Job ID = 5790709 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,775,165 reads read : 25,775,165 reads written : 25,775,165 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR8982442.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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:06 25775165 reads; of these: 25775165 (100.00%) were unpaired; of these: 4908762 (19.04%) aligned 0 times 17606302 (68.31%) aligned exactly 1 time 3260101 (12.65%) aligned >1 times 80.96% overall alignment rate Time searching: 00:05:07 Overall time: 00:05:07 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] 10777731 / 20866403 = 0.5165 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 06:31:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.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 06:31:22: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:31:22: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:31:28: 1000000 INFO @ Wed, 22 Apr 2020 06:31:34: 2000000 INFO @ Wed, 22 Apr 2020 06:31:39: 3000000 INFO @ Wed, 22 Apr 2020 06:31:45: 4000000 INFO @ Wed, 22 Apr 2020 06:31:50: 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 06:31:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.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 06:31:52: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:31:52: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:31:57: 6000000 INFO @ Wed, 22 Apr 2020 06:32:00: 1000000 INFO @ Wed, 22 Apr 2020 06:32:03: 7000000 INFO @ Wed, 22 Apr 2020 06:32:07: 2000000 INFO @ Wed, 22 Apr 2020 06:32:10: 8000000 INFO @ Wed, 22 Apr 2020 06:32:15: 3000000 INFO @ Wed, 22 Apr 2020 06:32:17: 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 06:32:22: 4000000 INFO @ Wed, 22 Apr 2020 06:32:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.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 06:32:22: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:32:22: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:32:24: 10000000 INFO @ Wed, 22 Apr 2020 06:32:24: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:32:24: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:32:24: #1 total tags in treatment: 10088672 INFO @ Wed, 22 Apr 2020 06:32:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:32:24: #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 06:32:25: #1 tags after filtering in treatment: 10088411 INFO @ Wed, 22 Apr 2020 06:32:25: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:32:25: #1 finished! INFO @ Wed, 22 Apr 2020 06:32:25: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:32:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:32:26: #2 number of paired peaks: 19649 INFO @ Wed, 22 Apr 2020 06:32:26: start model_add_line... INFO @ Wed, 22 Apr 2020 06:32:26: start X-correlation... INFO @ Wed, 22 Apr 2020 06:32:26: end of X-cor INFO @ Wed, 22 Apr 2020 06:32:26: #2 finished! INFO @ Wed, 22 Apr 2020 06:32:26: #2 predicted fragment length is 177 bps INFO @ Wed, 22 Apr 2020 06:32:26: #2 alternative fragment length(s) may be 177 bps INFO @ Wed, 22 Apr 2020 06:32:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.05_model.r INFO @ Wed, 22 Apr 2020 06:32:26: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:32:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:32:30: 5000000 INFO @ Wed, 22 Apr 2020 06:32:30: 1000000 INFO @ Wed, 22 Apr 2020 06:32:37: 6000000 INFO @ Wed, 22 Apr 2020 06:32:37: 2000000 INFO @ Wed, 22 Apr 2020 06:32:45: 7000000 INFO @ Wed, 22 Apr 2020 06:32:45: 3000000 INFO @ Wed, 22 Apr 2020 06:32:49: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:32:52: 8000000 INFO @ Wed, 22 Apr 2020 06:32:52: 4000000 INFO @ Wed, 22 Apr 2020 06:33:00: 5000000 INFO @ Wed, 22 Apr 2020 06:33:00: 9000000 INFO @ Wed, 22 Apr 2020 06:33:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:33:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:33:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.05_summits.bed INFO @ Wed, 22 Apr 2020 06:33:01: Done! pass1 - making usageList (142 chroms): 3 millis pass2 - checking and writing primary data (19824 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:33:07: 6000000 INFO @ Wed, 22 Apr 2020 06:33:07: 10000000 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: 10088672 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: 10088411 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 06:33:10: #2 number of paired peaks: 19649 INFO @ Wed, 22 Apr 2020 06:33:10: start model_add_line... INFO @ Wed, 22 Apr 2020 06:33:10: start X-correlation... INFO @ Wed, 22 Apr 2020 06:33:10: end of X-cor INFO @ Wed, 22 Apr 2020 06:33:10: #2 finished! INFO @ Wed, 22 Apr 2020 06:33:10: #2 predicted fragment length is 177 bps INFO @ Wed, 22 Apr 2020 06:33:10: #2 alternative fragment length(s) may be 177 bps INFO @ Wed, 22 Apr 2020 06:33:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.10_model.r INFO @ Wed, 22 Apr 2020 06:33:10: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:33:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:33:14: 7000000 INFO @ Wed, 22 Apr 2020 06:33:21: 8000000 INFO @ Wed, 22 Apr 2020 06:33:28: 9000000 INFO @ Wed, 22 Apr 2020 06:33:32: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:33:36: 10000000 INFO @ Wed, 22 Apr 2020 06:33:36: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:33:36: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:33:36: #1 total tags in treatment: 10088672 INFO @ Wed, 22 Apr 2020 06:33:36: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:33:36: #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 06:33:36: #1 tags after filtering in treatment: 10088411 INFO @ Wed, 22 Apr 2020 06:33:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:33:36: #1 finished! INFO @ Wed, 22 Apr 2020 06:33:36: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:33:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:33:38: #2 number of paired peaks: 19649 INFO @ Wed, 22 Apr 2020 06:33:38: start model_add_line... INFO @ Wed, 22 Apr 2020 06:33:38: start X-correlation... INFO @ Wed, 22 Apr 2020 06:33:38: end of X-cor INFO @ Wed, 22 Apr 2020 06:33:38: #2 finished! INFO @ Wed, 22 Apr 2020 06:33:38: #2 predicted fragment length is 177 bps INFO @ Wed, 22 Apr 2020 06:33:38: #2 alternative fragment length(s) may be 177 bps INFO @ Wed, 22 Apr 2020 06:33:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.20_model.r INFO @ Wed, 22 Apr 2020 06:33:38: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:33:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:33:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:33:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:33:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.10_summits.bed INFO @ Wed, 22 Apr 2020 06:33:44: Done! pass1 - making usageList (117 chroms): 3 millis pass2 - checking and writing primary data (17152 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 06:34:03: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:34:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:34:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:34:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761740/SRX5761740.20_summits.bed INFO @ Wed, 22 Apr 2020 06:34:16: Done! pass1 - making usageList (95 chroms): 2 millis pass2 - checking and writing primary data (14525 records, 4 fields): 15 millis CompletedMACS2peakCalling