Job ID = 5790664 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,212,808 reads read : 23,212,808 reads written : 23,212,808 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: 00:05:53 23212808 reads; of these: 23212808 (100.00%) were unpaired; of these: 5019695 (21.62%) aligned 0 times 14605932 (62.92%) aligned exactly 1 time 3587181 (15.45%) aligned >1 times 78.38% overall alignment rate Time searching: 00:05:55 Overall time: 00:05:55 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] 4491472 / 18193113 = 0.2469 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 05:45:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.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 05:45:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:45:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:45:59: 1000000 INFO @ Wed, 22 Apr 2020 05:46:03: 2000000 INFO @ Wed, 22 Apr 2020 05:46:08: 3000000 INFO @ Wed, 22 Apr 2020 05:46:12: 4000000 INFO @ Wed, 22 Apr 2020 05:46:17: 5000000 INFO @ Wed, 22 Apr 2020 05:46:22: 6000000 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 05:46:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.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 05:46:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:46:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:46:27: 7000000 INFO @ Wed, 22 Apr 2020 05:46:30: 1000000 INFO @ Wed, 22 Apr 2020 05:46:32: 8000000 INFO @ Wed, 22 Apr 2020 05:46:35: 2000000 INFO @ Wed, 22 Apr 2020 05:46:38: 9000000 INFO @ Wed, 22 Apr 2020 05:46:41: 3000000 INFO @ Wed, 22 Apr 2020 05:46:43: 10000000 INFO @ Wed, 22 Apr 2020 05:46:47: 4000000 INFO @ Wed, 22 Apr 2020 05:46:48: 11000000 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 05:46:52: 5000000 INFO @ Wed, 22 Apr 2020 05:46:53: 12000000 INFO @ Wed, 22 Apr 2020 05:46:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.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 05:46:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:46:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:46:58: 6000000 INFO @ Wed, 22 Apr 2020 05:46:58: 13000000 INFO @ Wed, 22 Apr 2020 05:47:00: 1000000 INFO @ Wed, 22 Apr 2020 05:47:02: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 05:47:02: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 05:47:02: #1 total tags in treatment: 13701641 INFO @ Wed, 22 Apr 2020 05:47:02: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:47:02: #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 05:47:03: #1 tags after filtering in treatment: 13701419 INFO @ Wed, 22 Apr 2020 05:47:03: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:47:03: #1 finished! INFO @ Wed, 22 Apr 2020 05:47:03: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:47:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:47:03: 7000000 INFO @ Wed, 22 Apr 2020 05:47:04: #2 number of paired peaks: 18637 INFO @ Wed, 22 Apr 2020 05:47:04: start model_add_line... INFO @ Wed, 22 Apr 2020 05:47:04: start X-correlation... INFO @ Wed, 22 Apr 2020 05:47:04: end of X-cor INFO @ Wed, 22 Apr 2020 05:47:04: #2 finished! INFO @ Wed, 22 Apr 2020 05:47:04: #2 predicted fragment length is 210 bps INFO @ Wed, 22 Apr 2020 05:47:04: #2 alternative fragment length(s) may be 210 bps INFO @ Wed, 22 Apr 2020 05:47:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.05_model.r INFO @ Wed, 22 Apr 2020 05:47:04: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:47:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:47:05: 2000000 INFO @ Wed, 22 Apr 2020 05:47:09: 8000000 INFO @ Wed, 22 Apr 2020 05:47:11: 3000000 INFO @ Wed, 22 Apr 2020 05:47:15: 9000000 INFO @ Wed, 22 Apr 2020 05:47:16: 4000000 INFO @ Wed, 22 Apr 2020 05:47:20: 10000000 INFO @ Wed, 22 Apr 2020 05:47:22: 5000000 INFO @ Wed, 22 Apr 2020 05:47:26: 11000000 INFO @ Wed, 22 Apr 2020 05:47:27: 6000000 INFO @ Wed, 22 Apr 2020 05:47:32: 12000000 INFO @ Wed, 22 Apr 2020 05:47:33: 7000000 INFO @ Wed, 22 Apr 2020 05:47:35: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:47:38: 13000000 INFO @ Wed, 22 Apr 2020 05:47:38: 8000000 INFO @ Wed, 22 Apr 2020 05:47:42: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 05:47:42: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 05:47:42: #1 total tags in treatment: 13701641 INFO @ Wed, 22 Apr 2020 05:47:42: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:47:42: #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 05:47:42: #1 tags after filtering in treatment: 13701419 INFO @ Wed, 22 Apr 2020 05:47:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:47:42: #1 finished! INFO @ Wed, 22 Apr 2020 05:47:42: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:47:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:47:44: #2 number of paired peaks: 18637 INFO @ Wed, 22 Apr 2020 05:47:44: start model_add_line... INFO @ Wed, 22 Apr 2020 05:47:44: start X-correlation... INFO @ Wed, 22 Apr 2020 05:47:44: 9000000 INFO @ Wed, 22 Apr 2020 05:47:44: end of X-cor INFO @ Wed, 22 Apr 2020 05:47:44: #2 finished! INFO @ Wed, 22 Apr 2020 05:47:44: #2 predicted fragment length is 210 bps INFO @ Wed, 22 Apr 2020 05:47:44: #2 alternative fragment length(s) may be 210 bps INFO @ Wed, 22 Apr 2020 05:47:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.10_model.r INFO @ Wed, 22 Apr 2020 05:47:44: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:47:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:47:49: 10000000 INFO @ Wed, 22 Apr 2020 05:47:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.05_peaks.xls INFO @ Wed, 22 Apr 2020 05:47:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:47:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.05_summits.bed INFO @ Wed, 22 Apr 2020 05:47:52: Done! pass1 - making usageList (131 chroms): 3 millis pass2 - checking and writing primary data (19127 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:47:55: 11000000 INFO @ Wed, 22 Apr 2020 05:48:00: 12000000 INFO @ Wed, 22 Apr 2020 05:48:06: 13000000 INFO @ Wed, 22 Apr 2020 05:48:10: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 05:48:10: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 05:48:10: #1 total tags in treatment: 13701641 INFO @ Wed, 22 Apr 2020 05:48:10: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:48:10: #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 05:48:10: #1 tags after filtering in treatment: 13701419 INFO @ Wed, 22 Apr 2020 05:48:10: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:48:10: #1 finished! INFO @ Wed, 22 Apr 2020 05:48:10: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:48:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:48:12: #2 number of paired peaks: 18637 INFO @ Wed, 22 Apr 2020 05:48:12: start model_add_line... INFO @ Wed, 22 Apr 2020 05:48:12: start X-correlation... INFO @ Wed, 22 Apr 2020 05:48:12: end of X-cor INFO @ Wed, 22 Apr 2020 05:48:12: #2 finished! INFO @ Wed, 22 Apr 2020 05:48:12: #2 predicted fragment length is 210 bps INFO @ Wed, 22 Apr 2020 05:48:12: #2 alternative fragment length(s) may be 210 bps INFO @ Wed, 22 Apr 2020 05:48:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.20_model.r INFO @ Wed, 22 Apr 2020 05:48:12: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:48:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:48:15: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:48:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.10_peaks.xls INFO @ Wed, 22 Apr 2020 05:48:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:48:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.10_summits.bed INFO @ Wed, 22 Apr 2020 05:48:31: Done! pass1 - making usageList (113 chroms): 3 millis pass2 - checking and writing primary data (16599 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:48:44: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:49:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.20_peaks.xls INFO @ Wed, 22 Apr 2020 05:49:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:49:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761700/SRX5761700.20_summits.bed INFO @ Wed, 22 Apr 2020 05:49:01: Done! pass1 - making usageList (93 chroms): 2 millis pass2 - checking and writing primary data (14293 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。