Job ID = 5790712 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,058,728 reads read : 27,058,728 reads written : 27,058,728 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR8982444.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: 00:00:03 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:08:30 27058728 reads; of these: 27058728 (100.00%) were unpaired; of these: 8919400 (32.96%) aligned 0 times 12655094 (46.77%) aligned exactly 1 time 5484234 (20.27%) aligned >1 times 67.04% overall alignment rate Time searching: 00:08:37 Overall time: 00:08:37 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] 3284042 / 18139328 = 0.1810 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 06:36:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.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 06:36:55: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:36:55: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:37:01: 1000000 INFO @ Wed, 22 Apr 2020 06:37:06: 2000000 INFO @ Wed, 22 Apr 2020 06:37:12: 3000000 INFO @ Wed, 22 Apr 2020 06:37:17: 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 06:37:23: 5000000 INFO @ Wed, 22 Apr 2020 06:37:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.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 06:37:26: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:37:26: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:37:29: 6000000 INFO @ Wed, 22 Apr 2020 06:37:32: 1000000 INFO @ Wed, 22 Apr 2020 06:37:35: 7000000 INFO @ Wed, 22 Apr 2020 06:37:39: 2000000 INFO @ Wed, 22 Apr 2020 06:37:42: 8000000 INFO @ Wed, 22 Apr 2020 06:37:45: 3000000 INFO @ Wed, 22 Apr 2020 06:37:48: 9000000 INFO @ Wed, 22 Apr 2020 06:37:52: 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 06:37:55: 10000000 INFO @ Wed, 22 Apr 2020 06:37:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.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 06:37:56: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:37:56: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:37:58: 5000000 INFO @ Wed, 22 Apr 2020 06:38:01: 11000000 INFO @ Wed, 22 Apr 2020 06:38:02: 1000000 INFO @ Wed, 22 Apr 2020 06:38:04: 6000000 INFO @ Wed, 22 Apr 2020 06:38:08: 12000000 INFO @ Wed, 22 Apr 2020 06:38:09: 2000000 INFO @ Wed, 22 Apr 2020 06:38:11: 7000000 INFO @ Wed, 22 Apr 2020 06:38:14: 13000000 INFO @ Wed, 22 Apr 2020 06:38:15: 3000000 INFO @ Wed, 22 Apr 2020 06:38:18: 8000000 INFO @ Wed, 22 Apr 2020 06:38:21: 14000000 INFO @ Wed, 22 Apr 2020 06:38:22: 4000000 INFO @ Wed, 22 Apr 2020 06:38:24: 9000000 INFO @ Wed, 22 Apr 2020 06:38:27: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:38:27: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:38:27: #1 total tags in treatment: 14855286 INFO @ Wed, 22 Apr 2020 06:38:27: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:38:27: #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 06:38:27: #1 tags after filtering in treatment: 14855143 INFO @ Wed, 22 Apr 2020 06:38:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:38:27: #1 finished! INFO @ Wed, 22 Apr 2020 06:38:27: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:38:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:38:28: 5000000 INFO @ Wed, 22 Apr 2020 06:38:29: #2 number of paired peaks: 15400 INFO @ Wed, 22 Apr 2020 06:38:29: start model_add_line... INFO @ Wed, 22 Apr 2020 06:38:29: start X-correlation... INFO @ Wed, 22 Apr 2020 06:38:29: end of X-cor INFO @ Wed, 22 Apr 2020 06:38:29: #2 finished! INFO @ Wed, 22 Apr 2020 06:38:29: #2 predicted fragment length is 207 bps INFO @ Wed, 22 Apr 2020 06:38:29: #2 alternative fragment length(s) may be 207 bps INFO @ Wed, 22 Apr 2020 06:38:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.05_model.r INFO @ Wed, 22 Apr 2020 06:38:29: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:38:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:38:31: 10000000 INFO @ Wed, 22 Apr 2020 06:38:35: 6000000 INFO @ Wed, 22 Apr 2020 06:38:37: 11000000 INFO @ Wed, 22 Apr 2020 06:38:41: 7000000 INFO @ Wed, 22 Apr 2020 06:38:44: 12000000 INFO @ Wed, 22 Apr 2020 06:38:48: 8000000 INFO @ Wed, 22 Apr 2020 06:38:50: 13000000 INFO @ Wed, 22 Apr 2020 06:38:54: 9000000 INFO @ Wed, 22 Apr 2020 06:38:57: 14000000 INFO @ Wed, 22 Apr 2020 06:39:01: 10000000 INFO @ Wed, 22 Apr 2020 06:39:02: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:39:02: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:39:02: #1 total tags in treatment: 14855286 INFO @ Wed, 22 Apr 2020 06:39:02: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:39:02: #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 06:39:03: #1 tags after filtering in treatment: 14855143 INFO @ Wed, 22 Apr 2020 06:39:03: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:39:03: #1 finished! INFO @ Wed, 22 Apr 2020 06:39:03: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:39:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:39:03: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:39:05: #2 number of paired peaks: 15400 INFO @ Wed, 22 Apr 2020 06:39:05: start model_add_line... INFO @ Wed, 22 Apr 2020 06:39:05: start X-correlation... INFO @ Wed, 22 Apr 2020 06:39:05: end of X-cor INFO @ Wed, 22 Apr 2020 06:39:05: #2 finished! INFO @ Wed, 22 Apr 2020 06:39:05: #2 predicted fragment length is 207 bps INFO @ Wed, 22 Apr 2020 06:39:05: #2 alternative fragment length(s) may be 207 bps INFO @ Wed, 22 Apr 2020 06:39:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.10_model.r INFO @ Wed, 22 Apr 2020 06:39:05: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:39:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:39:07: 11000000 INFO @ Wed, 22 Apr 2020 06:39:12: 12000000 INFO @ Wed, 22 Apr 2020 06:39:18: 13000000 INFO @ Wed, 22 Apr 2020 06:39:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:39:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:39:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.05_summits.bed INFO @ Wed, 22 Apr 2020 06:39:20: Done! pass1 - making usageList (73 chroms): 1 millis pass2 - checking and writing primary data (4085 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:39:24: 14000000 INFO @ Wed, 22 Apr 2020 06:39:29: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:39:29: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:39:29: #1 total tags in treatment: 14855286 INFO @ Wed, 22 Apr 2020 06:39:29: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:39:29: #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 06:39:29: #1 tags after filtering in treatment: 14855143 INFO @ Wed, 22 Apr 2020 06:39:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:39:29: #1 finished! INFO @ Wed, 22 Apr 2020 06:39:29: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:39:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:39:31: #2 number of paired peaks: 15400 INFO @ Wed, 22 Apr 2020 06:39:31: start model_add_line... INFO @ Wed, 22 Apr 2020 06:39:31: start X-correlation... INFO @ Wed, 22 Apr 2020 06:39:31: end of X-cor INFO @ Wed, 22 Apr 2020 06:39:31: #2 finished! INFO @ Wed, 22 Apr 2020 06:39:31: #2 predicted fragment length is 207 bps INFO @ Wed, 22 Apr 2020 06:39:31: #2 alternative fragment length(s) may be 207 bps INFO @ Wed, 22 Apr 2020 06:39:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.20_model.r INFO @ Wed, 22 Apr 2020 06:39:31: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:39:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:39:37: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:39:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:39:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:39:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.10_summits.bed INFO @ Wed, 22 Apr 2020 06:39:54: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (1045 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:40:03: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:40:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:40:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:40:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761742/SRX5761742.20_summits.bed INFO @ Wed, 22 Apr 2020 06:40:20: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (275 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。