Job ID = 5790677 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,532,315 reads read : 16,532,315 reads written : 16,532,315 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: 00:06:47 16532315 reads; of these: 16532315 (100.00%) were unpaired; of these: 3150147 (19.05%) aligned 0 times 7245212 (43.82%) aligned exactly 1 time 6136956 (37.12%) aligned >1 times 80.95% overall alignment rate Time searching: 00:06:49 Overall time: 00:06:49 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 1456543 / 13382168 = 0.1088 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 06:10:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.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 06:10:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:10:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:10:25: 1000000 INFO @ Wed, 22 Apr 2020 06:10:29: 2000000 INFO @ Wed, 22 Apr 2020 06:10:34: 3000000 INFO @ Wed, 22 Apr 2020 06:10:39: 4000000 INFO @ Wed, 22 Apr 2020 06:10:44: 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 06:10:49: 6000000 INFO @ Wed, 22 Apr 2020 06:10:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.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 06:10:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:10:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:10:54: 7000000 INFO @ Wed, 22 Apr 2020 06:10:55: 1000000 INFO @ Wed, 22 Apr 2020 06:10:59: 8000000 INFO @ Wed, 22 Apr 2020 06:11:00: 2000000 INFO @ Wed, 22 Apr 2020 06:11:04: 9000000 INFO @ Wed, 22 Apr 2020 06:11:05: 3000000 INFO @ Wed, 22 Apr 2020 06:11:09: 10000000 INFO @ Wed, 22 Apr 2020 06:11:10: 4000000 INFO @ Wed, 22 Apr 2020 06:11:14: 11000000 INFO @ Wed, 22 Apr 2020 06:11:15: 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 06:11:19: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:11:19: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:11:19: #1 total tags in treatment: 11925625 INFO @ Wed, 22 Apr 2020 06:11:19: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:11:19: #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 06:11:20: #1 tags after filtering in treatment: 11925484 INFO @ Wed, 22 Apr 2020 06:11:20: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:11:20: #1 finished! INFO @ Wed, 22 Apr 2020 06:11:20: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:11:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:11:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.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 06:11:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:11:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:11:20: 6000000 INFO @ Wed, 22 Apr 2020 06:11:22: #2 number of paired peaks: 29981 INFO @ Wed, 22 Apr 2020 06:11:22: start model_add_line... INFO @ Wed, 22 Apr 2020 06:11:22: start X-correlation... INFO @ Wed, 22 Apr 2020 06:11:22: end of X-cor INFO @ Wed, 22 Apr 2020 06:11:22: #2 finished! INFO @ Wed, 22 Apr 2020 06:11:22: #2 predicted fragment length is 199 bps INFO @ Wed, 22 Apr 2020 06:11:22: #2 alternative fragment length(s) may be 199 bps INFO @ Wed, 22 Apr 2020 06:11:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.05_model.r INFO @ Wed, 22 Apr 2020 06:11:22: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:11:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:11:25: 1000000 INFO @ Wed, 22 Apr 2020 06:11:25: 7000000 INFO @ Wed, 22 Apr 2020 06:11:30: 8000000 INFO @ Wed, 22 Apr 2020 06:11:30: 2000000 INFO @ Wed, 22 Apr 2020 06:11:35: 9000000 INFO @ Wed, 22 Apr 2020 06:11:35: 3000000 INFO @ Wed, 22 Apr 2020 06:11:40: 10000000 INFO @ Wed, 22 Apr 2020 06:11:40: 4000000 INFO @ Wed, 22 Apr 2020 06:11:45: 5000000 INFO @ Wed, 22 Apr 2020 06:11:45: 11000000 INFO @ Wed, 22 Apr 2020 06:11:50: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:11:50: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:11:50: #1 total tags in treatment: 11925625 INFO @ Wed, 22 Apr 2020 06:11:50: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:11:50: #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 06:11:50: 6000000 INFO @ Wed, 22 Apr 2020 06:11:50: #1 tags after filtering in treatment: 11925484 INFO @ Wed, 22 Apr 2020 06:11:50: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:11:50: #1 finished! INFO @ Wed, 22 Apr 2020 06:11:50: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:11:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:11:51: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:11:52: #2 number of paired peaks: 29981 INFO @ Wed, 22 Apr 2020 06:11:52: start model_add_line... INFO @ Wed, 22 Apr 2020 06:11:52: start X-correlation... INFO @ Wed, 22 Apr 2020 06:11:52: end of X-cor INFO @ Wed, 22 Apr 2020 06:11:52: #2 finished! INFO @ Wed, 22 Apr 2020 06:11:52: #2 predicted fragment length is 199 bps INFO @ Wed, 22 Apr 2020 06:11:52: #2 alternative fragment length(s) may be 199 bps INFO @ Wed, 22 Apr 2020 06:11:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.10_model.r INFO @ Wed, 22 Apr 2020 06:11:52: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:11:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:11:55: 7000000 INFO @ Wed, 22 Apr 2020 06:11:59: 8000000 INFO @ Wed, 22 Apr 2020 06:12:04: 9000000 INFO @ Wed, 22 Apr 2020 06:12:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:12:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:12:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.05_summits.bed INFO @ Wed, 22 Apr 2020 06:12:05: Done! pass1 - making usageList (100 chroms): 3 millis pass2 - checking and writing primary data (12913 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:12:09: 10000000 INFO @ Wed, 22 Apr 2020 06:12:13: 11000000 INFO @ Wed, 22 Apr 2020 06:12:18: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:12:18: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:12:18: #1 total tags in treatment: 11925625 INFO @ Wed, 22 Apr 2020 06:12:18: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:12:18: #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 06:12:18: #1 tags after filtering in treatment: 11925484 INFO @ Wed, 22 Apr 2020 06:12:18: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:12:18: #1 finished! INFO @ Wed, 22 Apr 2020 06:12:18: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:12:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:12:20: #2 number of paired peaks: 29981 INFO @ Wed, 22 Apr 2020 06:12:20: start model_add_line... INFO @ Wed, 22 Apr 2020 06:12:20: start X-correlation... INFO @ Wed, 22 Apr 2020 06:12:20: end of X-cor INFO @ Wed, 22 Apr 2020 06:12:20: #2 finished! INFO @ Wed, 22 Apr 2020 06:12:20: #2 predicted fragment length is 199 bps INFO @ Wed, 22 Apr 2020 06:12:20: #2 alternative fragment length(s) may be 199 bps INFO @ Wed, 22 Apr 2020 06:12:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.20_model.r INFO @ Wed, 22 Apr 2020 06:12:20: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:12:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:12:21: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:12:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:12:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:12:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.10_summits.bed INFO @ Wed, 22 Apr 2020 06:12:35: Done! pass1 - making usageList (68 chroms): 2 millis pass2 - checking and writing primary data (7462 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:12:49: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:13:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:13:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:13:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761712/SRX5761712.20_summits.bed INFO @ Wed, 22 Apr 2020 06:13:03: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (3291 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。