Job ID = 5790697 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,883,813 reads read : 25,883,813 reads written : 25,883,813 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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:23 25883813 reads; of these: 25883813 (100.00%) were unpaired; of these: 7715421 (29.81%) aligned 0 times 14310561 (55.29%) aligned exactly 1 time 3857831 (14.90%) aligned >1 times 70.19% overall alignment rate Time searching: 00:05:24 Overall time: 00:05:24 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] 7917099 / 18168392 = 0.4358 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 06:31:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.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 06:31:08: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:31:08: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:31:14: 1000000 INFO @ Wed, 22 Apr 2020 06:31:20: 2000000 INFO @ Wed, 22 Apr 2020 06:31:26: 3000000 INFO @ Wed, 22 Apr 2020 06:31:33: 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 06:31:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.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 06:31:38: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:31:38: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:31:39: 5000000 INFO @ Wed, 22 Apr 2020 06:31:44: 1000000 INFO @ Wed, 22 Apr 2020 06:31:46: 6000000 INFO @ Wed, 22 Apr 2020 06:31:50: 2000000 INFO @ Wed, 22 Apr 2020 06:31:52: 7000000 INFO @ Wed, 22 Apr 2020 06:31:56: 3000000 INFO @ Wed, 22 Apr 2020 06:31:59: 8000000 INFO @ Wed, 22 Apr 2020 06:32:02: 4000000 INFO @ Wed, 22 Apr 2020 06:32:06: 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 06:32:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.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 06:32:08: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:32:08: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:32:09: 5000000 INFO @ Wed, 22 Apr 2020 06:32:13: 10000000 INFO @ Wed, 22 Apr 2020 06:32:14: 1000000 INFO @ Wed, 22 Apr 2020 06:32:15: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:32:15: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:32:15: #1 total tags in treatment: 10251293 INFO @ Wed, 22 Apr 2020 06:32:15: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:32:15: #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 06:32:15: 6000000 INFO @ Wed, 22 Apr 2020 06:32:15: #1 tags after filtering in treatment: 10251059 INFO @ Wed, 22 Apr 2020 06:32:15: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:32:15: #1 finished! INFO @ Wed, 22 Apr 2020 06:32:15: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:32:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:32:17: #2 number of paired peaks: 44036 INFO @ Wed, 22 Apr 2020 06:32:17: start model_add_line... INFO @ Wed, 22 Apr 2020 06:32:17: start X-correlation... INFO @ Wed, 22 Apr 2020 06:32:17: end of X-cor INFO @ Wed, 22 Apr 2020 06:32:17: #2 finished! INFO @ Wed, 22 Apr 2020 06:32:17: #2 predicted fragment length is 237 bps INFO @ Wed, 22 Apr 2020 06:32:17: #2 alternative fragment length(s) may be 237 bps INFO @ Wed, 22 Apr 2020 06:32:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.05_model.r INFO @ Wed, 22 Apr 2020 06:32:17: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:32:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:32:21: 2000000 INFO @ Wed, 22 Apr 2020 06:32:21: 7000000 INFO @ Wed, 22 Apr 2020 06:32:27: 8000000 INFO @ Wed, 22 Apr 2020 06:32:27: 3000000 INFO @ Wed, 22 Apr 2020 06:32:33: 9000000 INFO @ Wed, 22 Apr 2020 06:32:33: 4000000 INFO @ Wed, 22 Apr 2020 06:32:39: 10000000 INFO @ Wed, 22 Apr 2020 06:32:39: 5000000 INFO @ Wed, 22 Apr 2020 06:32:40: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:32:40: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:32:40: #1 total tags in treatment: 10251293 INFO @ Wed, 22 Apr 2020 06:32:40: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:32:40: #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 06:32:40: #1 tags after filtering in treatment: 10251059 INFO @ Wed, 22 Apr 2020 06:32:40: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:32:40: #1 finished! INFO @ Wed, 22 Apr 2020 06:32:40: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:32:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:32:41: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:32:43: #2 number of paired peaks: 44036 INFO @ Wed, 22 Apr 2020 06:32:43: start model_add_line... INFO @ Wed, 22 Apr 2020 06:32:43: start X-correlation... INFO @ Wed, 22 Apr 2020 06:32:43: end of X-cor INFO @ Wed, 22 Apr 2020 06:32:43: #2 finished! INFO @ Wed, 22 Apr 2020 06:32:43: #2 predicted fragment length is 237 bps INFO @ Wed, 22 Apr 2020 06:32:43: #2 alternative fragment length(s) may be 237 bps INFO @ Wed, 22 Apr 2020 06:32:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.10_model.r INFO @ Wed, 22 Apr 2020 06:32:43: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:32:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:32:45: 6000000 INFO @ Wed, 22 Apr 2020 06:32:50: 7000000 INFO @ Wed, 22 Apr 2020 06:32:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:32:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:32:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.05_summits.bed INFO @ Wed, 22 Apr 2020 06:32:54: Done! pass1 - making usageList (111 chroms): 3 millis pass2 - checking and writing primary data (15755 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:32:56: 8000000 INFO @ Wed, 22 Apr 2020 06:33:01: 9000000 INFO @ Wed, 22 Apr 2020 06:33:07: 10000000 INFO @ Wed, 22 Apr 2020 06:33:07: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:33:08: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:33:08: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:33:08: #1 total tags in treatment: 10251293 INFO @ Wed, 22 Apr 2020 06:33:08: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:33:08: #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 06:33:08: #1 tags after filtering in treatment: 10251059 INFO @ Wed, 22 Apr 2020 06:33:08: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:33:08: #1 finished! INFO @ Wed, 22 Apr 2020 06:33:08: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:33:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:33:11: #2 number of paired peaks: 44036 INFO @ Wed, 22 Apr 2020 06:33:11: start model_add_line... INFO @ Wed, 22 Apr 2020 06:33:11: start X-correlation... INFO @ Wed, 22 Apr 2020 06:33:11: end of X-cor INFO @ Wed, 22 Apr 2020 06:33:11: #2 finished! INFO @ Wed, 22 Apr 2020 06:33:11: #2 predicted fragment length is 237 bps INFO @ Wed, 22 Apr 2020 06:33:11: #2 alternative fragment length(s) may be 237 bps INFO @ Wed, 22 Apr 2020 06:33:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.20_model.r INFO @ Wed, 22 Apr 2020 06:33:11: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:33:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:33:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:33:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:33:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.10_summits.bed INFO @ Wed, 22 Apr 2020 06:33:19: Done! pass1 - making usageList (87 chroms): 2 millis pass2 - checking and writing primary data (12519 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:33:35: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:33:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:33:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:33:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761729/SRX5761729.20_summits.bed INFO @ Wed, 22 Apr 2020 06:33:48: Done! pass1 - making usageList (66 chroms): 2 millis pass2 - checking and writing primary data (9409 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。