Job ID = 6454984 SRX = SRX2618523 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:13:36 prefetch.2.10.7: 1) Downloading 'SRR5319077'... 2020-06-21T10:13:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:15:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:15:36 prefetch.2.10.7: 'SRR5319077' is valid 2020-06-21T10:15:36 prefetch.2.10.7: 1) 'SRR5319077' was downloaded successfully 2020-06-21T10:15:36 prefetch.2.10.7: 'SRR5319077' has 0 unresolved dependencies Read 12166303 spots for SRR5319077/SRR5319077.sra Written 12166303 spots for SRR5319077/SRR5319077.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: 00:02:45 12166303 reads; of these: 12166303 (100.00%) were unpaired; of these: 1205535 (9.91%) aligned 0 times 9661274 (79.41%) aligned exactly 1 time 1299494 (10.68%) aligned >1 times 90.09% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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 8 files... [bam_rmdupse_core] 1610922 / 10960768 = 0.1470 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 19:22:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.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 19:22:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:22:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:22:55: 1000000 INFO @ Sun, 21 Jun 2020 19:23:01: 2000000 INFO @ Sun, 21 Jun 2020 19:23:07: 3000000 INFO @ Sun, 21 Jun 2020 19:23:12: 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 @ Sun, 21 Jun 2020 19:23:18: 5000000 INFO @ Sun, 21 Jun 2020 19:23:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.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 19:23:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:23:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:25: 6000000 INFO @ Sun, 21 Jun 2020 19:23:26: 1000000 INFO @ Sun, 21 Jun 2020 19:23:31: 7000000 INFO @ Sun, 21 Jun 2020 19:23:32: 2000000 INFO @ Sun, 21 Jun 2020 19:23:38: 8000000 INFO @ Sun, 21 Jun 2020 19:23:39: 3000000 INFO @ Sun, 21 Jun 2020 19:23:45: 9000000 INFO @ Sun, 21 Jun 2020 19:23:45: 4000000 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 19:23:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:23:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:23:47: #1 total tags in treatment: 9349846 INFO @ Sun, 21 Jun 2020 19:23:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:23:47: #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 19:23:48: #1 tags after filtering in treatment: 9349780 INFO @ Sun, 21 Jun 2020 19:23:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:23:48: #1 finished! INFO @ Sun, 21 Jun 2020 19:23:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:23:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:23:49: #2 number of paired peaks: 2467 INFO @ Sun, 21 Jun 2020 19:23:49: start model_add_line... INFO @ Sun, 21 Jun 2020 19:23:49: start X-correlation... INFO @ Sun, 21 Jun 2020 19:23:49: end of X-cor INFO @ Sun, 21 Jun 2020 19:23:49: #2 finished! INFO @ Sun, 21 Jun 2020 19:23:49: #2 predicted fragment length is 163 bps INFO @ Sun, 21 Jun 2020 19:23:49: #2 alternative fragment length(s) may be 163 bps INFO @ Sun, 21 Jun 2020 19:23:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.05_model.r INFO @ Sun, 21 Jun 2020 19:23:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:23:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:23:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.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 19:23:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:23:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:52: 5000000 INFO @ Sun, 21 Jun 2020 19:23:56: 1000000 INFO @ Sun, 21 Jun 2020 19:23:58: 6000000 INFO @ Sun, 21 Jun 2020 19:24:03: 2000000 INFO @ Sun, 21 Jun 2020 19:24:05: 7000000 INFO @ Sun, 21 Jun 2020 19:24:09: 3000000 INFO @ Sun, 21 Jun 2020 19:24:12: 8000000 INFO @ Sun, 21 Jun 2020 19:24:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:24:16: 4000000 INFO @ Sun, 21 Jun 2020 19:24:19: 9000000 INFO @ Sun, 21 Jun 2020 19:24:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:24:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:24:21: #1 total tags in treatment: 9349846 INFO @ Sun, 21 Jun 2020 19:24:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:24:21: #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 19:24:22: #1 tags after filtering in treatment: 9349780 INFO @ Sun, 21 Jun 2020 19:24:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:24:22: #1 finished! INFO @ Sun, 21 Jun 2020 19:24:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:24:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:24:22: 5000000 INFO @ Sun, 21 Jun 2020 19:24:23: #2 number of paired peaks: 2467 INFO @ Sun, 21 Jun 2020 19:24:23: start model_add_line... INFO @ Sun, 21 Jun 2020 19:24:23: start X-correlation... INFO @ Sun, 21 Jun 2020 19:24:23: end of X-cor INFO @ Sun, 21 Jun 2020 19:24:23: #2 finished! INFO @ Sun, 21 Jun 2020 19:24:23: #2 predicted fragment length is 163 bps INFO @ Sun, 21 Jun 2020 19:24:23: #2 alternative fragment length(s) may be 163 bps INFO @ Sun, 21 Jun 2020 19:24:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.10_model.r INFO @ Sun, 21 Jun 2020 19:24:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:24:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:24:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:24:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:24:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.05_summits.bed INFO @ Sun, 21 Jun 2020 19:24:25: Done! pass1 - making usageList (372 chroms): 3 millis pass2 - checking and writing primary data (8853 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:24:28: 6000000 INFO @ Sun, 21 Jun 2020 19:24:34: 7000000 INFO @ Sun, 21 Jun 2020 19:24:41: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:24:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:24:47: 9000000 INFO @ Sun, 21 Jun 2020 19:24:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:24:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:24:49: #1 total tags in treatment: 9349846 INFO @ Sun, 21 Jun 2020 19:24:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:24:49: #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 19:24:50: #1 tags after filtering in treatment: 9349780 INFO @ Sun, 21 Jun 2020 19:24:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:24:50: #1 finished! INFO @ Sun, 21 Jun 2020 19:24:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:24:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:24:51: #2 number of paired peaks: 2467 INFO @ Sun, 21 Jun 2020 19:24:51: start model_add_line... INFO @ Sun, 21 Jun 2020 19:24:51: start X-correlation... INFO @ Sun, 21 Jun 2020 19:24:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:24:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:24:51: #2 predicted fragment length is 163 bps INFO @ Sun, 21 Jun 2020 19:24:51: #2 alternative fragment length(s) may be 163 bps INFO @ Sun, 21 Jun 2020 19:24:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.20_model.r INFO @ Sun, 21 Jun 2020 19:24:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:24:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:24:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:24:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:24:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.10_summits.bed INFO @ Sun, 21 Jun 2020 19:24:57: Done! pass1 - making usageList (229 chroms): 2 millis pass2 - checking and writing primary data (5229 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:25:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:25:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:25:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:25:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618523/SRX2618523.20_summits.bed INFO @ Sun, 21 Jun 2020 19:25:25: Done! pass1 - making usageList (126 chroms): 2 millis pass2 - checking and writing primary data (2287 records, 4 fields): 10 millis CompletedMACS2peakCalling