Job ID = 6454703 SRX = SRX2520649 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:37:40 prefetch.2.10.7: 1) Downloading 'SRR5206768'... 2020-06-21T09:37:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:44:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:44:57 prefetch.2.10.7: 1) 'SRR5206768' was downloaded successfully Read 29067252 spots for SRR5206768/SRR5206768.sra Written 29067252 spots for SRR5206768/SRR5206768.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: 00:07:04 29067252 reads; of these: 29067252 (100.00%) were unpaired; of these: 496007 (1.71%) aligned 0 times 22940121 (78.92%) aligned exactly 1 time 5631124 (19.37%) aligned >1 times 98.29% overall alignment rate Time searching: 00:07:05 Overall time: 00:07:05 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] 14845049 / 28571245 = 0.5196 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 18:58:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.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 18:58:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:58:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:17: 1000000 INFO @ Sun, 21 Jun 2020 18:58:22: 2000000 INFO @ Sun, 21 Jun 2020 18:58:28: 3000000 INFO @ Sun, 21 Jun 2020 18:58:34: 4000000 INFO @ Sun, 21 Jun 2020 18:58:39: 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 18:58:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.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 18:58:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:58:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:45: 6000000 INFO @ Sun, 21 Jun 2020 18:58:47: 1000000 INFO @ Sun, 21 Jun 2020 18:58:51: 7000000 INFO @ Sun, 21 Jun 2020 18:58:53: 2000000 INFO @ Sun, 21 Jun 2020 18:58:57: 8000000 INFO @ Sun, 21 Jun 2020 18:59:00: 3000000 INFO @ Sun, 21 Jun 2020 18:59:03: 9000000 INFO @ Sun, 21 Jun 2020 18:59:06: 4000000 INFO @ Sun, 21 Jun 2020 18:59:09: 10000000 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 18:59:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.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 18:59:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:59:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:59:12: 5000000 INFO @ Sun, 21 Jun 2020 18:59:15: 11000000 INFO @ Sun, 21 Jun 2020 18:59:18: 1000000 INFO @ Sun, 21 Jun 2020 18:59:18: 6000000 INFO @ Sun, 21 Jun 2020 18:59:22: 12000000 INFO @ Sun, 21 Jun 2020 18:59:24: 2000000 INFO @ Sun, 21 Jun 2020 18:59:24: 7000000 INFO @ Sun, 21 Jun 2020 18:59:28: 13000000 INFO @ Sun, 21 Jun 2020 18:59:30: 3000000 INFO @ Sun, 21 Jun 2020 18:59:31: 8000000 INFO @ Sun, 21 Jun 2020 18:59:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:59:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:59:33: #1 total tags in treatment: 13726196 INFO @ Sun, 21 Jun 2020 18:59:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:59:33: #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 18:59:34: #1 tags after filtering in treatment: 13726121 INFO @ Sun, 21 Jun 2020 18:59:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:59:34: #1 finished! INFO @ Sun, 21 Jun 2020 18:59:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:59:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:59:35: #2 number of paired peaks: 2602 INFO @ Sun, 21 Jun 2020 18:59:35: start model_add_line... INFO @ Sun, 21 Jun 2020 18:59:35: start X-correlation... INFO @ Sun, 21 Jun 2020 18:59:35: end of X-cor INFO @ Sun, 21 Jun 2020 18:59:35: #2 finished! INFO @ Sun, 21 Jun 2020 18:59:35: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 18:59:35: #2 alternative fragment length(s) may be 0,37,126 bps INFO @ Sun, 21 Jun 2020 18:59:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.05_model.r INFO @ Sun, 21 Jun 2020 18:59:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:59:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:59:37: 4000000 INFO @ Sun, 21 Jun 2020 18:59:37: 9000000 INFO @ Sun, 21 Jun 2020 18:59:43: 5000000 INFO @ Sun, 21 Jun 2020 18:59:43: 10000000 INFO @ Sun, 21 Jun 2020 18:59:49: 11000000 INFO @ Sun, 21 Jun 2020 18:59:49: 6000000 INFO @ Sun, 21 Jun 2020 18:59:55: 7000000 INFO @ Sun, 21 Jun 2020 18:59:55: 12000000 INFO @ Sun, 21 Jun 2020 19:00:01: 8000000 INFO @ Sun, 21 Jun 2020 19:00:01: 13000000 INFO @ Sun, 21 Jun 2020 19:00:03: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:00:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:00:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:00:06: #1 total tags in treatment: 13726196 INFO @ Sun, 21 Jun 2020 19:00:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:00:06: #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 19:00:06: #1 tags after filtering in treatment: 13726121 INFO @ Sun, 21 Jun 2020 19:00:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:00:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:00:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:00:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:00:07: 9000000 INFO @ Sun, 21 Jun 2020 19:00:08: #2 number of paired peaks: 2602 INFO @ Sun, 21 Jun 2020 19:00:08: start model_add_line... INFO @ Sun, 21 Jun 2020 19:00:08: start X-correlation... INFO @ Sun, 21 Jun 2020 19:00:08: end of X-cor INFO @ Sun, 21 Jun 2020 19:00:08: #2 finished! INFO @ Sun, 21 Jun 2020 19:00:08: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 19:00:08: #2 alternative fragment length(s) may be 0,37,126 bps INFO @ Sun, 21 Jun 2020 19:00:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.10_model.r INFO @ Sun, 21 Jun 2020 19:00:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:00:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:00:13: 10000000 INFO @ Sun, 21 Jun 2020 19:00:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:00:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:00:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.05_summits.bed INFO @ Sun, 21 Jun 2020 19:00:18: Done! pass1 - making usageList (209 chroms): 2 millis pass2 - checking and writing primary data (7654 records, 4 fields): 14 millis INFO @ Sun, 21 Jun 2020 19:00:18: 11000000 CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:00:24: 12000000 INFO @ Sun, 21 Jun 2020 19:00:29: 13000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:00:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:00:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:00:33: #1 total tags in treatment: 13726196 INFO @ Sun, 21 Jun 2020 19:00:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:00:33: #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 19:00:34: #1 tags after filtering in treatment: 13726121 INFO @ Sun, 21 Jun 2020 19:00:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:00:34: #1 finished! INFO @ Sun, 21 Jun 2020 19:00:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:00:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:00:35: #2 number of paired peaks: 2602 INFO @ Sun, 21 Jun 2020 19:00:35: start model_add_line... INFO @ Sun, 21 Jun 2020 19:00:35: start X-correlation... INFO @ Sun, 21 Jun 2020 19:00:35: end of X-cor INFO @ Sun, 21 Jun 2020 19:00:35: #2 finished! INFO @ Sun, 21 Jun 2020 19:00:35: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 19:00:35: #2 alternative fragment length(s) may be 0,37,126 bps INFO @ Sun, 21 Jun 2020 19:00:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.20_model.r INFO @ Sun, 21 Jun 2020 19:00:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:00:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:00:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:00:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:00:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:00:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.10_summits.bed INFO @ Sun, 21 Jun 2020 19:00:53: Done! pass1 - making usageList (144 chroms): 1 millis pass2 - checking and writing primary data (2603 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:01:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:01:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:01:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:01:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520649/SRX2520649.20_summits.bed INFO @ Sun, 21 Jun 2020 19:01:21: Done! pass1 - making usageList (68 chroms): 1 millis pass2 - checking and writing primary data (413 records, 4 fields): 4 millis CompletedMACS2peakCalling