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 --------------------------------------------------------------------------------
