Job ID = 6365840 SRX = ERX1999210 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:15:27 prefetch.2.10.7: 1) Downloading 'ERR1938677'... 2020-06-15T22:15:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:16:10 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:16:10 prefetch.2.10.7: 'ERR1938677' is valid 2020-06-15T22:16:10 prefetch.2.10.7: 1) 'ERR1938677' was downloaded successfully Read 10051313 spots for ERR1938677/ERR1938677.sra Written 10051313 spots for ERR1938677/ERR1938677.sra 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: 00:00:00 Multiseed full-index search: 00:02:55 10051313 reads; of these: 10051313 (100.00%) were unpaired; of these: 217875 (2.17%) aligned 0 times 4286784 (42.65%) aligned exactly 1 time 5546654 (55.18%) aligned >1 times 97.83% overall alignment rate Time searching: 00:02:55 Overall time: 00:02:55 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 6316971 / 9833438 = 0.6424 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 @ Tue, 16 Jun 2020 07:21:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 07:21:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:21:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:21:55: 1000000 INFO @ Tue, 16 Jun 2020 07:22:02: 2000000 INFO @ Tue, 16 Jun 2020 07:22:09: 3000000 INFO @ Tue, 16 Jun 2020 07:22:12: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:22:12: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:22:12: #1 total tags in treatment: 3516467 INFO @ Tue, 16 Jun 2020 07:22:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:22:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:22:12: #1 tags after filtering in treatment: 3516467 INFO @ Tue, 16 Jun 2020 07:22:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:22:12: #1 finished! INFO @ Tue, 16 Jun 2020 07:22:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:22:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:22:13: #2 number of paired peaks: 7271 INFO @ Tue, 16 Jun 2020 07:22:13: start model_add_line... INFO @ Tue, 16 Jun 2020 07:22:13: start X-correlation... INFO @ Tue, 16 Jun 2020 07:22:13: end of X-cor INFO @ Tue, 16 Jun 2020 07:22:13: #2 finished! INFO @ Tue, 16 Jun 2020 07:22:13: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 07:22:13: #2 alternative fragment length(s) may be 4,163 bps INFO @ Tue, 16 Jun 2020 07:22:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.05_model.r INFO @ Tue, 16 Jun 2020 07:22:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:22:13: #3 Pre-compute pvalue-qvalue table... 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 @ Tue, 16 Jun 2020 07:22:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 07:22:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:22:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:22:24: 1000000 INFO @ Tue, 16 Jun 2020 07:22:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:22:30: 2000000 INFO @ Tue, 16 Jun 2020 07:22:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:22:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:22:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.05_summits.bed INFO @ Tue, 16 Jun 2020 07:22:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3334 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:22:35: 3000000 INFO @ Tue, 16 Jun 2020 07:22:38: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:22:38: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:22:38: #1 total tags in treatment: 3516467 INFO @ Tue, 16 Jun 2020 07:22:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:22:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:22:38: #1 tags after filtering in treatment: 3516467 INFO @ Tue, 16 Jun 2020 07:22:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:22:38: #1 finished! INFO @ Tue, 16 Jun 2020 07:22:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:22:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:22:39: #2 number of paired peaks: 7271 INFO @ Tue, 16 Jun 2020 07:22:39: start model_add_line... INFO @ Tue, 16 Jun 2020 07:22:39: start X-correlation... INFO @ Tue, 16 Jun 2020 07:22:39: end of X-cor INFO @ Tue, 16 Jun 2020 07:22:39: #2 finished! INFO @ Tue, 16 Jun 2020 07:22:39: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 07:22:39: #2 alternative fragment length(s) may be 4,163 bps INFO @ Tue, 16 Jun 2020 07:22:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.10_model.r INFO @ Tue, 16 Jun 2020 07:22:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:22:39: #3 Pre-compute pvalue-qvalue table... 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 @ Tue, 16 Jun 2020 07:22:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 07:22:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:22:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:22:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:22:54: 1000000 INFO @ Tue, 16 Jun 2020 07:22:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:22:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:22:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.10_summits.bed INFO @ Tue, 16 Jun 2020 07:22:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1450 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:23:00: 2000000 INFO @ Tue, 16 Jun 2020 07:23:05: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:23:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:23:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:23:08: #1 total tags in treatment: 3516467 INFO @ Tue, 16 Jun 2020 07:23:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:23:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:23:08: #1 tags after filtering in treatment: 3516467 INFO @ Tue, 16 Jun 2020 07:23:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:23:08: #1 finished! INFO @ Tue, 16 Jun 2020 07:23:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:23:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:23:09: #2 number of paired peaks: 7271 INFO @ Tue, 16 Jun 2020 07:23:09: start model_add_line... INFO @ Tue, 16 Jun 2020 07:23:09: start X-correlation... INFO @ Tue, 16 Jun 2020 07:23:09: end of X-cor INFO @ Tue, 16 Jun 2020 07:23:09: #2 finished! INFO @ Tue, 16 Jun 2020 07:23:09: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 07:23:09: #2 alternative fragment length(s) may be 4,163 bps INFO @ Tue, 16 Jun 2020 07:23:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.20_model.r INFO @ Tue, 16 Jun 2020 07:23:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:23:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:23:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:23:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:23:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:23:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1999210/ERX1999210.20_summits.bed INFO @ Tue, 16 Jun 2020 07:23:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (393 records, 4 fields): 1 millis CompletedMACS2peakCalling