Job ID = 6367746 SRX = SRX4082360 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:35:35 prefetch.2.10.7: 1) Downloading 'SRR7164178'... 2020-06-15T23:35:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:37:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:37:31 prefetch.2.10.7: 'SRR7164178' is valid 2020-06-15T23:37:31 prefetch.2.10.7: 1) 'SRR7164178' was downloaded successfully 2020-06-15T23:37:31 prefetch.2.10.7: 'SRR7164178' has 0 unresolved dependencies Read 13268521 spots for SRR7164178/SRR7164178.sra Written 13268521 spots for SRR7164178/SRR7164178.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: 00:02:44 13268521 reads; of these: 13268521 (100.00%) were unpaired; of these: 1756334 (13.24%) aligned 0 times 10451129 (78.77%) aligned exactly 1 time 1061058 (8.00%) aligned >1 times 86.76% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:44 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] 2404783 / 11512187 = 0.2089 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 08:43:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.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 08:43:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:43:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:43:57: 1000000 INFO @ Tue, 16 Jun 2020 08:44:02: 2000000 INFO @ Tue, 16 Jun 2020 08:44:06: 3000000 INFO @ Tue, 16 Jun 2020 08:44:11: 4000000 INFO @ Tue, 16 Jun 2020 08:44:16: 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 @ Tue, 16 Jun 2020 08:44:20: 6000000 INFO @ Tue, 16 Jun 2020 08:44:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.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 08:44:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:25: 7000000 INFO @ Tue, 16 Jun 2020 08:44:27: 1000000 INFO @ Tue, 16 Jun 2020 08:44:30: 8000000 INFO @ Tue, 16 Jun 2020 08:44:32: 2000000 INFO @ Tue, 16 Jun 2020 08:44:35: 9000000 INFO @ Tue, 16 Jun 2020 08:44:36: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:44:36: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:44:36: #1 total tags in treatment: 9107404 INFO @ Tue, 16 Jun 2020 08:44:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:44:36: #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 08:44:36: #1 tags after filtering in treatment: 9107404 INFO @ Tue, 16 Jun 2020 08:44:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:44:36: #1 finished! INFO @ Tue, 16 Jun 2020 08:44:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:44:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:44:37: #2 number of paired peaks: 4779 INFO @ Tue, 16 Jun 2020 08:44:37: start model_add_line... INFO @ Tue, 16 Jun 2020 08:44:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:44:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:44:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:44:37: #2 predicted fragment length is 176 bps INFO @ Tue, 16 Jun 2020 08:44:37: #2 alternative fragment length(s) may be 4,176 bps INFO @ Tue, 16 Jun 2020 08:44:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.05_model.r INFO @ Tue, 16 Jun 2020 08:44:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:44:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:44:37: 3000000 INFO @ Tue, 16 Jun 2020 08:44:42: 4000000 INFO @ Tue, 16 Jun 2020 08:44:47: 5000000 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 08:44:51: 6000000 INFO @ Tue, 16 Jun 2020 08:44:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.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 08:44:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:56: 7000000 INFO @ Tue, 16 Jun 2020 08:44:57: 1000000 INFO @ Tue, 16 Jun 2020 08:44:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:01: 8000000 INFO @ Tue, 16 Jun 2020 08:45:02: 2000000 INFO @ Tue, 16 Jun 2020 08:45:06: 9000000 INFO @ Tue, 16 Jun 2020 08:45:07: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:45:07: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:45:07: #1 total tags in treatment: 9107404 INFO @ Tue, 16 Jun 2020 08:45:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:07: #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 08:45:07: #1 tags after filtering in treatment: 9107404 INFO @ Tue, 16 Jun 2020 08:45:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:07: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:07: 3000000 INFO @ Tue, 16 Jun 2020 08:45:08: #2 number of paired peaks: 4779 INFO @ Tue, 16 Jun 2020 08:45:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:08: #2 predicted fragment length is 176 bps INFO @ Tue, 16 Jun 2020 08:45:08: #2 alternative fragment length(s) may be 4,176 bps INFO @ Tue, 16 Jun 2020 08:45:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.10_model.r INFO @ Tue, 16 Jun 2020 08:45:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:45:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.05_summits.bed INFO @ Tue, 16 Jun 2020 08:45:09: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (9272 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:45:12: 4000000 INFO @ Tue, 16 Jun 2020 08:45:16: 5000000 INFO @ Tue, 16 Jun 2020 08:45:21: 6000000 INFO @ Tue, 16 Jun 2020 08:45:26: 7000000 INFO @ Tue, 16 Jun 2020 08:45:30: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:45:30: 8000000 INFO @ Tue, 16 Jun 2020 08:45:35: 9000000 INFO @ Tue, 16 Jun 2020 08:45:36: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:45:36: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:45:36: #1 total tags in treatment: 9107404 INFO @ Tue, 16 Jun 2020 08:45:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:36: #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 08:45:36: #1 tags after filtering in treatment: 9107404 INFO @ Tue, 16 Jun 2020 08:45:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:36: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:37: #2 number of paired peaks: 4779 INFO @ Tue, 16 Jun 2020 08:45:37: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:37: #2 predicted fragment length is 176 bps INFO @ Tue, 16 Jun 2020 08:45:37: #2 alternative fragment length(s) may be 4,176 bps INFO @ Tue, 16 Jun 2020 08:45:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.20_model.r INFO @ Tue, 16 Jun 2020 08:45:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:45:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.10_summits.bed INFO @ Tue, 16 Jun 2020 08:45:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5725 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:45:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:46:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082360/SRX4082360.20_summits.bed INFO @ Tue, 16 Jun 2020 08:46:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2051 records, 4 fields): 3 millis CompletedMACS2peakCalling