Job ID = 6366548 SRX = SRX188614 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:48:07 prefetch.2.10.7: 1) Downloading 'SRR573720'... 2020-06-15T22:48:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:48:36 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:48:37 prefetch.2.10.7: 'SRR573720' is valid 2020-06-15T22:48:37 prefetch.2.10.7: 1) 'SRR573720' was downloaded successfully Read 6486474 spots for SRR573720/SRR573720.sra Written 6486474 spots for SRR573720/SRR573720.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: 00:00:49 6486474 reads; of these: 6486474 (100.00%) were unpaired; of these: 2115905 (32.62%) aligned 0 times 3962420 (61.09%) aligned exactly 1 time 408149 (6.29%) aligned >1 times 67.38% overall alignment rate Time searching: 00:00:49 Overall time: 00:00:49 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] 681728 / 4370569 = 0.1560 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 07:51:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.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 07:51:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:23: 1000000 INFO @ Tue, 16 Jun 2020 07:51:28: 2000000 INFO @ Tue, 16 Jun 2020 07:51:33: 3000000 INFO @ Tue, 16 Jun 2020 07:51:37: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:51:37: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:51:37: #1 total tags in treatment: 3688841 INFO @ Tue, 16 Jun 2020 07:51:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:51:37: #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 07:51:37: #1 tags after filtering in treatment: 3688841 INFO @ Tue, 16 Jun 2020 07:51:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:51:37: #1 finished! INFO @ Tue, 16 Jun 2020 07:51:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:51:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:51:37: #2 number of paired peaks: 3248 INFO @ Tue, 16 Jun 2020 07:51:37: start model_add_line... INFO @ Tue, 16 Jun 2020 07:51:37: start X-correlation... INFO @ Tue, 16 Jun 2020 07:51:37: end of X-cor INFO @ Tue, 16 Jun 2020 07:51:37: #2 finished! INFO @ Tue, 16 Jun 2020 07:51:37: #2 predicted fragment length is 140 bps INFO @ Tue, 16 Jun 2020 07:51:37: #2 alternative fragment length(s) may be 4,140 bps INFO @ Tue, 16 Jun 2020 07:51:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.05_model.r INFO @ Tue, 16 Jun 2020 07:51:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:51:37: #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 07:51:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:51:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.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 07:51:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:51:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:51:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.05_summits.bed INFO @ Tue, 16 Jun 2020 07:51:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3027 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:51:53: 1000000 INFO @ Tue, 16 Jun 2020 07:51:58: 2000000 INFO @ Tue, 16 Jun 2020 07:52:03: 3000000 INFO @ Tue, 16 Jun 2020 07:52:07: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:52:07: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:52:07: #1 total tags in treatment: 3688841 INFO @ Tue, 16 Jun 2020 07:52:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:07: #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 07:52:07: #1 tags after filtering in treatment: 3688841 INFO @ Tue, 16 Jun 2020 07:52:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:07: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:07: #2 number of paired peaks: 3248 INFO @ Tue, 16 Jun 2020 07:52:07: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:07: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:07: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:07: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:07: #2 predicted fragment length is 140 bps INFO @ Tue, 16 Jun 2020 07:52:07: #2 alternative fragment length(s) may be 4,140 bps INFO @ Tue, 16 Jun 2020 07:52:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.10_model.r INFO @ Tue, 16 Jun 2020 07:52:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:07: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... INFO @ Tue, 16 Jun 2020 07:52:17: #3 Call peaks for each chromosome... 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 07:52:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.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 07:52:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:52:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:52:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:52:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.10_summits.bed INFO @ Tue, 16 Jun 2020 07:52:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1002 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:52:23: 1000000 INFO @ Tue, 16 Jun 2020 07:52:28: 2000000 INFO @ Tue, 16 Jun 2020 07:52:33: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:52:37: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:52:37: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:52:37: #1 total tags in treatment: 3688841 INFO @ Tue, 16 Jun 2020 07:52:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:37: #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 07:52:37: #1 tags after filtering in treatment: 3688841 INFO @ Tue, 16 Jun 2020 07:52:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:37: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:37: #2 number of paired peaks: 3248 INFO @ Tue, 16 Jun 2020 07:52:37: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:38: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:38: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:38: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:38: #2 predicted fragment length is 140 bps INFO @ Tue, 16 Jun 2020 07:52:38: #2 alternative fragment length(s) may be 4,140 bps INFO @ Tue, 16 Jun 2020 07:52:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.20_model.r INFO @ Tue, 16 Jun 2020 07:52:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:52:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:52:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:52:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:52:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX188614/SRX188614.20_summits.bed INFO @ Tue, 16 Jun 2020 07:52:51: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (250 records, 4 fields): 1 millis CompletedMACS2peakCalling