp-devel/dbs/hg38-db/filtering/hg38.fa.sa
output: Preprocessing/mt.r1.trimmed.rna_filtered.hg38_filtered.fq, Preprocessing/mt.r2.trimmed.rna_filtered.hg38_filtered.fq, Preprocessing/mt
.se.trimmed.rna_filtered.hg38_filtered.fq
jobid: 13
TMP_FILE=$(mktemp --tmpdir=/tmp -t "alignment_XXXXXX.bam")
BUFFER=$(mktemp --tmpdir=/tmp -t "alignment_XXXXXX.bam")
bwa mem -v 1 -t 26 /home/users/claczny/projects/imp-devel/dbs/hg38-db/filtering/hg38.fa Preprocessing/mt.r1.trimmed.rna_filtered.fq Prepro
cessing/mt.r2.trimmed.rna_filtered.fq | samtools view -@ 26 -bS - > $TMP_FILE
samtools merge -@ 26 -u - <(samtools view -@ 26 -u -f 4 -F 264 $TMP_FILE) <(samtools view -@ 26 -u -f 8 -F 260 $TMP_FILE)
<(samtools view -@ 26 -u -f 12 -F 256 $TMP_FILE) | samtools view -@ 26 -bF 0x800 - | samtools sort -o -@ 26 -m 2G -n - $BUFFER -
| bamToFastq -i stdin -fq Preprocessing/mt.r1.trimmed.rna_filtered.hg38_filtered.fq -fq2 Preprocessing/mt.r2.trimmed.rna_filtered.hg38_fi
ltered.fq
if [[ -s Preprocessing/mt.se.trimmed.rna_filtered.fq ]]
then
bwa mem -v 1 -t 26 /home/users/claczny/projects/imp-devel/dbs/hg38-db/filtering/hg38.fa Preprocessing/mt.se.trimmed.rna_filtered.fq | samt
ools view -@ 26 -bS - | samtools view -@ 26 -uf 4 - | bamToFastq -i stdin -fq Preprocessing/mt.se.trimmed.rna_filtered.hg38_filtered.fq
else
echo "Preprocessing/mt.se.trimmed.rna_filtered.fq is empty, skipping single end human sequence filtering, but creating it anyway..."
touch Preprocessing/mt.se.trimmed.rna_filtered.hg38_filtered.fq
fi
rm -rf $BUFFER* $TMP_FILE
[...]
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[main] Version: 0.7.9a-r786
[main] CMD: bwa mem -v 1 -t 26 /home/users/claczny/projects/imp-devel/dbs/hg38-db/filtering/hg38.fa Preprocessing/mt.r1.trimmed.rna_filtered.fq Preprocessing/mt.r2.trimmed.rna_filtered.fq
[main] Real time: 255.606 sec; CPU: 4680.023 sec
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-n Sort by read name
-t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set)
-o FILE Write final output to FILE rather than standard output
-T PREFIX Write temporary files to PREFIX.nnnn.bam
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
--output-fmt-option OPT[=VAL]
Specify a single output file format option in the form
of OPTION or OPTION=VALUE
--reference FILE
Reference sequence FASTA FILE [null]
-@, --threads INT
Number of additional threads to use [0]
[W::bam_merge_core2] No @HD tag found.
Error in rule mt_filtering:
jobid: 13
output: Preprocessing/mt.r1.trimmed.rna_filtered.hg38_filtered.fq, Preprocessing/mt.r2.trimmed.rna_filtered.hg38_filtered.fq, Preprocessing/mt.se.trimmed.rna_filtered.hg38_filtered.fqThis needs further inspection.