Job ID = 6456628 SRX = SRX375353 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:56:01 prefetch.2.10.7: 1) Downloading 'SRR1027843'... 2020-06-21T10:56:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:04:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:04:52 prefetch.2.10.7: 1) 'SRR1027843' was downloaded successfully Read 41739672 spots for SRR1027843/SRR1027843.sra Written 41739672 spots for SRR1027843/SRR1027843.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: 00:10:37 41739672 reads; of these: 41739672 (100.00%) were unpaired; of these: 18528236 (44.39%) aligned 0 times 13757427 (32.96%) aligned exactly 1 time 9454009 (22.65%) aligned >1 times 55.61% overall alignment rate Time searching: 00:10:37 Overall time: 00:10:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 14421209 / 23211436 = 0.6213 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 20:23:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.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 20:23:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:23:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:23:56: 1000000 INFO @ Sun, 21 Jun 2020 20:24:05: 2000000 INFO @ Sun, 21 Jun 2020 20:24:14: 3000000 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 20:24:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.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 20:24:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:24:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:24:23: 4000000 INFO @ Sun, 21 Jun 2020 20:24:25: 1000000 INFO @ Sun, 21 Jun 2020 20:24:32: 2000000 INFO @ Sun, 21 Jun 2020 20:24:32: 5000000 INFO @ Sun, 21 Jun 2020 20:24:40: 3000000 INFO @ Sun, 21 Jun 2020 20:24:41: 6000000 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 20:24:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.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 20:24:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:24:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:24:48: 4000000 INFO @ Sun, 21 Jun 2020 20:24:50: 7000000 INFO @ Sun, 21 Jun 2020 20:24:56: 1000000 INFO @ Sun, 21 Jun 2020 20:24:57: 5000000 INFO @ Sun, 21 Jun 2020 20:24:59: 8000000 INFO @ Sun, 21 Jun 2020 20:25:04: 2000000 INFO @ Sun, 21 Jun 2020 20:25:06: 6000000 INFO @ Sun, 21 Jun 2020 20:25:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:25:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:25:07: #1 total tags in treatment: 8790227 INFO @ Sun, 21 Jun 2020 20:25:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:25:07: #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 20:25:07: #1 tags after filtering in treatment: 8790219 INFO @ Sun, 21 Jun 2020 20:25:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:25:07: #1 finished! INFO @ Sun, 21 Jun 2020 20:25:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:25:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:25:08: #2 number of paired peaks: 1225 INFO @ Sun, 21 Jun 2020 20:25:08: start model_add_line... INFO @ Sun, 21 Jun 2020 20:25:08: start X-correlation... INFO @ Sun, 21 Jun 2020 20:25:08: end of X-cor INFO @ Sun, 21 Jun 2020 20:25:08: #2 finished! INFO @ Sun, 21 Jun 2020 20:25:08: #2 predicted fragment length is 153 bps INFO @ Sun, 21 Jun 2020 20:25:08: #2 alternative fragment length(s) may be 153 bps INFO @ Sun, 21 Jun 2020 20:25:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.05_model.r INFO @ Sun, 21 Jun 2020 20:25:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:25:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:25:13: 3000000 INFO @ Sun, 21 Jun 2020 20:25:15: 7000000 INFO @ Sun, 21 Jun 2020 20:25:22: 4000000 INFO @ Sun, 21 Jun 2020 20:25:24: 8000000 INFO @ Sun, 21 Jun 2020 20:25:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:25:31: 5000000 INFO @ Sun, 21 Jun 2020 20:25:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:25:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:25:31: #1 total tags in treatment: 8790227 INFO @ Sun, 21 Jun 2020 20:25:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:25:31: #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 20:25:32: #1 tags after filtering in treatment: 8790219 INFO @ Sun, 21 Jun 2020 20:25:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:25:32: #1 finished! INFO @ Sun, 21 Jun 2020 20:25:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:25:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:25:33: #2 number of paired peaks: 1225 INFO @ Sun, 21 Jun 2020 20:25:33: start model_add_line... INFO @ Sun, 21 Jun 2020 20:25:33: start X-correlation... INFO @ Sun, 21 Jun 2020 20:25:33: end of X-cor INFO @ Sun, 21 Jun 2020 20:25:33: #2 finished! INFO @ Sun, 21 Jun 2020 20:25:33: #2 predicted fragment length is 153 bps INFO @ Sun, 21 Jun 2020 20:25:33: #2 alternative fragment length(s) may be 153 bps INFO @ Sun, 21 Jun 2020 20:25:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.10_model.r INFO @ Sun, 21 Jun 2020 20:25:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:25:33: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:25:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:25:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:25:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.05_summits.bed INFO @ Sun, 21 Jun 2020 20:25:36: Done! pass1 - making usageList (651 chroms): 2 millis pass2 - checking and writing primary data (4030 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:25:39: 6000000 INFO @ Sun, 21 Jun 2020 20:25:48: 7000000 INFO @ Sun, 21 Jun 2020 20:25:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:25:57: 8000000 INFO @ Sun, 21 Jun 2020 20:26:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:26:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:26:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.10_summits.bed INFO @ Sun, 21 Jun 2020 20:26:01: Done! pass1 - making usageList (574 chroms): 2 millis pass2 - checking and writing primary data (2717 records, 4 fields): 33 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:26:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:26:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:26:04: #1 total tags in treatment: 8790227 INFO @ Sun, 21 Jun 2020 20:26:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:26:04: #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 20:26:05: #1 tags after filtering in treatment: 8790219 INFO @ Sun, 21 Jun 2020 20:26:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:26:05: #1 finished! INFO @ Sun, 21 Jun 2020 20:26:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:26:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:26:05: #2 number of paired peaks: 1225 INFO @ Sun, 21 Jun 2020 20:26:05: start model_add_line... INFO @ Sun, 21 Jun 2020 20:26:05: start X-correlation... INFO @ Sun, 21 Jun 2020 20:26:05: end of X-cor INFO @ Sun, 21 Jun 2020 20:26:05: #2 finished! INFO @ Sun, 21 Jun 2020 20:26:05: #2 predicted fragment length is 153 bps INFO @ Sun, 21 Jun 2020 20:26:05: #2 alternative fragment length(s) may be 153 bps INFO @ Sun, 21 Jun 2020 20:26:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.20_model.r INFO @ Sun, 21 Jun 2020 20:26:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:26:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:26:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:26:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:26:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:26:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX375353/SRX375353.20_summits.bed INFO @ Sun, 21 Jun 2020 20:26:34: Done! pass1 - making usageList (496 chroms): 2 millis pass2 - checking and writing primary data (1955 records, 4 fields): 28 millis CompletedMACS2peakCalling