MissingOutputException for "samtools index" with 0.0.13
smoe opened this issue · comments
Hello,
[Sat Jun 5 17:28:07 2021]
rule index_bam:
input: /home/moeller/pigx-rnaseq/pigx-rnaseq/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam
output: /home/moeller/pigx-rnaseq/pigx-rnaseq/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai
log: /home/moeller/pigx-rnaseq/pigx-rnaseq/tests/output/logs/samtools_index_UHR_Rep3.log
jobid: 38
wildcards: sample=UHR_Rep3
/usr/bin/samtools index /home/moeller/pigx-rnaseq/pigx-rnaseq/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam /home/moeller/pigx-rnaseq/pigx-rnaseq/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai >> /home/moeller/pigx-rnaseq/pigx-rnaseq/tests/output/logs/samtools_index_HBR_Rep3.log 2>&1
Waiting at most 5 seconds for missing files.
MissingOutputException in line 369 of /home/moeller/pigx-rnaseq/pigx-rnaseq/snakefile.py:
Job completed successfully, but some output files are missing. Missing files after 5 seconds:
/home/moeller/pigx-rnaseq/pigx-rnaseq/tests/output/salmon_index/sa.bin
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.
File "/usr/lib/python3/dist-packages/snakemake/executors/__init__.py", line 544, in handle_job_success
File "/usr/lib/python3/dist-packages/snakemake/executors/__init__.py", line 225, in handle_job_success
with
$ /usr/bin/samtools --version
samtools 1.11
Using htslib 1.11-4
Copyright (C) 2020 Genome Research Ltd.
and
$ ./pigx-rnaseq --version
PiGx RNAseq Pipeline.
Version: 0.0.13
I had solved that issue before, just had a look at my previous patches that had not applied to the new version:
Index: pigx-rnaseq/tests/test_salmon/test_salmon_index.sh.in
===================================================================
--- pigx-rnaseq.orig/tests/test_salmon/test_salmon_index.sh.in
+++ pigx-rnaseq/tests/test_salmon/test_salmon_index.sh.in
@@ -26,7 +26,7 @@ head -n 2 ${samplesheet} > ${tmp_samples
${builddir}/pigx-rnaseq -s ${tmp_settings} --target salmon_index ${tmp_samplesheet}
rm ${tmp_settings} ${tmp_samplesheet}
-if ! test -f ${testfolder}/salmon_index/sa.bin
+if ! test -f ${testfolder}/salmon_index/pos.bin
then
echo "ERROR: failed the SALMON indexing test"
exit 1
Index: pigx-rnaseq/snakefile.py
===================================================================
--- pigx-rnaseq.orig/snakefile.py
+++ pigx-rnaseq/snakefile.py
@@ -187,7 +187,7 @@ targets = {
'salmon_index' : {
'description': "Create SALMON index file.",
'files':
- [os.path.join(OUTPUT_DIR, 'salmon_index', "sa.bin")]
+ [os.path.join(OUTPUT_DIR, 'salmon_index', "pos.bin")]
},
'salmon_quant' : {
'description': "Calculate read counts per transcript using SALMON.",
@@ -370,7 +370,7 @@ rule salmon_index:
input:
CDNA_FASTA
output:
- salmon_index_file = os.path.join(OUTPUT_DIR, 'salmon_index', "sa.bin")
+ salmon_index_file = os.path.join(OUTPUT_DIR, 'salmon_index', "pos.bin")
params:
salmon_index_dir = os.path.join(OUTPUT_DIR, 'salmon_index')
log: os.path.join(LOG_DIR, "salmon", 'salmon_index.log')
The reason is likely that Debian ships
$ salmon --version
salmon 1.4.0
while guix is on 0.13.1 - released in March 2019 (just checked on https://github.com/COMBINE-lab/salmon/releases).
Oops, I guess I should finally make some time to upgrade salmon in Guix. Thanks for the hint!