Job ID = 6366637 SRX = SRX2144184 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:49:37 prefetch.2.10.7: 1) Downloading 'SRR4188788'... 2020-06-15T22:49:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:50:05 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:50:06 prefetch.2.10.7: 'SRR4188788' is valid 2020-06-15T22:50:06 prefetch.2.10.7: 1) 'SRR4188788' was downloaded successfully Read 5526585 spots for SRR4188788/SRR4188788.sra Written 5526585 spots for SRR4188788/SRR4188788.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:07 5526585 reads; of these: 5526585 (100.00%) were unpaired; of these: 1181787 (21.38%) aligned 0 times 3684153 (66.66%) aligned exactly 1 time 660645 (11.95%) aligned >1 times 78.62% overall alignment rate Time searching: 00:01:07 Overall time: 00:01:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 321388 / 4344798 = 0.0740 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 07:52:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 07:52:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:02: 1000000 INFO @ Tue, 16 Jun 2020 07:53:07: 2000000 INFO @ Tue, 16 Jun 2020 07:53:13: 3000000 INFO @ Tue, 16 Jun 2020 07:53:18: 4000000 INFO @ Tue, 16 Jun 2020 07:53:18: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:53:18: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:53:18: #1 total tags in treatment: 4023410 INFO @ Tue, 16 Jun 2020 07:53:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:53:19: #1 tags after filtering in treatment: 4023410 INFO @ Tue, 16 Jun 2020 07:53:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:19: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:19: #2 number of paired peaks: 2003 INFO @ Tue, 16 Jun 2020 07:53:19: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:19: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:19: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:19: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:19: #2 predicted fragment length is 122 bps INFO @ Tue, 16 Jun 2020 07:53:19: #2 alternative fragment length(s) may be 122 bps INFO @ Tue, 16 Jun 2020 07:53:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.05_model.r INFO @ Tue, 16 Jun 2020 07:53:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:19: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 07:53:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 07:53:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:32: 1000000 INFO @ Tue, 16 Jun 2020 07:53:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.05_summits.bed INFO @ Tue, 16 Jun 2020 07:53:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2209 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:53:37: 2000000 INFO @ Tue, 16 Jun 2020 07:53:43: 3000000 INFO @ Tue, 16 Jun 2020 07:53:48: 4000000 INFO @ Tue, 16 Jun 2020 07:53:48: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:53:48: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:53:48: #1 total tags in treatment: 4023410 INFO @ Tue, 16 Jun 2020 07:53:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:53:48: #1 tags after filtering in treatment: 4023410 INFO @ Tue, 16 Jun 2020 07:53:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:48: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:49: #2 number of paired peaks: 2003 INFO @ Tue, 16 Jun 2020 07:53:49: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:49: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:49: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:49: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:49: #2 predicted fragment length is 122 bps INFO @ Tue, 16 Jun 2020 07:53:49: #2 alternative fragment length(s) may be 122 bps INFO @ Tue, 16 Jun 2020 07:53:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.10_model.r INFO @ Tue, 16 Jun 2020 07:53:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:49: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 07:53:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 07:53:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:01: 1000000 INFO @ Tue, 16 Jun 2020 07:54:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.10_summits.bed INFO @ Tue, 16 Jun 2020 07:54:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (942 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:54:06: 2000000 INFO @ Tue, 16 Jun 2020 07:54:11: 3000000 INFO @ Tue, 16 Jun 2020 07:54:16: 4000000 INFO @ Tue, 16 Jun 2020 07:54:16: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:54:16: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:54:16: #1 total tags in treatment: 4023410 INFO @ Tue, 16 Jun 2020 07:54:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:54:16: #1 tags after filtering in treatment: 4023410 INFO @ Tue, 16 Jun 2020 07:54:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:16: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:16: #2 number of paired peaks: 2003 INFO @ Tue, 16 Jun 2020 07:54:16: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:16: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:16: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:16: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:16: #2 predicted fragment length is 122 bps INFO @ Tue, 16 Jun 2020 07:54:16: #2 alternative fragment length(s) may be 122 bps INFO @ Tue, 16 Jun 2020 07:54:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.20_model.r INFO @ Tue, 16 Jun 2020 07:54:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:16: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:54:25: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:54:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144184/SRX2144184.20_summits.bed INFO @ Tue, 16 Jun 2020 07:54:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (320 records, 4 fields): 1 millis CompletedMACS2peakCalling