Job ID = 5790634 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 47,293,972 reads read : 47,293,972 reads written : 47,293,972 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR4018123.sra.cache’: 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: 00:00:02 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:25:03 47293972 reads; of these: 47293972 (100.00%) were unpaired; of these: 1847746 (3.91%) aligned 0 times 38698081 (81.82%) aligned exactly 1 time 6748145 (14.27%) aligned >1 times 96.09% overall alignment rate Time searching: 00:25:08 Overall time: 00:25:08 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 20 files... [bam_rmdupse_core] 26986794 / 45446226 = 0.5938 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 05:00:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.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 05:00:17: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:00:17: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:00:23: 1000000 INFO @ Wed, 22 Apr 2020 05:00:28: 2000000 INFO @ Wed, 22 Apr 2020 05:00:34: 3000000 INFO @ Wed, 22 Apr 2020 05:00:40: 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 05:00:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.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 05:00:45: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:00:45: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:00:46: 5000000 INFO @ Wed, 22 Apr 2020 05:00:51: 1000000 INFO @ Wed, 22 Apr 2020 05:00:52: 6000000 INFO @ Wed, 22 Apr 2020 05:00:57: 2000000 INFO @ Wed, 22 Apr 2020 05:00:58: 7000000 INFO @ Wed, 22 Apr 2020 05:01:04: 3000000 INFO @ Wed, 22 Apr 2020 05:01:05: 8000000 INFO @ Wed, 22 Apr 2020 05:01:10: 4000000 INFO @ Wed, 22 Apr 2020 05:01:11: 9000000 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 05:01:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.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 05:01:15: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:01:15: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:01:17: 5000000 INFO @ Wed, 22 Apr 2020 05:01:17: 10000000 INFO @ Wed, 22 Apr 2020 05:01:22: 1000000 INFO @ Wed, 22 Apr 2020 05:01:23: 6000000 INFO @ Wed, 22 Apr 2020 05:01:24: 11000000 INFO @ Wed, 22 Apr 2020 05:01:28: 2000000 INFO @ Wed, 22 Apr 2020 05:01:30: 7000000 INFO @ Wed, 22 Apr 2020 05:01:31: 12000000 INFO @ Wed, 22 Apr 2020 05:01:35: 3000000 INFO @ Wed, 22 Apr 2020 05:01:37: 8000000 INFO @ Wed, 22 Apr 2020 05:01:37: 13000000 INFO @ Wed, 22 Apr 2020 05:01:42: 4000000 INFO @ Wed, 22 Apr 2020 05:01:43: 9000000 INFO @ Wed, 22 Apr 2020 05:01:44: 14000000 INFO @ Wed, 22 Apr 2020 05:01:48: 5000000 INFO @ Wed, 22 Apr 2020 05:01:50: 10000000 INFO @ Wed, 22 Apr 2020 05:01:50: 15000000 INFO @ Wed, 22 Apr 2020 05:01:55: 6000000 INFO @ Wed, 22 Apr 2020 05:01:56: 11000000 INFO @ Wed, 22 Apr 2020 05:01:57: 16000000 INFO @ Wed, 22 Apr 2020 05:02:01: 7000000 INFO @ Wed, 22 Apr 2020 05:02:03: 12000000 INFO @ Wed, 22 Apr 2020 05:02:03: 17000000 INFO @ Wed, 22 Apr 2020 05:02:08: 8000000 INFO @ Wed, 22 Apr 2020 05:02:09: 13000000 INFO @ Wed, 22 Apr 2020 05:02:10: 18000000 INFO @ Wed, 22 Apr 2020 05:02:13: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 05:02:13: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 05:02:13: #1 total tags in treatment: 18459432 INFO @ Wed, 22 Apr 2020 05:02:13: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:02:13: #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 05:02:14: #1 tags after filtering in treatment: 18459275 INFO @ Wed, 22 Apr 2020 05:02:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:02:14: #1 finished! INFO @ Wed, 22 Apr 2020 05:02:14: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:02:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:02:14: 9000000 INFO @ Wed, 22 Apr 2020 05:02:16: 14000000 INFO @ Wed, 22 Apr 2020 05:02:17: #2 number of paired peaks: 51810 INFO @ Wed, 22 Apr 2020 05:02:17: start model_add_line... INFO @ Wed, 22 Apr 2020 05:02:17: start X-correlation... INFO @ Wed, 22 Apr 2020 05:02:17: end of X-cor INFO @ Wed, 22 Apr 2020 05:02:17: #2 finished! INFO @ Wed, 22 Apr 2020 05:02:17: #2 predicted fragment length is 163 bps INFO @ Wed, 22 Apr 2020 05:02:17: #2 alternative fragment length(s) may be 163 bps INFO @ Wed, 22 Apr 2020 05:02:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.05_model.r INFO @ Wed, 22 Apr 2020 05:02:17: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:02:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:02:21: 10000000 INFO @ Wed, 22 Apr 2020 05:02:22: 15000000 INFO @ Wed, 22 Apr 2020 05:02:27: 11000000 INFO @ Wed, 22 Apr 2020 05:02:29: 16000000 INFO @ Wed, 22 Apr 2020 05:02:34: 12000000 INFO @ Wed, 22 Apr 2020 05:02:35: 17000000 INFO @ Wed, 22 Apr 2020 05:02:40: 13000000 INFO @ Wed, 22 Apr 2020 05:02:42: 18000000 INFO @ Wed, 22 Apr 2020 05:02:45: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 05:02:45: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 05:02:45: #1 total tags in treatment: 18459432 INFO @ Wed, 22 Apr 2020 05:02:45: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:02:45: #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 05:02:45: #1 tags after filtering in treatment: 18459275 INFO @ Wed, 22 Apr 2020 05:02:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:02:45: #1 finished! INFO @ Wed, 22 Apr 2020 05:02:45: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:02:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:02:47: 14000000 INFO @ Wed, 22 Apr 2020 05:02:49: #2 number of paired peaks: 51810 INFO @ Wed, 22 Apr 2020 05:02:49: start model_add_line... INFO @ Wed, 22 Apr 2020 05:02:49: start X-correlation... INFO @ Wed, 22 Apr 2020 05:02:49: end of X-cor INFO @ Wed, 22 Apr 2020 05:02:49: #2 finished! INFO @ Wed, 22 Apr 2020 05:02:49: #2 predicted fragment length is 163 bps INFO @ Wed, 22 Apr 2020 05:02:49: #2 alternative fragment length(s) may be 163 bps INFO @ Wed, 22 Apr 2020 05:02:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.10_model.r INFO @ Wed, 22 Apr 2020 05:02:49: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:02:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:02:53: 15000000 INFO @ Wed, 22 Apr 2020 05:02:58: 16000000 INFO @ Wed, 22 Apr 2020 05:03:00: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:03:04: 17000000 INFO @ Wed, 22 Apr 2020 05:03:10: 18000000 INFO @ Wed, 22 Apr 2020 05:03:13: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 05:03:13: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 05:03:13: #1 total tags in treatment: 18459432 INFO @ Wed, 22 Apr 2020 05:03:13: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:03:13: #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 05:03:13: #1 tags after filtering in treatment: 18459275 INFO @ Wed, 22 Apr 2020 05:03:13: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:03:13: #1 finished! INFO @ Wed, 22 Apr 2020 05:03:13: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:03:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:03:16: #2 number of paired peaks: 51810 INFO @ Wed, 22 Apr 2020 05:03:16: start model_add_line... INFO @ Wed, 22 Apr 2020 05:03:17: start X-correlation... INFO @ Wed, 22 Apr 2020 05:03:17: end of X-cor INFO @ Wed, 22 Apr 2020 05:03:17: #2 finished! INFO @ Wed, 22 Apr 2020 05:03:17: #2 predicted fragment length is 163 bps INFO @ Wed, 22 Apr 2020 05:03:17: #2 alternative fragment length(s) may be 163 bps INFO @ Wed, 22 Apr 2020 05:03:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.20_model.r INFO @ Wed, 22 Apr 2020 05:03:17: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:03:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:03:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.05_peaks.xls INFO @ Wed, 22 Apr 2020 05:03:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:03:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.05_summits.bed INFO @ Wed, 22 Apr 2020 05:03:22: Done! pass1 - making usageList (136 chroms): 4 millis pass2 - checking and writing primary data (27796 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:03:33: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:03:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.10_peaks.xls INFO @ Wed, 22 Apr 2020 05:03:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:03:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.10_summits.bed INFO @ Wed, 22 Apr 2020 05:03:55: Done! INFO @ Wed, 22 Apr 2020 05:03:59: #3 Call peaks for each chromosome... pass1 - making usageList (108 chroms): 3 millis pass2 - checking and writing primary data (22527 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:04:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.20_peaks.xls INFO @ Wed, 22 Apr 2020 05:04:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:04:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX2011881/SRX2011881.20_summits.bed INFO @ Wed, 22 Apr 2020 05:04:23: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (88 chroms): 3 millis pass2 - checking and writing primary data (17195 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。