Job ID = 6368113 SRX = SRX466576 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:08:39 prefetch.2.10.7: 1) Downloading 'SRR1163642'... 2020-06-16T00:08:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:10:39 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:10:40 prefetch.2.10.7: 'SRR1163642' is valid 2020-06-16T00:10:40 prefetch.2.10.7: 1) 'SRR1163642' was downloaded successfully Read 22369021 spots for SRR1163642/SRR1163642.sra Written 22369021 spots for SRR1163642/SRR1163642.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: 00:03:32 22369021 reads; of these: 22369021 (100.00%) were unpaired; of these: 4353070 (19.46%) aligned 0 times 14559678 (65.09%) aligned exactly 1 time 3456273 (15.45%) aligned >1 times 80.54% overall alignment rate Time searching: 00:03:32 Overall time: 00:03:32 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] 8071545 / 18015951 = 0.4480 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 09:18:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.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 09:18:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:40: 1000000 INFO @ Tue, 16 Jun 2020 09:18:45: 2000000 INFO @ Tue, 16 Jun 2020 09:18:51: 3000000 INFO @ Tue, 16 Jun 2020 09:18:57: 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 @ Tue, 16 Jun 2020 09:19:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.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 09:19:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:03: 5000000 INFO @ Tue, 16 Jun 2020 09:19:09: 1000000 INFO @ Tue, 16 Jun 2020 09:19:11: 6000000 INFO @ Tue, 16 Jun 2020 09:19:17: 2000000 INFO @ Tue, 16 Jun 2020 09:19:17: 7000000 INFO @ Tue, 16 Jun 2020 09:19:24: 3000000 INFO @ Tue, 16 Jun 2020 09:19:25: 8000000 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 09:19:31: 4000000 INFO @ Tue, 16 Jun 2020 09:19:32: 9000000 INFO @ Tue, 16 Jun 2020 09:19:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.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 09:19:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:38: 5000000 INFO @ Tue, 16 Jun 2020 09:19:39: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:19:39: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:19:39: #1 total tags in treatment: 9944406 INFO @ Tue, 16 Jun 2020 09:19:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:19:39: #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 09:19:39: #1 tags after filtering in treatment: 9944406 INFO @ Tue, 16 Jun 2020 09:19:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:19:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:19:40: 1000000 INFO @ Tue, 16 Jun 2020 09:19:40: #2 number of paired peaks: 1154 INFO @ Tue, 16 Jun 2020 09:19:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:19:40: start X-correlation... INFO @ Tue, 16 Jun 2020 09:19:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:19:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:19:40: #2 predicted fragment length is 184 bps INFO @ Tue, 16 Jun 2020 09:19:40: #2 alternative fragment length(s) may be 3,184 bps INFO @ Tue, 16 Jun 2020 09:19:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.05_model.r INFO @ Tue, 16 Jun 2020 09:19:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:19:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:19:45: 6000000 INFO @ Tue, 16 Jun 2020 09:19:47: 2000000 INFO @ Tue, 16 Jun 2020 09:19:52: 7000000 INFO @ Tue, 16 Jun 2020 09:19:54: 3000000 INFO @ Tue, 16 Jun 2020 09:20:00: 8000000 INFO @ Tue, 16 Jun 2020 09:20:02: 4000000 INFO @ Tue, 16 Jun 2020 09:20:07: 9000000 INFO @ Tue, 16 Jun 2020 09:20:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:09: 5000000 INFO @ Tue, 16 Jun 2020 09:20:13: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:20:13: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:20:13: #1 total tags in treatment: 9944406 INFO @ Tue, 16 Jun 2020 09:20:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:13: #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 09:20:14: #1 tags after filtering in treatment: 9944406 INFO @ Tue, 16 Jun 2020 09:20:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:14: #2 number of paired peaks: 1154 INFO @ Tue, 16 Jun 2020 09:20:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:14: #2 predicted fragment length is 184 bps INFO @ Tue, 16 Jun 2020 09:20:14: #2 alternative fragment length(s) may be 3,184 bps INFO @ Tue, 16 Jun 2020 09:20:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.10_model.r INFO @ Tue, 16 Jun 2020 09:20:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:14: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:20:16: 6000000 INFO @ Tue, 16 Jun 2020 09:20:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.05_summits.bed INFO @ Tue, 16 Jun 2020 09:20:18: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1101 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:20:22: 7000000 INFO @ Tue, 16 Jun 2020 09:20:29: 8000000 INFO @ Tue, 16 Jun 2020 09:20:36: 9000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:20:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:42: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:20:42: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:20:42: #1 total tags in treatment: 9944406 INFO @ Tue, 16 Jun 2020 09:20:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:42: #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 09:20:42: #1 tags after filtering in treatment: 9944406 INFO @ Tue, 16 Jun 2020 09:20:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:43: #2 number of paired peaks: 1154 INFO @ Tue, 16 Jun 2020 09:20:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:43: #2 predicted fragment length is 184 bps INFO @ Tue, 16 Jun 2020 09:20:43: #2 alternative fragment length(s) may be 3,184 bps INFO @ Tue, 16 Jun 2020 09:20:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.20_model.r INFO @ Tue, 16 Jun 2020 09:20:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.10_summits.bed INFO @ Tue, 16 Jun 2020 09:20:51: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (790 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:21:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466576/SRX466576.20_summits.bed INFO @ Tue, 16 Jun 2020 09:21:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (540 records, 4 fields): 1 millis CompletedMACS2peakCalling