Job ID = 5790671 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,348,342 reads read : 19,348,342 reads written : 19,348,342 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: 00:07:10 19348342 reads; of these: 19348342 (100.00%) were unpaired; of these: 3135602 (16.21%) aligned 0 times 9405422 (48.61%) aligned exactly 1 time 6807318 (35.18%) aligned >1 times 83.79% overall alignment rate Time searching: 00:07:12 Overall time: 00:07:12 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] 1507768 / 16212740 = 0.0930 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 06:16:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.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 06:16:31: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:16:31: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:16:37: 1000000 INFO @ Wed, 22 Apr 2020 06:16:42: 2000000 INFO @ Wed, 22 Apr 2020 06:16:48: 3000000 INFO @ Wed, 22 Apr 2020 06:16:53: 4000000 INFO @ Wed, 22 Apr 2020 06:16:59: 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 06:17:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.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 06:17:01: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:17:01: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:17:05: 6000000 INFO @ Wed, 22 Apr 2020 06:17:07: 1000000 INFO @ Wed, 22 Apr 2020 06:17:11: 7000000 INFO @ Wed, 22 Apr 2020 06:17:14: 2000000 INFO @ Wed, 22 Apr 2020 06:17:17: 8000000 INFO @ Wed, 22 Apr 2020 06:17:20: 3000000 INFO @ Wed, 22 Apr 2020 06:17:24: 9000000 INFO @ Wed, 22 Apr 2020 06:17:27: 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 06:17:30: 10000000 INFO @ Wed, 22 Apr 2020 06:17:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.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 06:17:31: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:17:31: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:17:33: 5000000 INFO @ Wed, 22 Apr 2020 06:17:36: 11000000 INFO @ Wed, 22 Apr 2020 06:17:37: 1000000 INFO @ Wed, 22 Apr 2020 06:17:39: 6000000 INFO @ Wed, 22 Apr 2020 06:17:43: 12000000 INFO @ Wed, 22 Apr 2020 06:17:44: 2000000 INFO @ Wed, 22 Apr 2020 06:17:46: 7000000 INFO @ Wed, 22 Apr 2020 06:17:49: 13000000 INFO @ Wed, 22 Apr 2020 06:17:50: 3000000 INFO @ Wed, 22 Apr 2020 06:17:52: 8000000 INFO @ Wed, 22 Apr 2020 06:17:56: 14000000 INFO @ Wed, 22 Apr 2020 06:17:57: 4000000 INFO @ Wed, 22 Apr 2020 06:17:58: 9000000 INFO @ Wed, 22 Apr 2020 06:18:00: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:18:00: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:18:00: #1 total tags in treatment: 14704972 INFO @ Wed, 22 Apr 2020 06:18:00: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:18:00: #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 06:18:00: #1 tags after filtering in treatment: 14704830 INFO @ Wed, 22 Apr 2020 06:18:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:18:00: #1 finished! INFO @ Wed, 22 Apr 2020 06:18:00: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:18:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:18:02: #2 number of paired peaks: 22691 INFO @ Wed, 22 Apr 2020 06:18:02: start model_add_line... INFO @ Wed, 22 Apr 2020 06:18:03: start X-correlation... INFO @ Wed, 22 Apr 2020 06:18:03: end of X-cor INFO @ Wed, 22 Apr 2020 06:18:03: #2 finished! INFO @ Wed, 22 Apr 2020 06:18:03: #2 predicted fragment length is 179 bps INFO @ Wed, 22 Apr 2020 06:18:03: #2 alternative fragment length(s) may be 179 bps INFO @ Wed, 22 Apr 2020 06:18:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.05_model.r INFO @ Wed, 22 Apr 2020 06:18:03: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:18:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:18:03: 5000000 INFO @ Wed, 22 Apr 2020 06:18:05: 10000000 INFO @ Wed, 22 Apr 2020 06:18:09: 6000000 INFO @ Wed, 22 Apr 2020 06:18:11: 11000000 INFO @ Wed, 22 Apr 2020 06:18:16: 7000000 INFO @ Wed, 22 Apr 2020 06:18:17: 12000000 INFO @ Wed, 22 Apr 2020 06:18:22: 8000000 INFO @ Wed, 22 Apr 2020 06:18:24: 13000000 INFO @ Wed, 22 Apr 2020 06:18:28: 9000000 INFO @ Wed, 22 Apr 2020 06:18:30: 14000000 INFO @ Wed, 22 Apr 2020 06:18:35: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:18:35: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:18:35: #1 total tags in treatment: 14704972 INFO @ Wed, 22 Apr 2020 06:18:35: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:18:35: #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 06:18:35: 10000000 INFO @ Wed, 22 Apr 2020 06:18:35: #1 tags after filtering in treatment: 14704830 INFO @ Wed, 22 Apr 2020 06:18:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:18:35: #1 finished! INFO @ Wed, 22 Apr 2020 06:18:35: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:18:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:18:37: #2 number of paired peaks: 22691 INFO @ Wed, 22 Apr 2020 06:18:37: start model_add_line... INFO @ Wed, 22 Apr 2020 06:18:37: start X-correlation... INFO @ Wed, 22 Apr 2020 06:18:37: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:18:37: end of X-cor INFO @ Wed, 22 Apr 2020 06:18:37: #2 finished! INFO @ Wed, 22 Apr 2020 06:18:37: #2 predicted fragment length is 179 bps INFO @ Wed, 22 Apr 2020 06:18:37: #2 alternative fragment length(s) may be 179 bps INFO @ Wed, 22 Apr 2020 06:18:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.10_model.r INFO @ Wed, 22 Apr 2020 06:18:37: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:18:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:18:41: 11000000 INFO @ Wed, 22 Apr 2020 06:18:46: 12000000 INFO @ Wed, 22 Apr 2020 06:18:52: 13000000 INFO @ Wed, 22 Apr 2020 06:18:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:18:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:18:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.05_summits.bed INFO @ Wed, 22 Apr 2020 06:18:54: Done! pass1 - making usageList (89 chroms): 2 millis pass2 - checking and writing primary data (9634 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:18:58: 14000000 INFO @ Wed, 22 Apr 2020 06:19:01: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:19:01: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:19:01: #1 total tags in treatment: 14704972 INFO @ Wed, 22 Apr 2020 06:19:01: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:19:01: #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 06:19:02: #1 tags after filtering in treatment: 14704830 INFO @ Wed, 22 Apr 2020 06:19:02: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:19:02: #1 finished! INFO @ Wed, 22 Apr 2020 06:19:02: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:19:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:19:04: #2 number of paired peaks: 22691 INFO @ Wed, 22 Apr 2020 06:19:04: start model_add_line... INFO @ Wed, 22 Apr 2020 06:19:04: start X-correlation... INFO @ Wed, 22 Apr 2020 06:19:04: end of X-cor INFO @ Wed, 22 Apr 2020 06:19:04: #2 finished! INFO @ Wed, 22 Apr 2020 06:19:04: #2 predicted fragment length is 179 bps INFO @ Wed, 22 Apr 2020 06:19:04: #2 alternative fragment length(s) may be 179 bps INFO @ Wed, 22 Apr 2020 06:19:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.20_model.r INFO @ Wed, 22 Apr 2020 06:19:04: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:19:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:19:12: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:19:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:19:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:19:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.10_summits.bed INFO @ Wed, 22 Apr 2020 06:19:28: Done! pass1 - making usageList (50 chroms): 0 millis pass2 - checking and writing primary data (1445 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:19:38: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:19:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:19:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:19:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761706/SRX5761706.20_summits.bed INFO @ Wed, 22 Apr 2020 06:19:54: Done! pass1 - making usageList (39 chroms): 0 millis pass2 - checking and writing primary data (420 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。