Package: src:pigx-rnaseq
Version: 0.1.0-1.1
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules binary
dh binary
dh_update_autotools_config
debian/rules execute_before_dh_autoreconf
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p /<<PKGBUILDDIR>>/pigx-common
cp -a debian/common /<<PKGBUILDDIR>>/pigx-common
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_autoreconf
find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o
-path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o
-type l -printf "symlink %p
" > debian/autoreconf.before
grep -q ^XDT_ configure.ac
autoreconf -f -i
aclocal: warning: couldn't open directory 'm4': No such file or directory
[... snipped ...]
rule index_bam:
input:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam
output:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai
log: /<<PKGBUILDDIR>>/tests/output/logs/samtools_index_UHR_Rep2.log
jobid: 35
reason: Missing output files:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai;
Input files updated by another job:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam
wildcards: sample=UHR_Rep2
resources: tmpdir=/tmp, mem_mb=500, mem_mib=477
/usr/bin/samtools index /<<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 >>
/<<PKGBUILDDIR>>/tests/output/logs/samtools_index_UHR_Rep2.log 2>&1
[Fri May 17 17:27:28 2024]
Finished job 39.
18 of 48 steps (38%) done
Select jobs to execute...
[Fri May 17 17:27:28 2024]
rule coverage_megadepth:
input:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai
output:
/<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw
log:
/<<PKGBUILDDIR>>/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep2.log
jobid: 40
reason: Missing output files:
/<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw; Input files updated by
another job:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam
wildcards: sample=HBR_Rep2
resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2
/usr/bin/megadepth /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam
--threads 2 --bigwig --prefix /<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2 >>
/<<PKGBUILDDIR>>/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep2.log 2>&1
[Fri May 17 17:27:28 2024]
Finished job 35.
19 of 48 steps (40%) done
Select jobs to execute...
[Fri May 17 17:27:28 2024]
rule coverage_megadepth:
input:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai
output:
/<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw
log:
/<<PKGBUILDDIR>>/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep3.log
jobid: 44
reason: Missing output files:
/<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw; Input files updated by
another job:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam
wildcards: sample=UHR_Rep3
resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2
/usr/bin/megadepth /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam
--threads 2 --bigwig --prefix /<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3 >>
/<<PKGBUILDDIR>>/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep3.log 2>&1
[Fri May 17 17:27:28 2024]
Finished job 40.
20 of 48 steps (42%) done
Select jobs to execute...
[Fri May 17 17:27:28 2024]
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 May 17 17:27:28 2024]
Finished job 44.
21 of 48 steps (44%) done
Select jobs to execute...
[Fri May 17 17:27:28 2024]
rule index_bam:
input:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam
output:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai
log: /<<PKGBUILDDIR>>/tests/output/logs/samtools_index_HBR_Rep3.log
jobid: 31
reason: Missing output files:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai;
Input files updated by another job:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam
wildcards: sample=HBR_Rep3
resources: tmpdir=/tmp, mem_mb=500, mem_mib=477
/usr/bin/samtools index /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai >>
/<<PKGBUILDDIR>>/tests/output/logs/samtools_index_HBR_Rep3.log 2>&1
[Fri May 17 17:27:28 2024]
Finished job 31.
22 of 48 steps (46%) done
Select jobs to execute...
[Fri May 17 17:27:28 2024]
rule coverage_megadepth:
input:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai
output:
/<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw
log:
/<<PKGBUILDDIR>>/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep3.log
jobid: 41
reason: Missing output files:
/<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw; Input files updated by
another job: /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai
wildcards: sample=HBR_Rep3
resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2
/usr/bin/megadepth /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam
--threads 2 --bigwig --prefix /<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3 >>
/<<PKGBUILDDIR>>/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep3.log 2>&1
[Fri May 17 17:27:28 2024]
Finished job 41.
23 of 48 steps (48%) done
Select jobs to execute...
[Fri May 17 17:27:28 2024]
rule count_reads:
input:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai
output:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv
log: /<<PKGBUILDDIR>>/tests/output/logs/hisat2/HBR_Rep3.count_reads.log
jobid: 30
reason: Missing output files:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv; Input files updated by
another job: /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai
wildcards: sample=HBR_Rep3
resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723
/usr/bin/Rscript --vanilla /<<PKGBUILDDIR>>/scripts//count_reads.R HBR_Rep3
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam
/<<PKGBUILDDIR>>/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >>
/<<PKGBUILDDIR>>/tests/output/logs/hisat2/HBR_Rep3.count_reads.log 2>&1
[Fri May 17 17:27:28 2024]
Finished job 20.
24 of 48 steps (50%) done
Select jobs to execute...
[Fri May 17 17:27:28 2024]
rule count_reads:
input:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai
output:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv
log: /<<PKGBUILDDIR>>/tests/output/logs/hisat2/HBR_Rep2.count_reads.log
jobid: 28
reason: Missing output files:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv; Input files updated by
another job:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam
wildcards: sample=HBR_Rep2
resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723
/usr/bin/Rscript --vanilla /<<PKGBUILDDIR>>/scripts//count_reads.R HBR_Rep2
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam
/<<PKGBUILDDIR>>/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >>
/<<PKGBUILDDIR>>/tests/output/logs/hisat2/HBR_Rep2.count_reads.log 2>&1
[Fri May 17 17:28:06 2024]
Finished job 4.
25 of 48 steps (52%) done
Select jobs to execute...
[Fri May 17 17:28:06 2024]
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/salmon_index/pos.bin,
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz,
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.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 May 17 17:28:11 2024]
Finished job 10.
26 of 48 steps (54%) done
Select jobs to execute...
[Fri May 17 17:28:11 2024]
rule index_bam:
input:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam
output:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai
log: /<<PKGBUILDDIR>>/tests/output/logs/samtools_index_UHR_Rep1.log
jobid: 33
reason: Missing output files:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai;
Input files updated by another job:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam
wildcards: sample=UHR_Rep1
resources: tmpdir=/tmp, mem_mb=500, mem_mib=477
/usr/bin/samtools index /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai >>
/<<PKGBUILDDIR>>/tests/output/logs/samtools_index_UHR_Rep1.log 2>&1
[Fri May 17 17:28:12 2024]
Finished job 33.
27 of 48 steps (56%) done
Select jobs to execute...
[Fri May 17 17:28:12 2024]
rule coverage_megadepth:
input:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai
output:
/<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw
log:
/<<PKGBUILDDIR>>/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep1.log
jobid: 42
reason: Missing output files:
/<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw; Input files updated by
another job: /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai
wildcards: sample=UHR_Rep1
resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2
/usr/bin/megadepth /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam
--threads 2 --bigwig --prefix /<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1 >>
/<<PKGBUILDDIR>>/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep1.log 2>&1
[Fri May 17 17:28:12 2024]
Finished job 42.
28 of 48 steps (58%) done
Select jobs to execute...
[Fri May 17 17:28:12 2024]
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.genes.sf,
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep3/quant.sf; Input files updated by another job:
/<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin,
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz,
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz
wildcards: sample=HBR_Rep3
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/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 May 17 17:28:15 2024]
Finished job 36.
29 of 48 steps (60%) done
Select jobs to execute...
[Fri May 17 17:28:15 2024]
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.sf,
/<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep3/quant.genes.sf; Input files updated by another job:
/<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin,
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz
wildcards: sample=UHR_Rep3
resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723
[Fri May 17 17:28:15 2024]
Finished job 26.
30 of 48 steps (62%) done
Select jobs to execute...
[Fri May 17 17:28:15 2024]
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/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
wildcards: sample=HBR_Rep2
resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723
[Fri May 17 17:28:16 2024]
Finished job 34.
31 of 48 steps (65%) done
Select jobs to execute...
[Fri May 17 17:28:16 2024]
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.sf,
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep1/quant.genes.sf; Input files updated by another job:
/<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin,
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz
wildcards: sample=HBR_Rep1
resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723
[Fri May 17 17:28:16 2024]
Finished job 28.
32 of 48 steps (67%) done
Select jobs to execute...
[Fri May 17 17:28:16 2024]
rule salmon_quant:
input: /<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin,
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz,
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz
output: /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep2/quant.sf,
/<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep2/quant.genes.sf
log: /<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_UHR_Rep2.log
jobid: 12
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/salmon_index/pos.bin,
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz,
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz
wildcards: sample=UHR_Rep2
resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723
[Fri May 17 17:28:16 2024]
Finished job 30.
33 of 48 steps (69%) done
Select jobs to execute...
[Fri May 17 17:28:16 2024]
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
[Fri May 17 17:28:16 2024]
Finished job 43.
34 of 48 steps (71%) done
Select jobs to execute...
[Fri May 17 17:28:16 2024]
rule count_reads:
input:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai
output:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv
log: /<<PKGBUILDDIR>>/tests/output/logs/hisat2/UHR_Rep1.count_reads.log
jobid: 32
reason: Missing output files:
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv; Input files updated by
another job: /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai
wildcards: sample=UHR_Rep1
resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723
/usr/bin/Rscript --vanilla /<<PKGBUILDDIR>>/scripts//count_reads.R UHR_Rep1
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam
/<<PKGBUILDDIR>>/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >>
/<<PKGBUILDDIR>>/tests/output/logs/hisat2/UHR_Rep1.count_reads.log 2>&1
[Fri May 17 17:28:16 2024]
Finished job 8.
35 of 48 steps (73%) done
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...
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...
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_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
/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/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 May 17 17:28:19 2024]
Finished job 14.
36 of 48 steps (75%) done
[Fri May 17 17:28:19 2024]
Finished job 3.
37 of 48 steps (77%) done
[Fri May 17 17:28:19 2024]
Finished job 12.
38 of 48 steps (79%) done
[Fri May 17 17:28:19 2024]
Finished job 6.
39 of 48 steps (81%) done
Select jobs to execute...
[Fri May 17 17:28:19 2024]
rule multiqc:
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/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep3_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/output/multiqc/multiqc_report.html; Input files updated by another job: /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep3/quant.sf,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep1/quant.sf,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep3/quant.sf,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep1/quant.sf,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep2/quant.sf,
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep2/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 May 17 17:28:19 2024]
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/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; Input files updated by another job:
/<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep3/quant.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep1/quant.genes.sf,
/<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep1/quant.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep3/quant.sf,
/<<PKGBUILDDIR>>/tests/output/colData.tsv, /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep2/quant.genes.sf,
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep1/quant.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep2/quant.sf,
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep2/quant.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 May 17 17:28:25 2024]
Finished job 2.
40 of 48 steps (83%) done
[Fri May 17 17:28:29 2024]
Finished job 32.
41 of 48 steps (85%) done
Select jobs to execute...
[Fri May 17 17:28:29 2024]
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/colData.tsv, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv, /<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv,
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2.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 May 17 17:28:29 2024]
Finished job 25.
42 of 48 steps (88%) done
Select jobs to execute...
[Fri May 17 17:28:29 2024]
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_normalized_counts.tsv,
/<<PKGBUILDDIR>>/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt; Input files updated by
another job: /<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv,
/<<PKGBUILDDIR>>/tests/output/colData.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 May 17 17:28:29 2024]
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/feature_counts/raw_counts/hisat2/counts.tsv,
/<<PKGBUILDDIR>>/tests/output/colData.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 May 17 17:28:31 2024]
Finished job 23.
43 of 48 steps (90%) done
Select jobs to execute...
[Fri May 17 17:28:31 2024]
rule report3:
input:
/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv,
/<<PKGBUILDDIR>>/tests/output/colData.tsv
output:
/<<PKGBUILDDIR>>/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html
log:
/<<PKGBUILDDIR>>/tests/output/logs/salmon/analysis1.report.salmon.genes.log
jobid: 47
reason: Missing output files:
/<<PKGBUILDDIR>>/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html; Input files
updated by another job:
/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv,
/<<PKGBUILDDIR>>/tests/output/colData.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.salmon.genes'
--reportFile=/<<PKGBUILDDIR>>/scripts/deseqReport.Rmd --countDataFile=/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv
--colDataFile=/<<PKGBUILDDIR>>/tests/output/colData.tsv --gtfFile=/<<PKGBUILDDIR>>/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR'
--covariates='' --workdir=/<<PKGBUILDDIR>>/tests/output/report/salmon --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.'
--selfContained='True' >> /<<PKGBUILDDIR>>/tests/output/logs/salmon/analysis1.report.salmon.genes.log 2>&1
[Fri May 17 17:28:31 2024]
rule report2:
input:
/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv,
/<<PKGBUILDDIR>>/tests/output/colData.tsv
output:
/<<PKGBUILDDIR>>/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html
log:
/<<PKGBUILDDIR>>/tests/output/logs/salmon/analysis1.report.salmon.transcripts.log
jobid: 46
reason: Missing output files:
/<<PKGBUILDDIR>>/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html; Input files
updated by another job: /<<PKGBUILDDIR>>/tests/output/colData.tsv,
/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.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.salmon.transcripts'
--reportFile=/<<PKGBUILDDIR>>/scripts/deseqReport.Rmd
--countDataFile=/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv
--colDataFile=/<<PKGBUILDDIR>>/tests/output/colData.tsv --gtfFile=/<<PKGBUILDDIR>>/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR'
--covariates='' --workdir=/<<PKGBUILDDIR>>/tests/output/report/salmon --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.'
--selfContained='True' >> /<<PKGBUILDDIR>>/tests/output/logs/salmon/analysis1.report.salmon.transcripts.log 2>&1
[Fri May 17 17:28:43 2024]
Finished job 38.
44 of 48 steps (92%) done
[Fri May 17 17:29:01 2024]
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 May 17 17:29:01 2024]
Error in rule report3:
jobid: 47
input:
/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv,
/<<PKGBUILDDIR>>/tests/output/colData.tsv
output:
/<<PKGBUILDDIR>>/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html
log:
/<<PKGBUILDDIR>>/tests/output/logs/salmon/analysis1.report.salmon.genes.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.salmon.genes'
--reportFile=/<<PKGBUILDDIR>>/scripts/deseqReport.Rmd --countDataFile=/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv
--colDataFile=/<<PKGBUILDDIR>>/tests/output/colData.tsv --gtfFile=/<<PKGBUILDDIR>>/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR'
--covariates='' --workdir=/<<PKGBUILDDIR>>/tests/output/report/salmon --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.'
--selfContained='True' >> /<<PKGBUILDDIR>>/tests/output/logs/salmon/analysis1.report.salmon.genes.log 2>&1
(one of the commands exited with non-zero exit code; note that
snakemake uses bash strict mode!)
[Fri May 17 17:29:01 2024]
Error in rule report2:
jobid: 46
input:
/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv,
/<<PKGBUILDDIR>>/tests/output/colData.tsv
output:
/<<PKGBUILDDIR>>/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html
log:
/<<PKGBUILDDIR>>/tests/output/logs/salmon/analysis1.report.salmon.transcripts.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.salmon.transcripts'
--reportFile=/<<PKGBUILDDIR>>/scripts/deseqReport.Rmd
--countDataFile=/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv
--colDataFile=/<<PKGBUILDDIR>>/tests/output/colData.tsv --gtfFile=/<<PKGBUILDDIR>>/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR'
--covariates='' --workdir=/<<PKGBUILDDIR>>/tests/output/report/salmon --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.'
--selfContained='True' >> /<<PKGBUILDDIR>>/tests/output/logs/salmon/analysis1.report.salmon.transcripts.log 2>&1
(one of the commands exited with non-zero exit code; note that
snakemake uses bash strict mode!)
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-05-17T172711.682873.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
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202405/
About the archive rebuild: The build was made on virtual machines
of type m6a.large and r6a.large 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 affects, so that this is still visible in the BTS web
page for this package.
Thanks.
