Bug#1071333: marked as done (pigx-rnaseq: FTBFS: ERROR: could not find report for SALMON at transcript level)

Debian Bug Tracking System Sat, 07 Sep 2024 05:54:21 -0700

Your message dated Sat, 7 Sep 2024 14:49:57 +0200
with message-id <[email protected]>
and subject line Re: pigx-rnaseq: FTBFS: ERROR: could not find report for 
SALMON at transcript level
has caused the Debian Bug report #1071333,
regarding pigx-rnaseq: FTBFS: ERROR: could not find report for SALMON at 
transcript level
to be marked as done.


This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)


-- 
1071333: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1071333
Debian Bug Tracking System
Contact [email protected] with problems

--- Begin Message ---

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.

--- End Message ---

--- Begin Message ---
Version: 0.1.1-1

Fixed by new upstream release
OpenPGP_signature.asc
Description: OpenPGP digital signature

--- End Message ---

Bug#1071333: marked as done (pigx-rnaseq: FTBFS: ERROR: could not find report for SALMON at transcript level)

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