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run.log
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Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
count jobs
12 align_with_hisat_reps
1 build_hisat_index
1 count_reads
6 make_bigwig_tracks
6 merge_replicates
1 run_basic_rnaseq_workflow
27
[Sat Sep 21 16:03:51 2019]
rule build_hisat_index:
input: /projects/imb-pkbphil/sp/annotations/ensembl97/H.sap.GRCh38.chr10.fa
output: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l
jobid: 26
reason: Missing output files: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l
hisat2-build -q -p 1 --large-index /projects/imb-pkbphil/sp/annotations/ensembl97/H.sap.GRCh38.chr10.fa /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38
[Sat Sep 21 16:08:01 2019]
Finished job 26.
1 of 27 steps (4%) done
[Sat Sep 21 16:08:01 2019]
rule align_with_hisat_reps:
input: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/5-P5D3_S5_R1_rep2.fastq.gz, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/5-P5D3_S5_R2_rep2.fastq.gz
output: output/01hisat/5-P5D3_S5_rep2.splicesites, output/01hisat/5-P5D3_S5_rep2.sum.txt, output/bam_temp/5-P5D3_S5_rep2.sorted.bam
jobid: 23
reason: Missing output files: output/bam_temp/5-P5D3_S5_rep2.sorted.bam; Input files updated by another job: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l
wildcards: sample=5-P5D3_S5, replicate=rep2
hisat2 --dta-cufflinks --new-summary --threads 1 --novel-splicesite-outfile output/01hisat/5-P5D3_S5_rep2.splicesites --summary-file output/01hisat/5-P5D3_S5_rep2.sum.txt -x /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38 -1 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/5-P5D3_S5_R1_rep2.fastq.gz -2 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/5-P5D3_S5_R2_rep2.fastq.gz | samtools view -Su - | samtools sort - -o output/bam_temp/5-P5D3_S5_rep2.sorted.bam
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "C.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
HISAT2 summary stats:
Total pairs: 26477673
Aligned concordantly or discordantly 0 time: 25259612 (95.40%)
Aligned concordantly 1 time: 1159360 (4.38%)
Aligned concordantly >1 times: 39766 (0.15%)
Aligned discordantly 1 time: 18935 (0.07%)
Total unpaired reads: 50519224
Aligned 0 time: 49877185 (98.73%)
Aligned 1 time: 489293 (0.97%)
Aligned >1 times: 152746 (0.30%)
Overall alignment rate: 5.81%
[bam_sort_core] merging from 11 files and 1 in-memory blocks...
[Sat Sep 21 16:51:09 2019]
Finished job 23.
2 of 27 steps (7%) done
[Sat Sep 21 16:51:09 2019]
rule align_with_hisat_reps:
input: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/4-P5D1_S4_R1_rep2.fastq.gz, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/4-P5D1_S4_R2_rep2.fastq.gz
output: output/01hisat/4-P5D1_S4_rep2.splicesites, output/01hisat/4-P5D1_S4_rep2.sum.txt, output/bam_temp/4-P5D1_S4_rep2.sorted.bam
jobid: 21
reason: Missing output files: output/bam_temp/4-P5D1_S4_rep2.sorted.bam; Input files updated by another job: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l
wildcards: sample=4-P5D1_S4, replicate=rep2
hisat2 --dta-cufflinks --new-summary --threads 1 --novel-splicesite-outfile output/01hisat/4-P5D1_S4_rep2.splicesites --summary-file output/01hisat/4-P5D1_S4_rep2.sum.txt -x /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38 -1 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/4-P5D1_S4_R1_rep2.fastq.gz -2 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/4-P5D1_S4_R2_rep2.fastq.gz | samtools view -Su - | samtools sort - -o output/bam_temp/4-P5D1_S4_rep2.sorted.bam
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "C.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
HISAT2 summary stats:
Total pairs: 26279785
Aligned concordantly or discordantly 0 time: 25314478 (96.33%)
Aligned concordantly 1 time: 920208 (3.50%)
Aligned concordantly >1 times: 28250 (0.11%)
Aligned discordantly 1 time: 16849 (0.06%)
Total unpaired reads: 50628956
Aligned 0 time: 50022745 (98.80%)
Aligned 1 time: 457239 (0.90%)
Aligned >1 times: 148972 (0.29%)
Overall alignment rate: 4.83%
[bam_sort_core] merging from 11 files and 1 in-memory blocks...
[Sat Sep 21 17:29:20 2019]
Finished job 21.
3 of 27 steps (11%) done
[Sat Sep 21 17:29:20 2019]
rule align_with_hisat_reps:
input: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/5-P5D3_S5_R1_rep1.fastq.gz, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/5-P5D3_S5_R2_rep1.fastq.gz
output: output/01hisat/5-P5D3_S5_rep1.splicesites, output/01hisat/5-P5D3_S5_rep1.sum.txt, output/bam_temp/5-P5D3_S5_rep1.sorted.bam
jobid: 22
reason: Missing output files: output/bam_temp/5-P5D3_S5_rep1.sorted.bam; Input files updated by another job: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l
wildcards: sample=5-P5D3_S5, replicate=rep1
hisat2 --dta-cufflinks --new-summary --threads 1 --novel-splicesite-outfile output/01hisat/5-P5D3_S5_rep1.splicesites --summary-file output/01hisat/5-P5D3_S5_rep1.sum.txt -x /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38 -1 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/5-P5D3_S5_R1_rep1.fastq.gz -2 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/5-P5D3_S5_R2_rep1.fastq.gz | samtools view -Su - | samtools sort - -o output/bam_temp/5-P5D3_S5_rep1.sorted.bam
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "C.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
HISAT2 summary stats:
Total pairs: 25306297
Aligned concordantly or discordantly 0 time: 24143274 (95.40%)
Aligned concordantly 1 time: 1108865 (4.38%)
Aligned concordantly >1 times: 37819 (0.15%)
Aligned discordantly 1 time: 16339 (0.06%)
Total unpaired reads: 48286548
Aligned 0 time: 47714388 (98.82%)
Aligned 1 time: 434482 (0.90%)
Aligned >1 times: 137678 (0.29%)
Overall alignment rate: 5.73%
[bam_sort_core] merging from 11 files and 1 in-memory blocks...
[Sat Sep 21 18:11:53 2019]
Finished job 22.
4 of 27 steps (15%) done
[Sat Sep 21 18:11:53 2019]
rule merge_replicates:
input: output/bam_temp/5-P5D3_S5_rep1.sorted.bam, output/bam_temp/5-P5D3_S5_rep2.sorted.bam
output: output/01hisat/5-P5D3_S5.sorted.bam, output/01hisat/5-P5D3_S5.sorted.bam.bai
jobid: 12
reason: Missing output files: output/01hisat/5-P5D3_S5.sorted.bam, output/01hisat/5-P5D3_S5.sorted.bam.bai; Input files updated by another job: output/bam_temp/5-P5D3_S5_rep2.sorted.bam, output/bam_temp/5-P5D3_S5_rep1.sorted.bam
wildcards: sample=5-P5D3_S5
samtools merge output/01hisat/5-P5D3_S5.sorted.bam output/bam_temp/5-P5D3_S5_rep1.sorted.bam output/bam_temp/5-P5D3_S5_rep2.sorted.bam ; samtools index output/01hisat/5-P5D3_S5.sorted.bam output/01hisat/5-P5D3_S5.sorted.bam.bai
Removing temporary output file output/bam_temp/5-P5D3_S5_rep1.sorted.bam.
Removing temporary output file output/bam_temp/5-P5D3_S5_rep2.sorted.bam.
[Sat Sep 21 18:43:10 2019]
Finished job 12.
5 of 27 steps (19%) done
[Sat Sep 21 18:43:10 2019]
rule make_bigwig_tracks:
input: output/01hisat/5-P5D3_S5.sorted.bam, output/01hisat/5-P5D3_S5.sorted.bam.bai
output: output/01hisat/5-P5D3_S5.bw
jobid: 6
reason: Missing output files: output/01hisat/5-P5D3_S5.bw; Input files updated by another job: output/01hisat/5-P5D3_S5.sorted.bam, output/01hisat/5-P5D3_S5.sorted.bam.bai
wildcards: sample=5-P5D3_S5
bamCoverage -b output/01hisat/5-P5D3_S5.sorted.bam -o output/01hisat/5-P5D3_S5.bw --outFileFormat bigwig
bamFilesList: ['output/01hisat/5-P5D3_S5.sorted.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
[Sat Sep 21 18:44:55 2019]
Finished job 6.
6 of 27 steps (22%) done
[Sat Sep 21 18:44:55 2019]
rule align_with_hisat_reps:
input: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/4-P5D1_S4_R1_rep1.fastq.gz, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/4-P5D1_S4_R2_rep1.fastq.gz
output: output/01hisat/4-P5D1_S4_rep1.splicesites, output/01hisat/4-P5D1_S4_rep1.sum.txt, output/bam_temp/4-P5D1_S4_rep1.sorted.bam
jobid: 20
reason: Missing output files: output/bam_temp/4-P5D1_S4_rep1.sorted.bam; Input files updated by another job: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l
wildcards: sample=4-P5D1_S4, replicate=rep1
hisat2 --dta-cufflinks --new-summary --threads 1 --novel-splicesite-outfile output/01hisat/4-P5D1_S4_rep1.splicesites --summary-file output/01hisat/4-P5D1_S4_rep1.sum.txt -x /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38 -1 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/4-P5D1_S4_R1_rep1.fastq.gz -2 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/4-P5D1_S4_R2_rep1.fastq.gz | samtools view -Su - | samtools sort - -o output/bam_temp/4-P5D1_S4_rep1.sorted.bam
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "C.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
HISAT2 summary stats:
Total pairs: 25064852
Aligned concordantly or discordantly 0 time: 24144990 (96.33%)
Aligned concordantly 1 time: 878334 (3.50%)
Aligned concordantly >1 times: 26134 (0.10%)
Aligned discordantly 1 time: 15394 (0.06%)
Total unpaired reads: 48289980
Aligned 0 time: 47747635 (98.88%)
Aligned 1 time: 408437 (0.85%)
Aligned >1 times: 133908 (0.28%)
Overall alignment rate: 4.75%
[bam_sort_core] merging from 11 files and 1 in-memory blocks...
[Sat Sep 21 19:25:26 2019]
Finished job 20.
7 of 27 steps (26%) done
[Sat Sep 21 19:25:26 2019]
rule merge_replicates:
input: output/bam_temp/4-P5D1_S4_rep1.sorted.bam, output/bam_temp/4-P5D1_S4_rep2.sorted.bam
output: output/01hisat/4-P5D1_S4.sorted.bam, output/01hisat/4-P5D1_S4.sorted.bam.bai
jobid: 11
reason: Missing output files: output/01hisat/4-P5D1_S4.sorted.bam.bai, output/01hisat/4-P5D1_S4.sorted.bam; Input files updated by another job: output/bam_temp/4-P5D1_S4_rep1.sorted.bam, output/bam_temp/4-P5D1_S4_rep2.sorted.bam
wildcards: sample=4-P5D1_S4
samtools merge output/01hisat/4-P5D1_S4.sorted.bam output/bam_temp/4-P5D1_S4_rep1.sorted.bam output/bam_temp/4-P5D1_S4_rep2.sorted.bam ; samtools index output/01hisat/4-P5D1_S4.sorted.bam output/01hisat/4-P5D1_S4.sorted.bam.bai
Removing temporary output file output/bam_temp/4-P5D1_S4_rep1.sorted.bam.
Removing temporary output file output/bam_temp/4-P5D1_S4_rep2.sorted.bam.
[Sat Sep 21 19:57:15 2019]
Finished job 11.
8 of 27 steps (30%) done
[Sat Sep 21 19:57:15 2019]
rule make_bigwig_tracks:
input: output/01hisat/4-P5D1_S4.sorted.bam, output/01hisat/4-P5D1_S4.sorted.bam.bai
output: output/01hisat/4-P5D1_S4.bw
jobid: 5
reason: Missing output files: output/01hisat/4-P5D1_S4.bw; Input files updated by another job: output/01hisat/4-P5D1_S4.sorted.bam, output/01hisat/4-P5D1_S4.sorted.bam.bai
wildcards: sample=4-P5D1_S4
bamCoverage -b output/01hisat/4-P5D1_S4.sorted.bam -o output/01hisat/4-P5D1_S4.bw --outFileFormat bigwig
bamFilesList: ['output/01hisat/4-P5D1_S4.sorted.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
[Sat Sep 21 19:58:44 2019]
Finished job 5.
9 of 27 steps (33%) done
[Sat Sep 21 19:58:44 2019]
rule align_with_hisat_reps:
input: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/2-KD5NT_S2_R1_rep2.fastq.gz, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/2-KD5NT_S2_R2_rep2.fastq.gz
output: output/01hisat/2-KD5NT_S2_rep2.splicesites, output/01hisat/2-KD5NT_S2_rep2.sum.txt, output/bam_temp/2-KD5NT_S2_rep2.sorted.bam
jobid: 17
reason: Missing output files: output/bam_temp/2-KD5NT_S2_rep2.sorted.bam; Input files updated by another job: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l
wildcards: sample=2-KD5NT_S2, replicate=rep2
hisat2 --dta-cufflinks --new-summary --threads 1 --novel-splicesite-outfile output/01hisat/2-KD5NT_S2_rep2.splicesites --summary-file output/01hisat/2-KD5NT_S2_rep2.sum.txt -x /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38 -1 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/2-KD5NT_S2_R1_rep2.fastq.gz -2 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/2-KD5NT_S2_R2_rep2.fastq.gz | samtools view -Su - | samtools sort - -o output/bam_temp/2-KD5NT_S2_rep2.sorted.bam
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "C.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
HISAT2 summary stats:
Total pairs: 23443490
Aligned concordantly or discordantly 0 time: 22269032 (94.99%)
Aligned concordantly 1 time: 1134085 (4.84%)
Aligned concordantly >1 times: 24918 (0.11%)
Aligned discordantly 1 time: 15455 (0.07%)
Total unpaired reads: 44538064
Aligned 0 time: 43945709 (98.67%)
Aligned 1 time: 445515 (1.00%)
Aligned >1 times: 146840 (0.33%)
Overall alignment rate: 6.27%
[bam_sort_core] merging from 10 files and 1 in-memory blocks...
[Sat Sep 21 20:37:07 2019]
Finished job 17.
10 of 27 steps (37%) done
[Sat Sep 21 20:37:07 2019]
rule align_with_hisat_reps:
input: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/1-KD4NT_S1_R1_rep2.fastq.gz, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/1-KD4NT_S1_R2_rep2.fastq.gz
output: output/01hisat/1-KD4NT_S1_rep2.splicesites, output/01hisat/1-KD4NT_S1_rep2.sum.txt, output/bam_temp/1-KD4NT_S1_rep2.sorted.bam
jobid: 15
reason: Missing output files: output/bam_temp/1-KD4NT_S1_rep2.sorted.bam; Input files updated by another job: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l
wildcards: sample=1-KD4NT_S1, replicate=rep2
hisat2 --dta-cufflinks --new-summary --threads 1 --novel-splicesite-outfile output/01hisat/1-KD4NT_S1_rep2.splicesites --summary-file output/01hisat/1-KD4NT_S1_rep2.sum.txt -x /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38 -1 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/1-KD4NT_S1_R1_rep2.fastq.gz -2 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/1-KD4NT_S1_R2_rep2.fastq.gz | samtools view -Su - | samtools sort - -o output/bam_temp/1-KD4NT_S1_rep2.sorted.bam
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "C.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
HISAT2 summary stats:
Total pairs: 23407797
Aligned concordantly or discordantly 0 time: 22054678 (94.22%)
Aligned concordantly 1 time: 1289701 (5.51%)
Aligned concordantly >1 times: 32801 (0.14%)
Aligned discordantly 1 time: 30617 (0.13%)
Total unpaired reads: 44109356
Aligned 0 time: 43369460 (98.32%)
Aligned 1 time: 574748 (1.30%)
Aligned >1 times: 165148 (0.37%)
Overall alignment rate: 7.36%
[bam_sort_core] merging from 10 files and 1 in-memory blocks...
[Sat Sep 21 21:16:33 2019]
Finished job 15.
11 of 27 steps (41%) done
[Sat Sep 21 21:16:33 2019]
rule align_with_hisat_reps:
input: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/1-KD4NT_S1_R1_rep1.fastq.gz, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/1-KD4NT_S1_R2_rep1.fastq.gz
output: output/01hisat/1-KD4NT_S1_rep1.splicesites, output/01hisat/1-KD4NT_S1_rep1.sum.txt, output/bam_temp/1-KD4NT_S1_rep1.sorted.bam
jobid: 14
reason: Missing output files: output/bam_temp/1-KD4NT_S1_rep1.sorted.bam; Input files updated by another job: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l
wildcards: sample=1-KD4NT_S1, replicate=rep1
hisat2 --dta-cufflinks --new-summary --threads 1 --novel-splicesite-outfile output/01hisat/1-KD4NT_S1_rep1.splicesites --summary-file output/01hisat/1-KD4NT_S1_rep1.sum.txt -x /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38 -1 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/1-KD4NT_S1_R1_rep1.fastq.gz -2 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/1-KD4NT_S1_R2_rep1.fastq.gz | samtools view -Su - | samtools sort - -o output/bam_temp/1-KD4NT_S1_rep1.sorted.bam
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "C.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
HISAT2 summary stats:
Total pairs: 22360070
Aligned concordantly or discordantly 0 time: 21077707 (94.26%)
Aligned concordantly 1 time: 1227238 (5.49%)
Aligned concordantly >1 times: 28938 (0.13%)
Aligned discordantly 1 time: 26187 (0.12%)
Total unpaired reads: 42155414
Aligned 0 time: 41469457 (98.37%)
Aligned 1 time: 534517 (1.27%)
Aligned >1 times: 151440 (0.36%)
Overall alignment rate: 7.27%
[bam_sort_core] merging from 10 files and 1 in-memory blocks...
[Sat Sep 21 21:59:57 2019]
Finished job 14.
12 of 27 steps (44%) done
[Sat Sep 21 21:59:57 2019]
rule merge_replicates:
input: output/bam_temp/1-KD4NT_S1_rep1.sorted.bam, output/bam_temp/1-KD4NT_S1_rep2.sorted.bam
output: output/01hisat/1-KD4NT_S1.sorted.bam, output/01hisat/1-KD4NT_S1.sorted.bam.bai
jobid: 8
reason: Missing output files: output/01hisat/1-KD4NT_S1.sorted.bam.bai, output/01hisat/1-KD4NT_S1.sorted.bam; Input files updated by another job: output/bam_temp/1-KD4NT_S1_rep2.sorted.bam, output/bam_temp/1-KD4NT_S1_rep1.sorted.bam
wildcards: sample=1-KD4NT_S1
samtools merge output/01hisat/1-KD4NT_S1.sorted.bam output/bam_temp/1-KD4NT_S1_rep1.sorted.bam output/bam_temp/1-KD4NT_S1_rep2.sorted.bam ; samtools index output/01hisat/1-KD4NT_S1.sorted.bam output/01hisat/1-KD4NT_S1.sorted.bam.bai
Removing temporary output file output/bam_temp/1-KD4NT_S1_rep1.sorted.bam.
Removing temporary output file output/bam_temp/1-KD4NT_S1_rep2.sorted.bam.
[Sat Sep 21 22:44:33 2019]
Finished job 8.
13 of 27 steps (48%) done
[Sat Sep 21 22:44:33 2019]
rule make_bigwig_tracks:
input: output/01hisat/1-KD4NT_S1.sorted.bam, output/01hisat/1-KD4NT_S1.sorted.bam.bai
output: output/01hisat/1-KD4NT_S1.bw
jobid: 2
reason: Missing output files: output/01hisat/1-KD4NT_S1.bw; Input files updated by another job: output/01hisat/1-KD4NT_S1.sorted.bam.bai, output/01hisat/1-KD4NT_S1.sorted.bam
wildcards: sample=1-KD4NT_S1
bamCoverage -b output/01hisat/1-KD4NT_S1.sorted.bam -o output/01hisat/1-KD4NT_S1.bw --outFileFormat bigwig
bamFilesList: ['output/01hisat/1-KD4NT_S1.sorted.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
[Sat Sep 21 22:46:18 2019]
Finished job 2.
14 of 27 steps (52%) done
[Sat Sep 21 22:46:18 2019]
rule align_with_hisat_reps:
input: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/6-P5D9_S6_R1_rep2.fastq.gz, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/6-P5D9_S6_R2_rep2.fastq.gz
output: output/01hisat/6-P5D9_S6_rep2.splicesites, output/01hisat/6-P5D9_S6_rep2.sum.txt, output/bam_temp/6-P5D9_S6_rep2.sorted.bam
jobid: 25
reason: Missing output files: output/bam_temp/6-P5D9_S6_rep2.sorted.bam; Input files updated by another job: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l
wildcards: sample=6-P5D9_S6, replicate=rep2
hisat2 --dta-cufflinks --new-summary --threads 1 --novel-splicesite-outfile output/01hisat/6-P5D9_S6_rep2.splicesites --summary-file output/01hisat/6-P5D9_S6_rep2.sum.txt -x /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38 -1 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/6-P5D9_S6_R1_rep2.fastq.gz -2 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/6-P5D9_S6_R2_rep2.fastq.gz | samtools view -Su - | samtools sort - -o output/bam_temp/6-P5D9_S6_rep2.sorted.bam
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "C.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
HISAT2 summary stats:
Total pairs: 22664748
Aligned concordantly or discordantly 0 time: 21007586 (92.69%)
Aligned concordantly 1 time: 1612841 (7.12%)
Aligned concordantly >1 times: 29199 (0.13%)
Aligned discordantly 1 time: 15122 (0.07%)
Total unpaired reads: 42015172
Aligned 0 time: 41462173 (98.68%)
Aligned 1 time: 431365 (1.03%)
Aligned >1 times: 121634 (0.29%)
Overall alignment rate: 8.53%
[bam_sort_core] merging from 10 files and 1 in-memory blocks...
[Sat Sep 21 23:40:03 2019]
Finished job 25.
15 of 27 steps (56%) done
[Sat Sep 21 23:40:03 2019]
rule align_with_hisat_reps:
input: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/2-KD5NT_S2_R1_rep1.fastq.gz, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/2-KD5NT_S2_R2_rep1.fastq.gz
output: output/01hisat/2-KD5NT_S2_rep1.splicesites, output/01hisat/2-KD5NT_S2_rep1.sum.txt, output/bam_temp/2-KD5NT_S2_rep1.sorted.bam
jobid: 16
reason: Missing output files: output/bam_temp/2-KD5NT_S2_rep1.sorted.bam; Input files updated by another job: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l
wildcards: sample=2-KD5NT_S2, replicate=rep1
hisat2 --dta-cufflinks --new-summary --threads 1 --novel-splicesite-outfile output/01hisat/2-KD5NT_S2_rep1.splicesites --summary-file output/01hisat/2-KD5NT_S2_rep1.sum.txt -x /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38 -1 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/2-KD5NT_S2_R1_rep1.fastq.gz -2 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/2-KD5NT_S2_R2_rep1.fastq.gz | samtools view -Su - | samtools sort - -o output/bam_temp/2-KD5NT_S2_rep1.sorted.bam
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "C.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
HISAT2 summary stats:
Total pairs: 21973130
Aligned concordantly or discordantly 0 time: 20878448 (95.02%)
Aligned concordantly 1 time: 1059282 (4.82%)
Aligned concordantly >1 times: 22197 (0.10%)
Aligned discordantly 1 time: 13203 (0.06%)
Total unpaired reads: 41756896
Aligned 0 time: 41224731 (98.73%)
Aligned 1 time: 401992 (0.96%)
Aligned >1 times: 130173 (0.31%)
Overall alignment rate: 6.19%
[bam_sort_core] merging from 9 files and 1 in-memory blocks...
[Sun Sep 22 00:32:56 2019]
Finished job 16.
16 of 27 steps (59%) done
[Sun Sep 22 00:32:56 2019]
rule merge_replicates:
input: output/bam_temp/2-KD5NT_S2_rep1.sorted.bam, output/bam_temp/2-KD5NT_S2_rep2.sorted.bam
output: output/01hisat/2-KD5NT_S2.sorted.bam, output/01hisat/2-KD5NT_S2.sorted.bam.bai
jobid: 9
reason: Missing output files: output/01hisat/2-KD5NT_S2.sorted.bam, output/01hisat/2-KD5NT_S2.sorted.bam.bai; Input files updated by another job: output/bam_temp/2-KD5NT_S2_rep1.sorted.bam, output/bam_temp/2-KD5NT_S2_rep2.sorted.bam
wildcards: sample=2-KD5NT_S2
samtools merge output/01hisat/2-KD5NT_S2.sorted.bam output/bam_temp/2-KD5NT_S2_rep1.sorted.bam output/bam_temp/2-KD5NT_S2_rep2.sorted.bam ; samtools index output/01hisat/2-KD5NT_S2.sorted.bam output/01hisat/2-KD5NT_S2.sorted.bam.bai
Removing temporary output file output/bam_temp/2-KD5NT_S2_rep1.sorted.bam.
Removing temporary output file output/bam_temp/2-KD5NT_S2_rep2.sorted.bam.
[Sun Sep 22 01:20:31 2019]
Finished job 9.
17 of 27 steps (63%) done
[Sun Sep 22 01:20:31 2019]
rule make_bigwig_tracks:
input: output/01hisat/2-KD5NT_S2.sorted.bam, output/01hisat/2-KD5NT_S2.sorted.bam.bai
output: output/01hisat/2-KD5NT_S2.bw
jobid: 3
reason: Missing output files: output/01hisat/2-KD5NT_S2.bw; Input files updated by another job: output/01hisat/2-KD5NT_S2.sorted.bam, output/01hisat/2-KD5NT_S2.sorted.bam.bai
wildcards: sample=2-KD5NT_S2
bamCoverage -b output/01hisat/2-KD5NT_S2.sorted.bam -o output/01hisat/2-KD5NT_S2.bw --outFileFormat bigwig
bamFilesList: ['output/01hisat/2-KD5NT_S2.sorted.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
[Sun Sep 22 01:22:07 2019]
Finished job 3.
18 of 27 steps (67%) done
[Sun Sep 22 01:22:07 2019]
rule align_with_hisat_reps:
input: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/6-P5D9_S6_R1_rep1.fastq.gz, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/6-P5D9_S6_R2_rep1.fastq.gz
output: output/01hisat/6-P5D9_S6_rep1.splicesites, output/01hisat/6-P5D9_S6_rep1.sum.txt, output/bam_temp/6-P5D9_S6_rep1.sorted.bam
jobid: 24
reason: Missing output files: output/bam_temp/6-P5D9_S6_rep1.sorted.bam; Input files updated by another job: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l
wildcards: sample=6-P5D9_S6, replicate=rep1
hisat2 --dta-cufflinks --new-summary --threads 1 --novel-splicesite-outfile output/01hisat/6-P5D9_S6_rep1.splicesites --summary-file output/01hisat/6-P5D9_S6_rep1.sum.txt -x /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38 -1 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/6-P5D9_S6_R1_rep1.fastq.gz -2 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/6-P5D9_S6_R2_rep1.fastq.gz | samtools view -Su - | samtools sort - -o output/bam_temp/6-P5D9_S6_rep1.sorted.bam
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "C.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
HISAT2 summary stats:
Total pairs: 21636710
Aligned concordantly or discordantly 0 time: 20053326 (92.68%)
Aligned concordantly 1 time: 1539763 (7.12%)
Aligned concordantly >1 times: 29815 (0.14%)
Aligned discordantly 1 time: 13806 (0.06%)
Total unpaired reads: 40106652
Aligned 0 time: 39609382 (98.76%)
Aligned 1 time: 386313 (0.96%)
Aligned >1 times: 110957 (0.28%)
Overall alignment rate: 8.47%
[bam_sort_core] merging from 9 files and 1 in-memory blocks...
[Sun Sep 22 02:05:11 2019]
Finished job 24.
19 of 27 steps (70%) done
[Sun Sep 22 02:05:11 2019]
rule merge_replicates:
input: output/bam_temp/6-P5D9_S6_rep1.sorted.bam, output/bam_temp/6-P5D9_S6_rep2.sorted.bam
output: output/01hisat/6-P5D9_S6.sorted.bam, output/01hisat/6-P5D9_S6.sorted.bam.bai
jobid: 13
reason: Missing output files: output/01hisat/6-P5D9_S6.sorted.bam, output/01hisat/6-P5D9_S6.sorted.bam.bai; Input files updated by another job: output/bam_temp/6-P5D9_S6_rep1.sorted.bam, output/bam_temp/6-P5D9_S6_rep2.sorted.bam
wildcards: sample=6-P5D9_S6
samtools merge output/01hisat/6-P5D9_S6.sorted.bam output/bam_temp/6-P5D9_S6_rep1.sorted.bam output/bam_temp/6-P5D9_S6_rep2.sorted.bam ; samtools index output/01hisat/6-P5D9_S6.sorted.bam output/01hisat/6-P5D9_S6.sorted.bam.bai
Removing temporary output file output/bam_temp/6-P5D9_S6_rep1.sorted.bam.
Removing temporary output file output/bam_temp/6-P5D9_S6_rep2.sorted.bam.
[Sun Sep 22 02:33:06 2019]
Finished job 13.
20 of 27 steps (74%) done
[Sun Sep 22 02:33:06 2019]
rule make_bigwig_tracks:
input: output/01hisat/6-P5D9_S6.sorted.bam, output/01hisat/6-P5D9_S6.sorted.bam.bai
output: output/01hisat/6-P5D9_S6.bw
jobid: 7
reason: Missing output files: output/01hisat/6-P5D9_S6.bw; Input files updated by another job: output/01hisat/6-P5D9_S6.sorted.bam, output/01hisat/6-P5D9_S6.sorted.bam.bai
wildcards: sample=6-P5D9_S6
bamCoverage -b output/01hisat/6-P5D9_S6.sorted.bam -o output/01hisat/6-P5D9_S6.bw --outFileFormat bigwig
bamFilesList: ['output/01hisat/6-P5D9_S6.sorted.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
[Sun Sep 22 02:35:21 2019]
Finished job 7.
21 of 27 steps (78%) done
[Sun Sep 22 02:35:21 2019]
rule align_with_hisat_reps:
input: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/3-P5D0_S3_R1_rep2.fastq.gz, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/3-P5D0_S3_R2_rep2.fastq.gz
output: output/01hisat/3-P5D0_S3_rep2.splicesites, output/01hisat/3-P5D0_S3_rep2.sum.txt, output/bam_temp/3-P5D0_S3_rep2.sorted.bam
jobid: 19
reason: Missing output files: output/bam_temp/3-P5D0_S3_rep2.sorted.bam; Input files updated by another job: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l
wildcards: sample=3-P5D0_S3, replicate=rep2
hisat2 --dta-cufflinks --new-summary --threads 1 --novel-splicesite-outfile output/01hisat/3-P5D0_S3_rep2.splicesites --summary-file output/01hisat/3-P5D0_S3_rep2.sum.txt -x /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38 -1 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/3-P5D0_S3_R1_rep2.fastq.gz -2 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/3-P5D0_S3_R2_rep2.fastq.gz | samtools view -Su - | samtools sort - -o output/bam_temp/3-P5D0_S3_rep2.sorted.bam
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "C.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
HISAT2 summary stats:
Total pairs: 20890298
Aligned concordantly or discordantly 0 time: 20079355 (96.12%)
Aligned concordantly 1 time: 782207 (3.74%)
Aligned concordantly >1 times: 15945 (0.08%)
Aligned discordantly 1 time: 12791 (0.06%)
Total unpaired reads: 40158710
Aligned 0 time: 39731341 (98.94%)
Aligned 1 time: 327651 (0.82%)
Aligned >1 times: 99718 (0.25%)
Overall alignment rate: 4.90%
[bam_sort_core] merging from 9 files and 1 in-memory blocks...
[Sun Sep 22 03:09:13 2019]
Finished job 19.
22 of 27 steps (81%) done
[Sun Sep 22 03:09:13 2019]
rule align_with_hisat_reps:
input: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/3-P5D0_S3_R1_rep1.fastq.gz, /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/3-P5D0_S3_R2_rep1.fastq.gz
output: output/01hisat/3-P5D0_S3_rep1.splicesites, output/01hisat/3-P5D0_S3_rep1.sum.txt, output/bam_temp/3-P5D0_S3_rep1.sorted.bam
jobid: 18
reason: Missing output files: output/bam_temp/3-P5D0_S3_rep1.sorted.bam; Input files updated by another job: /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38.1.ht2l
wildcards: sample=3-P5D0_S3, replicate=rep1
hisat2 --dta-cufflinks --new-summary --threads 1 --novel-splicesite-outfile output/01hisat/3-P5D0_S3_rep1.splicesites --summary-file output/01hisat/3-P5D0_S3_rep1.sum.txt -x /projects/imb-pkbphil/sp/annotations/ensembl97/hisat2_index/chr10_hg38 -1 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/3-P5D0_S3_R1_rep1.fastq.gz -2 /projects/imb-pkbphil/sp/rnaseq/mar19_rnaseq/raw/3-P5D0_S3_R2_rep1.fastq.gz | samtools view -Su - | samtools sort - -o output/bam_temp/3-P5D0_S3_rep1.sorted.bam
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "C.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
HISAT2 summary stats:
Total pairs: 19176472
Aligned concordantly or discordantly 0 time: 18436790 (96.14%)
Aligned concordantly 1 time: 715563 (3.73%)
Aligned concordantly >1 times: 13791 (0.07%)
Aligned discordantly 1 time: 10328 (0.05%)
Total unpaired reads: 36873580
Aligned 0 time: 36506199 (99.00%)
Aligned 1 time: 280336 (0.76%)
Aligned >1 times: 87045 (0.24%)
Overall alignment rate: 4.82%
[bam_sort_core] merging from 8 files and 1 in-memory blocks...
[Sun Sep 22 03:43:50 2019]
Finished job 18.
23 of 27 steps (85%) done
[Sun Sep 22 03:43:50 2019]
rule merge_replicates:
input: output/bam_temp/3-P5D0_S3_rep1.sorted.bam, output/bam_temp/3-P5D0_S3_rep2.sorted.bam
output: output/01hisat/3-P5D0_S3.sorted.bam, output/01hisat/3-P5D0_S3.sorted.bam.bai
jobid: 10
reason: Missing output files: output/01hisat/3-P5D0_S3.sorted.bam.bai, output/01hisat/3-P5D0_S3.sorted.bam; Input files updated by another job: output/bam_temp/3-P5D0_S3_rep1.sorted.bam, output/bam_temp/3-P5D0_S3_rep2.sorted.bam
wildcards: sample=3-P5D0_S3
samtools merge output/01hisat/3-P5D0_S3.sorted.bam output/bam_temp/3-P5D0_S3_rep1.sorted.bam output/bam_temp/3-P5D0_S3_rep2.sorted.bam ; samtools index output/01hisat/3-P5D0_S3.sorted.bam output/01hisat/3-P5D0_S3.sorted.bam.bai
Removing temporary output file output/bam_temp/3-P5D0_S3_rep1.sorted.bam.
Removing temporary output file output/bam_temp/3-P5D0_S3_rep2.sorted.bam.
[Sun Sep 22 04:25:43 2019]
Finished job 10.
24 of 27 steps (89%) done
[Sun Sep 22 04:25:43 2019]
rule count_reads:
input: output/01hisat/1-KD4NT_S1.sorted.bam, output/01hisat/2-KD5NT_S2.sorted.bam, output/01hisat/3-P5D0_S3.sorted.bam, output/01hisat/4-P5D1_S4.sorted.bam, output/01hisat/5-P5D3_S5.sorted.bam, output/01hisat/6-P5D9_S6.sorted.bam, /projects/imb-pkbphil/sp/annotations/ensembl97/H.sap.GRCh38.97.chr10.gtf
output: output/02featureCounts/test_mar19_rnaseq.counts
jobid: 1
reason: Missing output files: output/02featureCounts/test_mar19_rnaseq.counts; Input files updated by another job: output/01hisat/4-P5D1_S4.sorted.bam, output/01hisat/6-P5D9_S6.sorted.bam, output/01hisat/5-P5D3_S5.sorted.bam, output/01hisat/2-KD5NT_S2.sorted.bam, output/01hisat/1-KD4NT_S1.sorted.bam, output/01hisat/3-P5D0_S3.sorted.bam
featureCounts -T 1 -p -s 2 -a /projects/imb-pkbphil/sp/annotations/ensembl97/H.sap.GRCh38.97.chr10.gtf -o output/02featureCounts/test_mar19_rnaseq.counts output/01hisat/1-KD4NT_S1.sorted.bam output/01hisat/2-KD5NT_S2.sorted.bam output/01hisat/3-P5D0_S3.sorted.bam output/01hisat/4-P5D1_S4.sorted.bam output/01hisat/5-P5D3_S5.sorted.bam output/01hisat/6-P5D9_S6.sorted.bam ;
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.4
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 6 BAM files ||
|| P 1-KD4NT_S1.sorted.bam ||
|| P 2-KD5NT_S2.sorted.bam ||
|| P 3-P5D0_S3.sorted.bam ||
|| P 4-P5D1_S4.sorted.bam ||
|| P 5-P5D3_S5.sorted.bam ||
|| P 6-P5D9_S6.sorted.bam ||
|| ||
|| Output file : test_mar19_rnaseq.counts ||
|| Summary : test_mar19_rnaseq.counts.summary ||
|| Annotation : H.sap.GRCh38.97.chr10.gtf (GTF) ||
|| Dir for temp files : output/02featureCounts ||
|| ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : yes ||
|| Multimapping reads : not counted ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| ||
|| Chimeric reads : counted ||
|| Both ends mapped : not required ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file H.sap.GRCh38.97.chr10.gtf ... ||
|| Features : 50494 ||
|| Meta-features : 2332 ||
|| Chromosomes/contigs : 1 ||
|| ||
|| Process BAM file 1-KD4NT_S1.sorted.bam... ||
|| Paired-end reads are included. ||
|| Strand specific : reversely stranded ||
|| Assign alignments (paired-end) to features... ||
|| ||
|| WARNING: reads from the same pair were found not adjacent to each ||
|| other in the input (due to read sorting by location or ||
|| reporting of multi-mapping read pairs). ||
|| ||
|| Pairing up the read pairs. ||
|| ||
|| Total alignments : 46435999 ||
|| Successfully assigned alignments : 3074484 (6.6%) ||
|| Running time : 7.71 minutes ||
|| ||
|| Process BAM file 2-KD5NT_S2.sorted.bam... ||
|| Paired-end reads are included. ||
|| Strand specific : reversely stranded ||
|| Assign alignments (paired-end) to features... ||
|| ||
|| WARNING: reads from the same pair were found not adjacent to each ||
|| other in the input (due to read sorting by location or ||
|| reporting of multi-mapping read pairs). ||
|| ||
|| Pairing up the read pairs. ||
|| ||
|| Total alignments : 46053871 ||
|| Successfully assigned alignments : 2485949 (5.4%) ||
|| Running time : 4.35 minutes ||
|| ||
|| Process BAM file 3-P5D0_S3.sorted.bam... ||
|| Paired-end reads are included. ||
|| Strand specific : reversely stranded ||
|| Assign alignments (paired-end) to features... ||
|| ||
|| WARNING: reads from the same pair were found not adjacent to each ||
|| other in the input (due to read sorting by location or ||
|| reporting of multi-mapping read pairs). ||
|| ||
|| Pairing up the read pairs. ||
|| ||
|| Total alignments : 40506385 ||
|| Successfully assigned alignments : 1720158 (4.2%) ||
|| Running time : 4.05 minutes ||
|| ||
|| Process BAM file 4-P5D1_S4.sorted.bam... ||
|| Paired-end reads are included. ||
|| Strand specific : reversely stranded ||
|| Assign alignments (paired-end) to features... ||
|| ||
|| WARNING: reads from the same pair were found not adjacent to each ||
|| other in the input (due to read sorting by location or ||
|| reporting of multi-mapping read pairs). ||
|| ||
|| Pairing up the read pairs. ||
|| ||
|| Total alignments : 52026825 ||
|| Successfully assigned alignments : 2104789 (4.0%) ||
|| Running time : 3.88 minutes ||
|| ||
|| Process BAM file 5-P5D3_S5.sorted.bam... ||
|| Paired-end reads are included. ||
|| Strand specific : reversely stranded ||
|| Assign alignments (paired-end) to features... ||
|| ||
|| WARNING: reads from the same pair were found not adjacent to each ||
|| other in the input (due to read sorting by location or ||
|| reporting of multi-mapping read pairs). ||
|| ||
|| Pairing up the read pairs. ||
|| ||
|| Total alignments : 52523096 ||
|| Successfully assigned alignments : 2596698 (4.9%) ||
|| Running time : 4.75 minutes ||
|| ||
|| Process BAM file 6-P5D9_S6.sorted.bam... ||
|| Paired-end reads are included. ||
|| Strand specific : reversely stranded ||
|| Assign alignments (paired-end) to features... ||
|| ||
|| WARNING: reads from the same pair were found not adjacent to each ||
|| other in the input (due to read sorting by location or ||
|| reporting of multi-mapping read pairs). ||
|| ||
|| Pairing up the read pairs. ||
|| ||
|| Total alignments : 44879224 ||
|| Successfully assigned alignments : 3508391 (7.8%) ||
|| Running time : 6.21 minutes ||
|| ||
|| ||
|| Summary of counting results can be found in file "output/02featureCounts/ ||
|| test_mar19_rnaseq.counts.summary" ||
|| ||
\\============================================================================//
[Sun Sep 22 04:56:41 2019]
Finished job 1.
25 of 27 steps (93%) done
[Sun Sep 22 04:56:41 2019]
rule make_bigwig_tracks:
input: output/01hisat/3-P5D0_S3.sorted.bam, output/01hisat/3-P5D0_S3.sorted.bam.bai
output: output/01hisat/3-P5D0_S3.bw
jobid: 4
reason: Missing output files: output/01hisat/3-P5D0_S3.bw; Input files updated by another job: output/01hisat/3-P5D0_S3.sorted.bam.bai, output/01hisat/3-P5D0_S3.sorted.bam
wildcards: sample=3-P5D0_S3
bamCoverage -b output/01hisat/3-P5D0_S3.sorted.bam -o output/01hisat/3-P5D0_S3.bw --outFileFormat bigwig
bamFilesList: ['output/01hisat/3-P5D0_S3.sorted.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
[Sun Sep 22 04:57:42 2019]
Finished job 4.
26 of 27 steps (96%) done
[Sun Sep 22 04:57:42 2019]
localrule run_basic_rnaseq_workflow:
input: output/02featureCounts/test_mar19_rnaseq.counts, output/01hisat/1-KD4NT_S1.bw, output/01hisat/2-KD5NT_S2.bw, output/01hisat/3-P5D0_S3.bw, output/01hisat/4-P5D1_S4.bw, output/01hisat/5-P5D3_S5.bw, output/01hisat/6-P5D9_S6.bw, output/01hisat/1-KD4NT_S1.sorted.bam.bai, output/01hisat/2-KD5NT_S2.sorted.bam.bai, output/01hisat/3-P5D0_S3.sorted.bam.bai, output/01hisat/4-P5D1_S4.sorted.bam.bai, output/01hisat/5-P5D3_S5.sorted.bam.bai, output/01hisat/6-P5D9_S6.sorted.bam.bai
jobid: 0
reason: Input files updated by another job: output/01hisat/5-P5D3_S5.bw, output/01hisat/4-P5D1_S4.bw, output/01hisat/4-P5D1_S4.sorted.bam.bai, output/01hisat/2-KD5NT_S2.bw, output/01hisat/3-P5D0_S3.sorted.bam.bai, output/01hisat/5-P5D3_S5.sorted.bam.bai, output/01hisat/6-P5D9_S6.sorted.bam.bai, output/01hisat/3-P5D0_S3.bw, output/01hisat/1-KD4NT_S1.bw, output/01hisat/6-P5D9_S6.bw, output/01hisat/2-KD5NT_S2.sorted.bam.bai, output/01hisat/1-KD4NT_S1.sorted.bam.bai, output/02featureCounts/test_mar19_rnaseq.counts
[Sun Sep 22 04:57:42 2019]
Finished job 0.
27 of 27 steps (100%) done
Complete log: /projects/imb-pkbphil/sp/dev/rnaseq-basic/.snakemake/log/2019-09-21T160351.827075.snakemake.log