Job ID = 5790699 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,798,993 reads read : 28,798,993 reads written : 28,798,993 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR8982433.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: 00:08:52 28798993 reads; of these: 28798993 (100.00%) were unpaired; of these: 5733046 (19.91%) aligned 0 times 15352060 (53.31%) aligned exactly 1 time 7713887 (26.79%) aligned >1 times 80.09% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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] 6286712 / 23065947 = 0.2726 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 06:29:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.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 06:29:23: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:29:23: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:29:27: 1000000 INFO @ Wed, 22 Apr 2020 06:29:32: 2000000 INFO @ Wed, 22 Apr 2020 06:29:37: 3000000 INFO @ Wed, 22 Apr 2020 06:29:42: 4000000 INFO @ Wed, 22 Apr 2020 06:29:47: 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 06:29:52: 6000000 INFO @ Wed, 22 Apr 2020 06:29:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.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 06:29:52: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:29:52: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:29:57: 7000000 INFO @ Wed, 22 Apr 2020 06:29:58: 1000000 INFO @ Wed, 22 Apr 2020 06:30:03: 8000000 INFO @ Wed, 22 Apr 2020 06:30:05: 2000000 INFO @ Wed, 22 Apr 2020 06:30:08: 9000000 INFO @ Wed, 22 Apr 2020 06:30:11: 3000000 INFO @ Wed, 22 Apr 2020 06:30:13: 10000000 INFO @ Wed, 22 Apr 2020 06:30:17: 4000000 INFO @ Wed, 22 Apr 2020 06:30:19: 11000000 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 06:30:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.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 06:30:22: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:30:22: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:30:23: 5000000 INFO @ Wed, 22 Apr 2020 06:30:24: 12000000 INFO @ Wed, 22 Apr 2020 06:30:28: 1000000 INFO @ Wed, 22 Apr 2020 06:30:29: 6000000 INFO @ Wed, 22 Apr 2020 06:30:30: 13000000 INFO @ Wed, 22 Apr 2020 06:30:33: 2000000 INFO @ Wed, 22 Apr 2020 06:30:35: 14000000 INFO @ Wed, 22 Apr 2020 06:30:36: 7000000 INFO @ Wed, 22 Apr 2020 06:30:39: 3000000 INFO @ Wed, 22 Apr 2020 06:30:41: 15000000 INFO @ Wed, 22 Apr 2020 06:30:42: 8000000 INFO @ Wed, 22 Apr 2020 06:30:44: 4000000 INFO @ Wed, 22 Apr 2020 06:30:46: 16000000 INFO @ Wed, 22 Apr 2020 06:30:48: 9000000 INFO @ Wed, 22 Apr 2020 06:30:50: 5000000 INFO @ Wed, 22 Apr 2020 06:30:51: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:30:51: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:30:51: #1 total tags in treatment: 16779235 INFO @ Wed, 22 Apr 2020 06:30:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:30:51: #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 06:30:51: #1 tags after filtering in treatment: 16779111 INFO @ Wed, 22 Apr 2020 06:30:51: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:30:51: #1 finished! INFO @ Wed, 22 Apr 2020 06:30:51: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:30:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:30:53: #2 number of paired peaks: 28289 INFO @ Wed, 22 Apr 2020 06:30:53: start model_add_line... INFO @ Wed, 22 Apr 2020 06:30:53: start X-correlation... INFO @ Wed, 22 Apr 2020 06:30:54: end of X-cor INFO @ Wed, 22 Apr 2020 06:30:54: #2 finished! INFO @ Wed, 22 Apr 2020 06:30:54: #2 predicted fragment length is 181 bps INFO @ Wed, 22 Apr 2020 06:30:54: #2 alternative fragment length(s) may be 181 bps INFO @ Wed, 22 Apr 2020 06:30:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.05_model.r INFO @ Wed, 22 Apr 2020 06:30:54: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:30:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:30:55: 10000000 INFO @ Wed, 22 Apr 2020 06:30:55: 6000000 INFO @ Wed, 22 Apr 2020 06:31:00: 7000000 INFO @ Wed, 22 Apr 2020 06:31:01: 11000000 INFO @ Wed, 22 Apr 2020 06:31:06: 8000000 INFO @ Wed, 22 Apr 2020 06:31:07: 12000000 INFO @ Wed, 22 Apr 2020 06:31:11: 9000000 INFO @ Wed, 22 Apr 2020 06:31:13: 13000000 INFO @ Wed, 22 Apr 2020 06:31:17: 10000000 INFO @ Wed, 22 Apr 2020 06:31:20: 14000000 INFO @ Wed, 22 Apr 2020 06:31:22: 11000000 INFO @ Wed, 22 Apr 2020 06:31:26: 15000000 INFO @ Wed, 22 Apr 2020 06:31:28: 12000000 INFO @ Wed, 22 Apr 2020 06:31:30: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:31:32: 16000000 INFO @ Wed, 22 Apr 2020 06:31:33: 13000000 INFO @ Wed, 22 Apr 2020 06:31:37: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:31:37: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:31:37: #1 total tags in treatment: 16779235 INFO @ Wed, 22 Apr 2020 06:31:37: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:31:37: #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 06:31:38: #1 tags after filtering in treatment: 16779111 INFO @ Wed, 22 Apr 2020 06:31:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:31:38: #1 finished! INFO @ Wed, 22 Apr 2020 06:31:38: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:31:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:31:38: 14000000 INFO @ Wed, 22 Apr 2020 06:31:40: #2 number of paired peaks: 28289 INFO @ Wed, 22 Apr 2020 06:31:40: start model_add_line... INFO @ Wed, 22 Apr 2020 06:31:40: start X-correlation... INFO @ Wed, 22 Apr 2020 06:31:40: end of X-cor INFO @ Wed, 22 Apr 2020 06:31:40: #2 finished! INFO @ Wed, 22 Apr 2020 06:31:40: #2 predicted fragment length is 181 bps INFO @ Wed, 22 Apr 2020 06:31:40: #2 alternative fragment length(s) may be 181 bps INFO @ Wed, 22 Apr 2020 06:31:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.10_model.r INFO @ Wed, 22 Apr 2020 06:31:40: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:31:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:31:44: 15000000 INFO @ Wed, 22 Apr 2020 06:31:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:31:49: 16000000 INFO @ Wed, 22 Apr 2020 06:31:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:31:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.05_summits.bed INFO @ Wed, 22 Apr 2020 06:31:49: Done! pass1 - making usageList (115 chroms): 2 millis pass2 - checking and writing primary data (11714 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:31:53: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:31:53: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:31:53: #1 total tags in treatment: 16779235 INFO @ Wed, 22 Apr 2020 06:31:53: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:31:53: #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 06:31:53: #1 tags after filtering in treatment: 16779111 INFO @ Wed, 22 Apr 2020 06:31:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:31:53: #1 finished! INFO @ Wed, 22 Apr 2020 06:31:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:31:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:31:55: #2 number of paired peaks: 28289 INFO @ Wed, 22 Apr 2020 06:31:55: start model_add_line... INFO @ Wed, 22 Apr 2020 06:31:55: start X-correlation... INFO @ Wed, 22 Apr 2020 06:31:55: end of X-cor INFO @ Wed, 22 Apr 2020 06:31:55: #2 finished! INFO @ Wed, 22 Apr 2020 06:31:55: #2 predicted fragment length is 181 bps INFO @ Wed, 22 Apr 2020 06:31:55: #2 alternative fragment length(s) may be 181 bps INFO @ Wed, 22 Apr 2020 06:31:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.20_model.r INFO @ Wed, 22 Apr 2020 06:31:55: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:31:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:32:18: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:32:34: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:32:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:32:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:32:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.10_summits.bed INFO @ Wed, 22 Apr 2020 06:32:37: Done! pass1 - making usageList (71 chroms): 1 millis pass2 - checking and writing primary data (2297 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:32:52: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:32:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:32:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761731/SRX5761731.20_summits.bed INFO @ Wed, 22 Apr 2020 06:32:52: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (461 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。