Job ID = 5790665 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,172,674 reads read : 23,172,674 reads written : 23,172,674 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:03 23172674 reads; of these: 23172674 (100.00%) were unpaired; of these: 4405269 (19.01%) aligned 0 times 14389888 (62.10%) aligned exactly 1 time 4377517 (18.89%) aligned >1 times 80.99% overall alignment rate Time searching: 00:07:06 Overall time: 00:07:06 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] 3678370 / 18767405 = 0.1960 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 05:52:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.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 05:52:10: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:52:10: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:52:15: 1000000 INFO @ Wed, 22 Apr 2020 05:52:20: 2000000 INFO @ Wed, 22 Apr 2020 05:52:25: 3000000 INFO @ Wed, 22 Apr 2020 05:52:29: 4000000 INFO @ Wed, 22 Apr 2020 05:52:34: 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 05:52:39: 6000000 INFO @ Wed, 22 Apr 2020 05:52:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.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 05:52:40: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:52:40: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:52:44: 7000000 INFO @ Wed, 22 Apr 2020 05:52:45: 1000000 INFO @ Wed, 22 Apr 2020 05:52:49: 8000000 INFO @ Wed, 22 Apr 2020 05:52:49: 2000000 INFO @ Wed, 22 Apr 2020 05:52:53: 9000000 INFO @ Wed, 22 Apr 2020 05:52:54: 3000000 INFO @ Wed, 22 Apr 2020 05:52:58: 10000000 INFO @ Wed, 22 Apr 2020 05:52:59: 4000000 INFO @ Wed, 22 Apr 2020 05:53:03: 11000000 INFO @ Wed, 22 Apr 2020 05:53:04: 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 05:53:08: 12000000 INFO @ Wed, 22 Apr 2020 05:53:09: 6000000 INFO @ Wed, 22 Apr 2020 05:53:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.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 05:53:10: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:53:10: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:53:13: 13000000 INFO @ Wed, 22 Apr 2020 05:53:14: 7000000 INFO @ Wed, 22 Apr 2020 05:53:15: 1000000 INFO @ Wed, 22 Apr 2020 05:53:18: 14000000 INFO @ Wed, 22 Apr 2020 05:53:19: 8000000 INFO @ Wed, 22 Apr 2020 05:53:20: 2000000 INFO @ Wed, 22 Apr 2020 05:53:23: 15000000 INFO @ Wed, 22 Apr 2020 05:53:24: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 05:53:24: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 05:53:24: #1 total tags in treatment: 15089035 INFO @ Wed, 22 Apr 2020 05:53:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:53:24: #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 05:53:24: 9000000 INFO @ Wed, 22 Apr 2020 05:53:24: #1 tags after filtering in treatment: 15088846 INFO @ Wed, 22 Apr 2020 05:53:24: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:53:24: #1 finished! INFO @ Wed, 22 Apr 2020 05:53:24: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:53:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:53:25: 3000000 INFO @ Wed, 22 Apr 2020 05:53:26: #2 number of paired peaks: 23091 INFO @ Wed, 22 Apr 2020 05:53:26: start model_add_line... INFO @ Wed, 22 Apr 2020 05:53:26: start X-correlation... INFO @ Wed, 22 Apr 2020 05:53:26: end of X-cor INFO @ Wed, 22 Apr 2020 05:53:26: #2 finished! INFO @ Wed, 22 Apr 2020 05:53:26: #2 predicted fragment length is 184 bps INFO @ Wed, 22 Apr 2020 05:53:26: #2 alternative fragment length(s) may be 184 bps INFO @ Wed, 22 Apr 2020 05:53:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.05_model.r INFO @ Wed, 22 Apr 2020 05:53:26: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:53:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:53:29: 10000000 INFO @ Wed, 22 Apr 2020 05:53:30: 4000000 INFO @ Wed, 22 Apr 2020 05:53:34: 11000000 INFO @ Wed, 22 Apr 2020 05:53:35: 5000000 INFO @ Wed, 22 Apr 2020 05:53:39: 12000000 INFO @ Wed, 22 Apr 2020 05:53:40: 6000000 INFO @ Wed, 22 Apr 2020 05:53:44: 13000000 INFO @ Wed, 22 Apr 2020 05:53:45: 7000000 INFO @ Wed, 22 Apr 2020 05:53:49: 14000000 INFO @ Wed, 22 Apr 2020 05:53:50: 8000000 INFO @ Wed, 22 Apr 2020 05:53:54: 15000000 INFO @ Wed, 22 Apr 2020 05:53:55: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 05:53:55: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 05:53:55: #1 total tags in treatment: 15089035 INFO @ Wed, 22 Apr 2020 05:53:55: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:53:55: #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 05:53:55: 9000000 INFO @ Wed, 22 Apr 2020 05:53:55: #1 tags after filtering in treatment: 15088846 INFO @ Wed, 22 Apr 2020 05:53:55: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:53:55: #1 finished! INFO @ Wed, 22 Apr 2020 05:53:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:53:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:53:57: #2 number of paired peaks: 23091 INFO @ Wed, 22 Apr 2020 05:53:57: start model_add_line... INFO @ Wed, 22 Apr 2020 05:53:57: start X-correlation... INFO @ Wed, 22 Apr 2020 05:53:57: end of X-cor INFO @ Wed, 22 Apr 2020 05:53:57: #2 finished! INFO @ Wed, 22 Apr 2020 05:53:57: #2 predicted fragment length is 184 bps INFO @ Wed, 22 Apr 2020 05:53:57: #2 alternative fragment length(s) may be 184 bps INFO @ Wed, 22 Apr 2020 05:53:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.10_model.r INFO @ Wed, 22 Apr 2020 05:53:57: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:53:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:53:59: 10000000 INFO @ Wed, 22 Apr 2020 05:54:01: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:54:04: 11000000 INFO @ Wed, 22 Apr 2020 05:54:09: 12000000 INFO @ Wed, 22 Apr 2020 05:54:14: 13000000 INFO @ Wed, 22 Apr 2020 05:54:19: 14000000 INFO @ Wed, 22 Apr 2020 05:54:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.05_peaks.xls INFO @ Wed, 22 Apr 2020 05:54:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:54:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.05_summits.bed INFO @ Wed, 22 Apr 2020 05:54:19: Done! pass1 - making usageList (143 chroms): 3 millis pass2 - checking and writing primary data (22724 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:54:24: 15000000 INFO @ Wed, 22 Apr 2020 05:54:24: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 05:54:24: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 05:54:24: #1 total tags in treatment: 15089035 INFO @ Wed, 22 Apr 2020 05:54:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:54:24: #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 05:54:24: #1 tags after filtering in treatment: 15088846 INFO @ Wed, 22 Apr 2020 05:54:24: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:54:24: #1 finished! INFO @ Wed, 22 Apr 2020 05:54:24: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:54:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:54:26: #2 number of paired peaks: 23091 INFO @ Wed, 22 Apr 2020 05:54:26: start model_add_line... INFO @ Wed, 22 Apr 2020 05:54:27: start X-correlation... INFO @ Wed, 22 Apr 2020 05:54:27: end of X-cor INFO @ Wed, 22 Apr 2020 05:54:27: #2 finished! INFO @ Wed, 22 Apr 2020 05:54:27: #2 predicted fragment length is 184 bps INFO @ Wed, 22 Apr 2020 05:54:27: #2 alternative fragment length(s) may be 184 bps INFO @ Wed, 22 Apr 2020 05:54:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.20_model.r INFO @ Wed, 22 Apr 2020 05:54:27: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:54:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:54:32: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:54:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.10_peaks.xls INFO @ Wed, 22 Apr 2020 05:54:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:54:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.10_summits.bed INFO @ Wed, 22 Apr 2020 05:54:50: Done! pass1 - making usageList (118 chroms): 3 millis pass2 - checking and writing primary data (17998 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:55:01: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:55:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.20_peaks.xls INFO @ Wed, 22 Apr 2020 05:55:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:55:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761701/SRX5761701.20_summits.bed INFO @ Wed, 22 Apr 2020 05:55:19: Done! pass1 - making usageList (100 chroms): 4 millis pass2 - checking and writing primary data (15046 records, 4 fields): 24 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。