Job ID = 5790690 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,596,611 reads read : 22,596,611 reads written : 22,596,611 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: 00:00:02 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:03 Multiseed full-index search: 00:06:49 22596611 reads; of these: 22596611 (100.00%) were unpaired; of these: 5684044 (25.15%) aligned 0 times 12240058 (54.17%) aligned exactly 1 time 4672509 (20.68%) aligned >1 times 74.85% overall alignment rate Time searching: 00:06:57 Overall time: 00:06:57 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] 6059988 / 16912567 = 0.3583 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 06:25:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.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 06:25:06: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:25:06: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:25:11: 1000000 INFO @ Wed, 22 Apr 2020 06:25:16: 2000000 INFO @ Wed, 22 Apr 2020 06:25:21: 3000000 INFO @ Wed, 22 Apr 2020 06:25:26: 4000000 INFO @ Wed, 22 Apr 2020 06:25:31: 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 06:25:36: 6000000 INFO @ Wed, 22 Apr 2020 06:25:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.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 06:25:37: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:25:37: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:25:41: 7000000 INFO @ Wed, 22 Apr 2020 06:25:42: 1000000 INFO @ Wed, 22 Apr 2020 06:25:47: 8000000 INFO @ Wed, 22 Apr 2020 06:25:47: 2000000 INFO @ Wed, 22 Apr 2020 06:25:52: 9000000 INFO @ Wed, 22 Apr 2020 06:25:52: 3000000 INFO @ Wed, 22 Apr 2020 06:25:57: 10000000 INFO @ Wed, 22 Apr 2020 06:25:58: 4000000 INFO @ Wed, 22 Apr 2020 06:26:02: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:26:02: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:26:02: #1 total tags in treatment: 10852579 INFO @ Wed, 22 Apr 2020 06:26:02: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:26:02: #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 06:26:02: #1 tags after filtering in treatment: 10852388 INFO @ Wed, 22 Apr 2020 06:26:02: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:26:02: #1 finished! INFO @ Wed, 22 Apr 2020 06:26:02: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:26:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:26:03: 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 06:26:04: #2 number of paired peaks: 37875 INFO @ Wed, 22 Apr 2020 06:26:04: start model_add_line... INFO @ Wed, 22 Apr 2020 06:26:04: start X-correlation... INFO @ Wed, 22 Apr 2020 06:26:04: end of X-cor INFO @ Wed, 22 Apr 2020 06:26:04: #2 finished! INFO @ Wed, 22 Apr 2020 06:26:04: #2 predicted fragment length is 234 bps INFO @ Wed, 22 Apr 2020 06:26:04: #2 alternative fragment length(s) may be 234 bps INFO @ Wed, 22 Apr 2020 06:26:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.05_model.r INFO @ Wed, 22 Apr 2020 06:26:04: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:26:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:26:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.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 06:26:07: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:26:07: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:26:08: 6000000 INFO @ Wed, 22 Apr 2020 06:26:12: 1000000 INFO @ Wed, 22 Apr 2020 06:26:14: 7000000 INFO @ Wed, 22 Apr 2020 06:26:18: 2000000 INFO @ Wed, 22 Apr 2020 06:26:19: 8000000 INFO @ Wed, 22 Apr 2020 06:26:23: 3000000 INFO @ Wed, 22 Apr 2020 06:26:24: 9000000 INFO @ Wed, 22 Apr 2020 06:26:28: 4000000 INFO @ Wed, 22 Apr 2020 06:26:29: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:26:30: 10000000 INFO @ Wed, 22 Apr 2020 06:26:34: 5000000 INFO @ Wed, 22 Apr 2020 06:26:34: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:26:34: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:26:34: #1 total tags in treatment: 10852579 INFO @ Wed, 22 Apr 2020 06:26:34: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:26:34: #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 06:26:35: #1 tags after filtering in treatment: 10852388 INFO @ Wed, 22 Apr 2020 06:26:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:26:35: #1 finished! INFO @ Wed, 22 Apr 2020 06:26:35: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:26:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:26:36: #2 number of paired peaks: 37875 INFO @ Wed, 22 Apr 2020 06:26:36: start model_add_line... INFO @ Wed, 22 Apr 2020 06:26:37: start X-correlation... INFO @ Wed, 22 Apr 2020 06:26:37: end of X-cor INFO @ Wed, 22 Apr 2020 06:26:37: #2 finished! INFO @ Wed, 22 Apr 2020 06:26:37: #2 predicted fragment length is 234 bps INFO @ Wed, 22 Apr 2020 06:26:37: #2 alternative fragment length(s) may be 234 bps INFO @ Wed, 22 Apr 2020 06:26:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.10_model.r INFO @ Wed, 22 Apr 2020 06:26:37: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:26:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:26:39: 6000000 INFO @ Wed, 22 Apr 2020 06:26:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:26:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:26:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.05_summits.bed INFO @ Wed, 22 Apr 2020 06:26:42: Done! INFO @ Wed, 22 Apr 2020 06:26:44: 7000000 pass1 - making usageList (97 chroms): 2 millis pass2 - checking and writing primary data (8638 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:26:49: 8000000 INFO @ Wed, 22 Apr 2020 06:26:54: 9000000 INFO @ Wed, 22 Apr 2020 06:26:59: 10000000 INFO @ Wed, 22 Apr 2020 06:27:02: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:27:03: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:27:03: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:27:03: #1 total tags in treatment: 10852579 INFO @ Wed, 22 Apr 2020 06:27:03: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:27:03: #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 06:27:04: #1 tags after filtering in treatment: 10852388 INFO @ Wed, 22 Apr 2020 06:27:04: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:27:04: #1 finished! INFO @ Wed, 22 Apr 2020 06:27:04: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:27:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:27:06: #2 number of paired peaks: 37875 INFO @ Wed, 22 Apr 2020 06:27:06: start model_add_line... INFO @ Wed, 22 Apr 2020 06:27:06: start X-correlation... INFO @ Wed, 22 Apr 2020 06:27:06: end of X-cor INFO @ Wed, 22 Apr 2020 06:27:06: #2 finished! INFO @ Wed, 22 Apr 2020 06:27:06: #2 predicted fragment length is 234 bps INFO @ Wed, 22 Apr 2020 06:27:06: #2 alternative fragment length(s) may be 234 bps INFO @ Wed, 22 Apr 2020 06:27:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.20_model.r INFO @ Wed, 22 Apr 2020 06:27:06: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:27:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:27:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:27:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:27:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.10_summits.bed INFO @ Wed, 22 Apr 2020 06:27:14: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (1655 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:27:30: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:27:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:27:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:27:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761722/SRX5761722.20_summits.bed INFO @ Wed, 22 Apr 2020 06:27:43: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (292 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。