Job ID = 6454367 SRX = SRX201901 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:03:19 prefetch.2.10.7: 1) Downloading 'SRR609691'... 2020-06-21T09:03:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:07:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:07:44 prefetch.2.10.7: 1) 'SRR609691' was downloaded successfully Read 38178192 spots for SRR609691/SRR609691.sra Written 38178192 spots for SRR609691/SRR609691.sra 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:37 38178192 reads; of these: 38178192 (100.00%) were unpaired; of these: 3669820 (9.61%) aligned 0 times 32121476 (84.14%) aligned exactly 1 time 2386896 (6.25%) aligned >1 times 90.39% overall alignment rate Time searching: 00:07:38 Overall time: 00:07:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 27470410 / 34508372 = 0.7961 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 @ Sun, 21 Jun 2020 18:23:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:23:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:23:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:23:08: 1000000 INFO @ Sun, 21 Jun 2020 18:23:13: 2000000 INFO @ Sun, 21 Jun 2020 18:23:18: 3000000 INFO @ Sun, 21 Jun 2020 18:23:24: 4000000 INFO @ Sun, 21 Jun 2020 18:23:29: 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 @ Sun, 21 Jun 2020 18:23:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:23:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:23:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:23:35: 6000000 INFO @ Sun, 21 Jun 2020 18:23:38: 1000000 INFO @ Sun, 21 Jun 2020 18:23:40: 7000000 INFO @ Sun, 21 Jun 2020 18:23:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:23:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:23:41: #1 total tags in treatment: 7037962 INFO @ Sun, 21 Jun 2020 18:23:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:23:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:23:41: #1 tags after filtering in treatment: 7037743 INFO @ Sun, 21 Jun 2020 18:23:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:23:41: #1 finished! INFO @ Sun, 21 Jun 2020 18:23:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:23:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:23:42: #2 number of paired peaks: 8044 INFO @ Sun, 21 Jun 2020 18:23:42: start model_add_line... INFO @ Sun, 21 Jun 2020 18:23:42: start X-correlation... INFO @ Sun, 21 Jun 2020 18:23:42: end of X-cor INFO @ Sun, 21 Jun 2020 18:23:42: #2 finished! INFO @ Sun, 21 Jun 2020 18:23:42: #2 predicted fragment length is 272 bps INFO @ Sun, 21 Jun 2020 18:23:42: #2 alternative fragment length(s) may be 272 bps INFO @ Sun, 21 Jun 2020 18:23:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.05_model.r INFO @ Sun, 21 Jun 2020 18:23:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:23:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:23:43: 2000000 INFO @ Sun, 21 Jun 2020 18:23:49: 3000000 INFO @ Sun, 21 Jun 2020 18:23:54: 4000000 INFO @ Sun, 21 Jun 2020 18:24:00: 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 @ Sun, 21 Jun 2020 18:24:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:24:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:24:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:24:06: 6000000 INFO @ Sun, 21 Jun 2020 18:24:07: 1000000 INFO @ Sun, 21 Jun 2020 18:24:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:24:12: 7000000 INFO @ Sun, 21 Jun 2020 18:24:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:24:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:24:12: #1 total tags in treatment: 7037962 INFO @ Sun, 21 Jun 2020 18:24:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:24:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:24:12: #1 tags after filtering in treatment: 7037743 INFO @ Sun, 21 Jun 2020 18:24:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:24:12: #1 finished! INFO @ Sun, 21 Jun 2020 18:24:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:24:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:24:13: 2000000 INFO @ Sun, 21 Jun 2020 18:24:13: #2 number of paired peaks: 8044 INFO @ Sun, 21 Jun 2020 18:24:13: start model_add_line... INFO @ Sun, 21 Jun 2020 18:24:14: start X-correlation... INFO @ Sun, 21 Jun 2020 18:24:14: end of X-cor INFO @ Sun, 21 Jun 2020 18:24:14: #2 finished! INFO @ Sun, 21 Jun 2020 18:24:14: #2 predicted fragment length is 272 bps INFO @ Sun, 21 Jun 2020 18:24:14: #2 alternative fragment length(s) may be 272 bps INFO @ Sun, 21 Jun 2020 18:24:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.10_model.r INFO @ Sun, 21 Jun 2020 18:24:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:24:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:24:18: 3000000 INFO @ Sun, 21 Jun 2020 18:24:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:24:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:24:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.05_summits.bed INFO @ Sun, 21 Jun 2020 18:24:21: Done! pass1 - making usageList (100 chroms): 2 millis pass2 - checking and writing primary data (7463 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:24:24: 4000000 INFO @ Sun, 21 Jun 2020 18:24:29: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:24:35: 6000000 INFO @ Sun, 21 Jun 2020 18:24:40: 7000000 INFO @ Sun, 21 Jun 2020 18:24:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:24:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:24:40: #1 total tags in treatment: 7037962 INFO @ Sun, 21 Jun 2020 18:24:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:24:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:24:41: #1 tags after filtering in treatment: 7037743 INFO @ Sun, 21 Jun 2020 18:24:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:24:41: #1 finished! INFO @ Sun, 21 Jun 2020 18:24:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:24:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:24:41: #2 number of paired peaks: 8044 INFO @ Sun, 21 Jun 2020 18:24:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:24:42: start X-correlation... INFO @ Sun, 21 Jun 2020 18:24:42: end of X-cor INFO @ Sun, 21 Jun 2020 18:24:42: #2 finished! INFO @ Sun, 21 Jun 2020 18:24:42: #2 predicted fragment length is 272 bps INFO @ Sun, 21 Jun 2020 18:24:42: #2 alternative fragment length(s) may be 272 bps INFO @ Sun, 21 Jun 2020 18:24:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.20_model.r INFO @ Sun, 21 Jun 2020 18:24:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:24:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:24:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:24:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:24:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:24:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.10_summits.bed INFO @ Sun, 21 Jun 2020 18:24:53: Done! pass1 - making usageList (75 chroms): 1 millis pass2 - checking and writing primary data (5675 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:25:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:25:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:25:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:25:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201901/SRX201901.20_summits.bed INFO @ Sun, 21 Jun 2020 18:25:20: Done! pass1 - making usageList (50 chroms): 1 millis pass2 - checking and writing primary data (3974 records, 4 fields): 7 millis CompletedMACS2peakCalling