[Debian-med-packaging] Bug#1114262: pigx-rnaseq: FTBFS: dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
Santiago Vila
sanvila at debian.org
Fri Sep 5 19:22:24 BST 2025
Package: src:pigx-rnaseq
Version: 0.1.1-1
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build.
Below you will find how the build ends (probably the most relevant part,
but not necessarily). If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202509/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:pigx-rnaseq, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
rm -rf pigx-common
rm -f config.log test.sh
rm -rf tests/output
rm -f Makefile.in aclocal.m4 build-aux/install-sh build-aux/missing build-aux/test-driver
rm -f scripts/jquery.min.js
rm -f conftest.tar confdefs.h
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
rm -f debian/debhelper-build-stamp
[... snipped ...]
reason: Missing output files: /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep2/quant.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep2/quant.genes.sf; Input files updated by another job: /<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz, /<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin
wildcards: sample=UHR_Rep2
resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 6
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=6000, mem_mib=5723
Select jobs to execute...
/usr/bin/salmon quant -i /<<PKGBUILDDIR>>/tests/output/salmon_index -l A -p 8 -1 /<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz -2 /<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz -o /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep2 --seqBias --gcBias -g /<<PKGBUILDDIR>>/tests/sample_data/sample.gtf >> /<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_UHR_Rep2.log 2>&1
[Fri Sep 5 00:06:02 2025]
Finished job 12.
28 of 49 steps (57%) done
Select jobs to execute...
[Fri Sep 5 00:06:02 2025]
rule salmon_quant:
input: /<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin, /<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz
output: /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep1/quant.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep1/quant.genes.sf
log: /<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_UHR_Rep1.log
jobid: 10
reason: Missing output files: /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep1/quant.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep1/quant.genes.sf; Input files updated by another job: /<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin, /<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz
wildcards: sample=UHR_Rep1
resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 6
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=6000, mem_mib=5723
Select jobs to execute...
/usr/bin/salmon quant -i /<<PKGBUILDDIR>>/tests/output/salmon_index -l A -p 8 -1 /<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz -2 /<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz -o /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep1 --seqBias --gcBias -g /<<PKGBUILDDIR>>/tests/sample_data/sample.gtf >> /<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_UHR_Rep1.log 2>&1
[Fri Sep 5 00:06:04 2025]
Finished job 10.
29 of 49 steps (59%) done
Select jobs to execute...
[Fri Sep 5 00:06:04 2025]
rule count_reads:
input: /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai
output: /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv
log: /<<PKGBUILDDIR>>/tests/output/logs/hisat2/UHR_Rep2.count_reads.log
jobid: 34
reason: Missing output files: /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv; Input files updated by another job: /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai
wildcards: sample=UHR_Rep2
resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723
/usr/bin/Rscript --vanilla /<<PKGBUILDDIR>>/scripts//count_reads.R UHR_Rep2 /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam /<<PKGBUILDDIR>>/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /<<PKGBUILDDIR>>/tests/output/logs/hisat2/UHR_Rep2.count_reads.log 2>&1
[Fri Sep 5 00:06:06 2025]
Finished job 28.
30 of 49 steps (61%) done
Select jobs to execute...
[Fri Sep 5 00:06:06 2025]
rule salmon_quant:
input: /<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin, /<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz
output: /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep1/quant.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep1/quant.genes.sf
log: /<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_HBR_Rep1.log
jobid: 3
reason: Missing output files: /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep1/quant.sf; Input files updated by another job: /<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz, /<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin
wildcards: sample=HBR_Rep1
resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723
[Fri Sep 5 00:06:06 2025]
Finished job 32.
31 of 49 steps (63%) done
Select jobs to execute...
[Fri Sep 5 00:06:06 2025]
rule salmon_quant:
input: /<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin, /<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz
output: /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep2/quant.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep2/quant.genes.sf
log: /<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_HBR_Rep2.log
jobid: 6
reason: Missing output files: /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep2/quant.sf; Input files updated by another job: /<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin
wildcards: sample=HBR_Rep2
resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723
[Fri Sep 5 00:06:07 2025]
Finished job 30.
32 of 49 steps (65%) done
Select jobs to execute...
[Fri Sep 5 00:06:07 2025]
rule salmon_quant:
input: /<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin, /<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz
output: /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep3/quant.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep3/quant.genes.sf
log: /<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_HBR_Rep3.log
jobid: 8
reason: Missing output files: /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep3/quant.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep3/quant.genes.sf; Input files updated by another job: /<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz, /<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin
wildcards: sample=HBR_Rep3
resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723
[Fri Sep 5 00:06:07 2025]
Finished job 26.
33 of 49 steps (67%) done
Select jobs to execute...
[Fri Sep 5 00:06:07 2025]
rule coverage_megadepth:
input: /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai
output: /<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw
log: /<<PKGBUILDDIR>>/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep2.log
jobid: 43
reason: Missing output files: /<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw; Input files updated by another job: /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai
wildcards: sample=UHR_Rep2
resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2
/usr/bin/megadepth /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2 >> /<<PKGBUILDDIR>>/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep2.log 2>&1
Building DAG of jobs...
[Fri Sep 5 00:06:07 2025]
Finished job 43.
34 of 49 steps (69%) done
Select jobs to execute...
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 6
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=6000, mem_mib=5723
Select jobs to execute...
Using shell: /usr/bin/bash
Provided cores: 6
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=6000, mem_mib=5723
Select jobs to execute...
[Fri Sep 5 00:06:07 2025]
rule salmon_quant:
input: /<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin, /<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz
output: /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep3/quant.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep3/quant.genes.sf
log: /<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_UHR_Rep3.log
jobid: 14
reason: Missing output files: /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep3/quant.sf; Input files updated by another job: /<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz, /<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin
wildcards: sample=UHR_Rep3
resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723
[Fri Sep 5 00:06:07 2025]
Finished job 36.
35 of 49 steps (71%) done
Select jobs to execute...
[Fri Sep 5 00:06:07 2025]
rule coverage_megadepth:
input: /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai
output: /<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw
log: /<<PKGBUILDDIR>>/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep1.log
jobid: 39
reason: Missing output files: /<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw; Input files updated by another job: /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai
wildcards: sample=HBR_Rep1
resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2
/usr/bin/megadepth /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1 >> /<<PKGBUILDDIR>>/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep1.log 2>&1
[Fri Sep 5 00:06:07 2025]
Finished job 39.
36 of 49 steps (73%) done
/usr/bin/salmon quant -i /<<PKGBUILDDIR>>/tests/output/salmon_index -l A -p 8 -r /<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz -o /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep1 --seqBias --gcBias -g /<<PKGBUILDDIR>>/tests/sample_data/sample.gtf >> /<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_HBR_Rep1.log 2>&1
/usr/bin/salmon quant -i /<<PKGBUILDDIR>>/tests/output/salmon_index -l A -p 8 -1 /<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz -2 /<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz -o /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep2 --seqBias --gcBias -g /<<PKGBUILDDIR>>/tests/sample_data/sample.gtf >> /<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_HBR_Rep2.log 2>&1
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 6
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=6000, mem_mib=5723
Select jobs to execute...
/usr/bin/salmon quant -i /<<PKGBUILDDIR>>/tests/output/salmon_index -l A -p 8 -r /<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz -o /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep3 --seqBias --gcBias -g /<<PKGBUILDDIR>>/tests/sample_data/sample.gtf >> /<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_UHR_Rep3.log 2>&1
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 6
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=6000, mem_mib=5723
Select jobs to execute...
/usr/bin/salmon quant -i /<<PKGBUILDDIR>>/tests/output/salmon_index -l A -p 8 -1 /<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz -2 /<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz -o /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep3 --seqBias --gcBias -g /<<PKGBUILDDIR>>/tests/sample_data/sample.gtf >> /<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_HBR_Rep3.log 2>&1
[Fri Sep 5 00:06:08 2025]
Finished job 3.
37 of 49 steps (76%) done
[Fri Sep 5 00:06:08 2025]
Finished job 6.
38 of 49 steps (78%) done
[Fri Sep 5 00:06:08 2025]
Finished job 14.
39 of 49 steps (80%) done
[Fri Sep 5 00:06:08 2025]
Finished job 8.
40 of 49 steps (82%) done
Select jobs to execute...
[Fri Sep 5 00:06:08 2025]
rule counts_from_SALMON:
input: /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep1/quant.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep2/quant.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep3/quant.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep1/quant.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep2/quant.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep3/quant.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /<<PKGBUILDDIR>>/tests/output/colData.tsv
output: /<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /<<PKGBUILDDIR>>/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /<<PKGBUILDDIR>>/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv
log: /<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_import_counts.log
jobid: 23
reason: Missing output files: /<<PKGBUILDDIR>>/tests/out [too-long-redacted] _output/UHR_Rep1/quant.genes.sf
resources: tmpdir=/tmp, mem_mb=200, mem_mib=191
/usr/bin/Rscript --vanilla /<<PKGBUILDDIR>>/scripts//counts_matrix_from_SALMON.R /<<PKGBUILDDIR>>/tests/output/salmon_output /<<PKGBUILDDIR>>/tests/output/feature_counts /<<PKGBUILDDIR>>/tests/output/colData.tsv >> /<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_import_counts.log 2>&1
[Fri Sep 5 00:06:08 2025]
rule multiqc:
input: /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_R [too-long-redacted] 3_Aligned.sortedByCoord.out.bam
output: /<<PKGBUILDDIR>>/tests/output/multiqc/multiqc_report.html
log: /<<PKGBUILDDIR>>/tests/output/logs/multiqc.hisat2.log
jobid: 2
reason: Missing output files: /<<PKGBUILDDIR>>/tests/out [too-long-redacted] salmon_output/UHR_Rep1/quant.sf
resources: tmpdir=/tmp, mem_mb=500, mem_mib=477
/usr/bin/multiqc -f -o /<<PKGBUILDDIR>>/tests/output/multiqc /<<PKGBUILDDIR>>/tests/output >> /<<PKGBUILDDIR>>/tests/output/logs/multiqc.hisat2.log 2>&1
[Fri Sep 5 00:06:10 2025]
Finished job 2.
41 of 49 steps (84%) done
[Fri Sep 5 00:06:13 2025]
Finished job 34.
42 of 49 steps (86%) done
Select jobs to execute...
[Fri Sep 5 00:06:13 2025]
rule collate_read_counts:
input: /<<PKGBUILDDIR>>/tests/output/colData.tsv, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv
output: /<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv
log: /<<PKGBUILDDIR>>/tests/output/logs/hisat2/collate_read_counts.log
jobid: 25
reason: Missing output files: /<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv; Input files updated by another job: /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv, /<<PKGBUILDDIR>>/tests/output/colData.tsv, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv
resources: tmpdir=/tmp, mem_mb=200, mem_mib=191
/usr/bin/Rscript --vanilla /<<PKGBUILDDIR>>/scripts/collate_read_counts.R /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2 /<<PKGBUILDDIR>>/tests/output/colData.tsv /<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv >> /<<PKGBUILDDIR>>/tests/output/logs/hisat2/collate_read_counts.log 2>&1
[Fri Sep 5 00:06:14 2025]
Finished job 25.
43 of 49 steps (88%) done
Select jobs to execute...
[Fri Sep 5 00:06:14 2025]
rule report1:
input: /<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /<<PKGBUILDDIR>>/tests/output/colData.tsv
output: /<<PKGBUILDDIR>>/tests/output/report/hisat2/analysis1.deseq.report.html
log: /<<PKGBUILDDIR>>/tests/output/logs/hisat2/analysis1.report.log
jobid: 45
reason: Missing output files: /<<PKGBUILDDIR>>/tests/output/report/hisat2/analysis1.deseq.report.html; Input files updated by another job: /<<PKGBUILDDIR>>/tests/output/colData.tsv, /<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv
wildcards: analysis=analysis1
resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815
/usr/bin/Rscript --vanilla /<<PKGBUILDDIR>>/scripts/runDeseqReport.R --logo=/<<PKGBUILDDIR>>/images/Logo_PiGx.png --prefix='analysis1' --reportFile=/<<PKGBUILDDIR>>/scripts/deseqReport.Rmd --countDataFile=/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv --colDataFile=/<<PKGBUILDDIR>>/tests/output/colData.tsv --gtfFile=/<<PKGBUILDDIR>>/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/<<PKGBUILDDIR>>/tests/output/report/hisat2 --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.' --selfContained='True' >> /<<PKGBUILDDIR>>/tests/output/logs/hisat2/analysis1.report.log 2>&1
[Fri Sep 5 00:06:14 2025]
rule norm_counts_deseq:
input: /<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /<<PKGBUILDDIR>>/tests/output/colData.tsv
output: /<<PKGBUILDDIR>>/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /<<PKGBUILDDIR>>/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv
log: /<<PKGBUILDDIR>>/tests/output/logs/hisat2/norm_counts_deseq.log
jobid: 38
reason: Missing output files: /<<PKGBUILDDIR>>/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /<<PKGBUILDDIR>>/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv; Input files updated by another job: /<<PKGBUILDDIR>>/tests/output/colData.tsv, /<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv
resources: tmpdir=/tmp, mem_mb=1000, mem_mib=954
/usr/bin/Rscript --vanilla /<<PKGBUILDDIR>>/scripts/norm_counts_deseq.R /<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv /<<PKGBUILDDIR>>/tests/output/colData.tsv /<<PKGBUILDDIR>>/tests/output/feature_counts/normalized/hisat2 >> /<<PKGBUILDDIR>>/tests/output/logs/hisat2/norm_counts_deseq.log 2>&1
[Fri Sep 5 00:06:14 2025]
Error in rule report1:
jobid: 45
input: /<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /<<PKGBUILDDIR>>/tests/output/colData.tsv
output: /<<PKGBUILDDIR>>/tests/output/report/hisat2/analysis1.deseq.report.html
log: /<<PKGBUILDDIR>>/tests/output/logs/hisat2/analysis1.report.log (check log file(s) for error details)
shell:
/usr/bin/Rscript --vanilla /<<PKGBUILDDIR>>/scripts/runDeseqReport.R --logo=/<<PKGBUILDDIR>>/images/Logo_PiGx.png --prefix='analysis1' --reportFile=/<<PKGBUILDDIR>>/scripts/deseqReport.Rmd --countDataFile=/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv --colDataFile=/<<PKGBUILDDIR>>/tests/output/colData.tsv --gtfFile=/<<PKGBUILDDIR>>/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/<<PKGBUILDDIR>>/tests/output/report/hisat2 --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.' --selfContained='True' >> /<<PKGBUILDDIR>>/tests/output/logs/hisat2/analysis1.report.log 2>&1
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
[Fri Sep 5 00:06:15 2025]
Finished job 23.
44 of 49 steps (90%) done
[Fri Sep 5 00:06:19 2025]
Finished job 38.
45 of 49 steps (92%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2025-09-05T000521.751761.snakemake.log
ERROR: could not find report for SALMON at transcript level
make[1]: *** [debian/rules:40: override_dh_auto_test] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:12: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
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