Job ID = 5790694 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,252,592 reads read : 23,252,592 reads written : 23,252,592 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:31 23252592 reads; of these: 23252592 (100.00%) were unpaired; of these: 5856401 (25.19%) aligned 0 times 12176492 (52.37%) aligned exactly 1 time 5219699 (22.45%) aligned >1 times 74.81% overall alignment rate Time searching: 00:08:32 Overall time: 00:08:32 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2874179 / 17396191 = 0.1652 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 @ Wed, 22 Apr 2020 06:31:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 06:31:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:31:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:31:25: 1000000 INFO @ Wed, 22 Apr 2020 06:31:30: 2000000 INFO @ Wed, 22 Apr 2020 06:31:35: 3000000 INFO @ Wed, 22 Apr 2020 06:31:40: 4000000 INFO @ Wed, 22 Apr 2020 06:31:45: 5000000 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 @ Wed, 22 Apr 2020 06:31:50: 6000000 INFO @ Wed, 22 Apr 2020 06:31:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 06:31:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:31:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:31:55: 7000000 INFO @ Wed, 22 Apr 2020 06:31:56: 1000000 INFO @ Wed, 22 Apr 2020 06:32:01: 8000000 INFO @ Wed, 22 Apr 2020 06:32:01: 2000000 INFO @ Wed, 22 Apr 2020 06:32:06: 9000000 INFO @ Wed, 22 Apr 2020 06:32:06: 3000000 INFO @ Wed, 22 Apr 2020 06:32:11: 10000000 INFO @ Wed, 22 Apr 2020 06:32:11: 4000000 INFO @ Wed, 22 Apr 2020 06:32:16: 11000000 INFO @ Wed, 22 Apr 2020 06:32:17: 5000000 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 @ Wed, 22 Apr 2020 06:32:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 06:32:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:32:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:32:22: 12000000 INFO @ Wed, 22 Apr 2020 06:32:22: 6000000 INFO @ Wed, 22 Apr 2020 06:32:26: 1000000 INFO @ Wed, 22 Apr 2020 06:32:27: 13000000 INFO @ Wed, 22 Apr 2020 06:32:27: 7000000 INFO @ Wed, 22 Apr 2020 06:32:33: 2000000 INFO @ Wed, 22 Apr 2020 06:32:33: 8000000 INFO @ Wed, 22 Apr 2020 06:32:33: 14000000 INFO @ Wed, 22 Apr 2020 06:32:36: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:32:36: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:32:36: #1 total tags in treatment: 14522012 INFO @ Wed, 22 Apr 2020 06:32:36: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:32:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:32:36: #1 tags after filtering in treatment: 14521849 INFO @ Wed, 22 Apr 2020 06:32:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:32:36: #1 finished! INFO @ Wed, 22 Apr 2020 06:32:36: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:32:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:32:38: #2 number of paired peaks: 18168 INFO @ Wed, 22 Apr 2020 06:32:38: start model_add_line... INFO @ Wed, 22 Apr 2020 06:32:38: start X-correlation... INFO @ Wed, 22 Apr 2020 06:32:38: end of X-cor INFO @ Wed, 22 Apr 2020 06:32:38: #2 finished! INFO @ Wed, 22 Apr 2020 06:32:38: #2 predicted fragment length is 215 bps INFO @ Wed, 22 Apr 2020 06:32:38: #2 alternative fragment length(s) may be 215 bps INFO @ Wed, 22 Apr 2020 06:32:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.05_model.r INFO @ Wed, 22 Apr 2020 06:32:38: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:32:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:32:38: 9000000 INFO @ Wed, 22 Apr 2020 06:32:39: 3000000 INFO @ Wed, 22 Apr 2020 06:32:44: 10000000 INFO @ Wed, 22 Apr 2020 06:32:45: 4000000 INFO @ Wed, 22 Apr 2020 06:32:49: 11000000 INFO @ Wed, 22 Apr 2020 06:32:51: 5000000 INFO @ Wed, 22 Apr 2020 06:32:55: 12000000 INFO @ Wed, 22 Apr 2020 06:32:57: 6000000 INFO @ Wed, 22 Apr 2020 06:33:00: 13000000 INFO @ Wed, 22 Apr 2020 06:33:03: 7000000 INFO @ Wed, 22 Apr 2020 06:33:06: 14000000 INFO @ Wed, 22 Apr 2020 06:33:09: 8000000 INFO @ Wed, 22 Apr 2020 06:33:09: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:33:09: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:33:09: #1 total tags in treatment: 14522012 INFO @ Wed, 22 Apr 2020 06:33:09: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:33:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:33:09: #1 tags after filtering in treatment: 14521849 INFO @ Wed, 22 Apr 2020 06:33:09: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:33:09: #1 finished! INFO @ Wed, 22 Apr 2020 06:33:09: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:33:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:33:11: #2 number of paired peaks: 18168 INFO @ Wed, 22 Apr 2020 06:33:11: start model_add_line... INFO @ Wed, 22 Apr 2020 06:33:11: start X-correlation... INFO @ Wed, 22 Apr 2020 06:33:11: end of X-cor INFO @ Wed, 22 Apr 2020 06:33:11: #2 finished! INFO @ Wed, 22 Apr 2020 06:33:11: #2 predicted fragment length is 215 bps INFO @ Wed, 22 Apr 2020 06:33:11: #2 alternative fragment length(s) may be 215 bps INFO @ Wed, 22 Apr 2020 06:33:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.10_model.r INFO @ Wed, 22 Apr 2020 06:33:11: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:33:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:33:11: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:33:14: 9000000 INFO @ Wed, 22 Apr 2020 06:33:20: 10000000 INFO @ Wed, 22 Apr 2020 06:33:26: 11000000 INFO @ Wed, 22 Apr 2020 06:33:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:33:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:33:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.05_summits.bed INFO @ Wed, 22 Apr 2020 06:33:29: Done! pass1 - making usageList (81 chroms): 1 millis pass2 - checking and writing primary data (5869 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:33:32: 12000000 INFO @ Wed, 22 Apr 2020 06:33:37: 13000000 INFO @ Wed, 22 Apr 2020 06:33:43: 14000000 INFO @ Wed, 22 Apr 2020 06:33:44: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:33:46: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:33:46: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:33:46: #1 total tags in treatment: 14522012 INFO @ Wed, 22 Apr 2020 06:33:46: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:33:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:33:47: #1 tags after filtering in treatment: 14521849 INFO @ Wed, 22 Apr 2020 06:33:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:33:47: #1 finished! INFO @ Wed, 22 Apr 2020 06:33:47: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:33:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:33:49: #2 number of paired peaks: 18168 INFO @ Wed, 22 Apr 2020 06:33:49: start model_add_line... INFO @ Wed, 22 Apr 2020 06:33:49: start X-correlation... INFO @ Wed, 22 Apr 2020 06:33:49: end of X-cor INFO @ Wed, 22 Apr 2020 06:33:49: #2 finished! INFO @ Wed, 22 Apr 2020 06:33:49: #2 predicted fragment length is 215 bps INFO @ Wed, 22 Apr 2020 06:33:49: #2 alternative fragment length(s) may be 215 bps INFO @ Wed, 22 Apr 2020 06:33:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.20_model.r INFO @ Wed, 22 Apr 2020 06:33:49: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:33:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:34:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:34:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:34:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.10_summits.bed INFO @ Wed, 22 Apr 2020 06:34:01: Done! pass1 - making usageList (55 chroms): 2 millis pass2 - checking and writing primary data (2148 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:34:22: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:34:38: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:34:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:34:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761726/SRX5761726.20_summits.bed INFO @ Wed, 22 Apr 2020 06:34:38: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (404 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。