Job ID = 5790708 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,963,443 reads read : 23,963,443 reads written : 23,963,443 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:38 23963443 reads; of these: 23963443 (100.00%) were unpaired; of these: 5131247 (21.41%) aligned 0 times 11918590 (49.74%) aligned exactly 1 time 6913606 (28.85%) aligned >1 times 78.59% overall alignment rate Time searching: 00:07:39 Overall time: 00:07:39 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] 2259197 / 18832196 = 0.1200 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 06:46:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.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 06:46:32: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:46:32: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:46:38: 1000000 INFO @ Wed, 22 Apr 2020 06:46:44: 2000000 INFO @ Wed, 22 Apr 2020 06:46:51: 3000000 INFO @ Wed, 22 Apr 2020 06:46:58: 4000000 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 06:47:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.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 06:47:02: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:47:02: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:47:04: 5000000 INFO @ Wed, 22 Apr 2020 06:47:08: 1000000 INFO @ Wed, 22 Apr 2020 06:47:11: 6000000 INFO @ Wed, 22 Apr 2020 06:47:14: 2000000 INFO @ Wed, 22 Apr 2020 06:47:18: 7000000 INFO @ Wed, 22 Apr 2020 06:47:20: 3000000 INFO @ Wed, 22 Apr 2020 06:47:24: 8000000 INFO @ Wed, 22 Apr 2020 06:47:26: 4000000 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 06:47:31: 9000000 INFO @ Wed, 22 Apr 2020 06:47:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.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 06:47:32: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:47:32: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:47:32: 5000000 INFO @ Wed, 22 Apr 2020 06:47:38: 10000000 INFO @ Wed, 22 Apr 2020 06:47:38: 6000000 INFO @ Wed, 22 Apr 2020 06:47:39: 1000000 INFO @ Wed, 22 Apr 2020 06:47:45: 7000000 INFO @ Wed, 22 Apr 2020 06:47:45: 11000000 INFO @ Wed, 22 Apr 2020 06:47:46: 2000000 INFO @ Wed, 22 Apr 2020 06:47:51: 8000000 INFO @ Wed, 22 Apr 2020 06:47:52: 12000000 INFO @ Wed, 22 Apr 2020 06:47:53: 3000000 INFO @ Wed, 22 Apr 2020 06:47:57: 9000000 INFO @ Wed, 22 Apr 2020 06:47:59: 13000000 INFO @ Wed, 22 Apr 2020 06:48:00: 4000000 INFO @ Wed, 22 Apr 2020 06:48:03: 10000000 INFO @ Wed, 22 Apr 2020 06:48:06: 14000000 INFO @ Wed, 22 Apr 2020 06:48:07: 5000000 INFO @ Wed, 22 Apr 2020 06:48:09: 11000000 INFO @ Wed, 22 Apr 2020 06:48:13: 15000000 INFO @ Wed, 22 Apr 2020 06:48:14: 6000000 INFO @ Wed, 22 Apr 2020 06:48:15: 12000000 INFO @ Wed, 22 Apr 2020 06:48:20: 16000000 INFO @ Wed, 22 Apr 2020 06:48:20: 7000000 INFO @ Wed, 22 Apr 2020 06:48:21: 13000000 INFO @ Wed, 22 Apr 2020 06:48:24: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:48:24: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:48:24: #1 total tags in treatment: 16572999 INFO @ Wed, 22 Apr 2020 06:48:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:48:24: #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 06:48:25: #1 tags after filtering in treatment: 16572872 INFO @ Wed, 22 Apr 2020 06:48:25: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:48:25: #1 finished! INFO @ Wed, 22 Apr 2020 06:48:25: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:48:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:48:27: #2 number of paired peaks: 27711 INFO @ Wed, 22 Apr 2020 06:48:27: start model_add_line... INFO @ Wed, 22 Apr 2020 06:48:27: start X-correlation... INFO @ Wed, 22 Apr 2020 06:48:27: end of X-cor INFO @ Wed, 22 Apr 2020 06:48:27: #2 finished! INFO @ Wed, 22 Apr 2020 06:48:27: #2 predicted fragment length is 170 bps INFO @ Wed, 22 Apr 2020 06:48:27: #2 alternative fragment length(s) may be 170 bps INFO @ Wed, 22 Apr 2020 06:48:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.05_model.r INFO @ Wed, 22 Apr 2020 06:48:27: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:48:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:48:27: 8000000 INFO @ Wed, 22 Apr 2020 06:48:28: 14000000 INFO @ Wed, 22 Apr 2020 06:48:34: 15000000 INFO @ Wed, 22 Apr 2020 06:48:34: 9000000 INFO @ Wed, 22 Apr 2020 06:48:40: 16000000 INFO @ Wed, 22 Apr 2020 06:48:41: 10000000 INFO @ Wed, 22 Apr 2020 06:48:44: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:48:44: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:48:44: #1 total tags in treatment: 16572999 INFO @ Wed, 22 Apr 2020 06:48:44: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:48:44: #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 06:48:44: #1 tags after filtering in treatment: 16572872 INFO @ Wed, 22 Apr 2020 06:48:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:48:44: #1 finished! INFO @ Wed, 22 Apr 2020 06:48:44: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:48:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:48:46: #2 number of paired peaks: 27711 INFO @ Wed, 22 Apr 2020 06:48:46: start model_add_line... INFO @ Wed, 22 Apr 2020 06:48:46: start X-correlation... INFO @ Wed, 22 Apr 2020 06:48:46: end of X-cor INFO @ Wed, 22 Apr 2020 06:48:46: #2 finished! INFO @ Wed, 22 Apr 2020 06:48:46: #2 predicted fragment length is 170 bps INFO @ Wed, 22 Apr 2020 06:48:46: #2 alternative fragment length(s) may be 170 bps INFO @ Wed, 22 Apr 2020 06:48:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.10_model.r INFO @ Wed, 22 Apr 2020 06:48:46: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:48:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:48:47: 11000000 INFO @ Wed, 22 Apr 2020 06:48:54: 12000000 INFO @ Wed, 22 Apr 2020 06:49:00: 13000000 INFO @ Wed, 22 Apr 2020 06:49:04: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:49:07: 14000000 INFO @ Wed, 22 Apr 2020 06:49:13: 15000000 INFO @ Wed, 22 Apr 2020 06:49:20: 16000000 INFO @ Wed, 22 Apr 2020 06:49:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:49:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:49:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.05_summits.bed INFO @ Wed, 22 Apr 2020 06:49:23: Done! INFO @ Wed, 22 Apr 2020 06:49:23: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:49:23: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:49:23: #1 total tags in treatment: 16572999 INFO @ Wed, 22 Apr 2020 06:49:23: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:49:23: #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 06:49:23: #3 Call peaks for each chromosome... pass1 - making usageList (120 chroms): 3 millis pass2 - checking and writing primary data (15001 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:49:24: #1 tags after filtering in treatment: 16572872 INFO @ Wed, 22 Apr 2020 06:49:24: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:49:24: #1 finished! INFO @ Wed, 22 Apr 2020 06:49:24: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:49:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:49:26: #2 number of paired peaks: 27711 INFO @ Wed, 22 Apr 2020 06:49:26: start model_add_line... INFO @ Wed, 22 Apr 2020 06:49:26: start X-correlation... INFO @ Wed, 22 Apr 2020 06:49:26: end of X-cor INFO @ Wed, 22 Apr 2020 06:49:26: #2 finished! INFO @ Wed, 22 Apr 2020 06:49:26: #2 predicted fragment length is 170 bps INFO @ Wed, 22 Apr 2020 06:49:26: #2 alternative fragment length(s) may be 170 bps INFO @ Wed, 22 Apr 2020 06:49:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.20_model.r INFO @ Wed, 22 Apr 2020 06:49:26: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:49:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:49:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:49:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:49:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.10_summits.bed INFO @ Wed, 22 Apr 2020 06:49:42: Done! pass1 - making usageList (74 chroms): 1 millis pass2 - checking and writing primary data (4356 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:50:04: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:50:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:50:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:50:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761739/SRX5761739.20_summits.bed INFO @ Wed, 22 Apr 2020 06:50:22: Done! pass1 - making usageList (45 chroms): 0 millis pass2 - checking and writing primary data (772 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。