Job ID = 6455700 SRX = SRX288001 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:09:51 prefetch.2.10.7: 1) Downloading 'SRR870190'... 2020-06-21T10:09:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:14:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:14:11 prefetch.2.10.7: 1) 'SRR870190' was downloaded successfully Read 22467727 spots for SRR870190/SRR870190.sra Written 22467727 spots for SRR870190/SRR870190.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: 00:04:07 22467727 reads; of these: 22467727 (100.00%) were unpaired; of these: 1823413 (8.12%) aligned 0 times 19337786 (86.07%) aligned exactly 1 time 1306528 (5.82%) aligned >1 times 91.88% overall alignment rate Time searching: 00:04:07 Overall time: 00:04:07 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] 3461204 / 20644314 = 0.1677 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 19:24:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.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 19:24:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:24:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:24:40: 1000000 INFO @ Sun, 21 Jun 2020 19:24:45: 2000000 INFO @ Sun, 21 Jun 2020 19:24:50: 3000000 INFO @ Sun, 21 Jun 2020 19:24:55: 4000000 INFO @ Sun, 21 Jun 2020 19:25:00: 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 19:25:05: 6000000 INFO @ Sun, 21 Jun 2020 19:25:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.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 19:25:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:25:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:25:09: 7000000 INFO @ Sun, 21 Jun 2020 19:25:11: 1000000 INFO @ Sun, 21 Jun 2020 19:25:14: 8000000 INFO @ Sun, 21 Jun 2020 19:25:17: 2000000 INFO @ Sun, 21 Jun 2020 19:25:19: 9000000 INFO @ Sun, 21 Jun 2020 19:25:23: 3000000 INFO @ Sun, 21 Jun 2020 19:25:24: 10000000 INFO @ Sun, 21 Jun 2020 19:25:28: 4000000 INFO @ Sun, 21 Jun 2020 19:25:29: 11000000 INFO @ Sun, 21 Jun 2020 19:25:34: 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 19:25:34: 12000000 INFO @ Sun, 21 Jun 2020 19:25:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.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 19:25:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:25:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:25:39: 6000000 INFO @ Sun, 21 Jun 2020 19:25:39: 13000000 INFO @ Sun, 21 Jun 2020 19:25:41: 1000000 INFO @ Sun, 21 Jun 2020 19:25:44: 14000000 INFO @ Sun, 21 Jun 2020 19:25:44: 7000000 INFO @ Sun, 21 Jun 2020 19:25:45: 2000000 INFO @ Sun, 21 Jun 2020 19:25:49: 15000000 INFO @ Sun, 21 Jun 2020 19:25:50: 8000000 INFO @ Sun, 21 Jun 2020 19:25:50: 3000000 INFO @ Sun, 21 Jun 2020 19:25:54: 16000000 INFO @ Sun, 21 Jun 2020 19:25:55: 4000000 INFO @ Sun, 21 Jun 2020 19:25:55: 9000000 INFO @ Sun, 21 Jun 2020 19:25:59: 17000000 INFO @ Sun, 21 Jun 2020 19:26:00: 5000000 INFO @ Sun, 21 Jun 2020 19:26:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:26:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:26:00: #1 total tags in treatment: 17183110 INFO @ Sun, 21 Jun 2020 19:26:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:26:00: #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 19:26:01: #1 tags after filtering in treatment: 17183007 INFO @ Sun, 21 Jun 2020 19:26:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:26:01: #1 finished! INFO @ Sun, 21 Jun 2020 19:26:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:26:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:26:01: 10000000 INFO @ Sun, 21 Jun 2020 19:26:02: #2 number of paired peaks: 4875 INFO @ Sun, 21 Jun 2020 19:26:02: start model_add_line... INFO @ Sun, 21 Jun 2020 19:26:02: start X-correlation... INFO @ Sun, 21 Jun 2020 19:26:02: end of X-cor INFO @ Sun, 21 Jun 2020 19:26:02: #2 finished! INFO @ Sun, 21 Jun 2020 19:26:02: #2 predicted fragment length is 204 bps INFO @ Sun, 21 Jun 2020 19:26:02: #2 alternative fragment length(s) may be 204 bps INFO @ Sun, 21 Jun 2020 19:26:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.05_model.r INFO @ Sun, 21 Jun 2020 19:26:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:26:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:26:05: 6000000 INFO @ Sun, 21 Jun 2020 19:26:07: 11000000 INFO @ Sun, 21 Jun 2020 19:26:10: 7000000 INFO @ Sun, 21 Jun 2020 19:26:12: 12000000 INFO @ Sun, 21 Jun 2020 19:26:15: 8000000 INFO @ Sun, 21 Jun 2020 19:26:18: 13000000 INFO @ Sun, 21 Jun 2020 19:26:20: 9000000 INFO @ Sun, 21 Jun 2020 19:26:23: 14000000 INFO @ Sun, 21 Jun 2020 19:26:24: 10000000 INFO @ Sun, 21 Jun 2020 19:26:29: 15000000 INFO @ Sun, 21 Jun 2020 19:26:29: 11000000 INFO @ Sun, 21 Jun 2020 19:26:34: 12000000 INFO @ Sun, 21 Jun 2020 19:26:35: 16000000 INFO @ Sun, 21 Jun 2020 19:26:39: 13000000 INFO @ Sun, 21 Jun 2020 19:26:40: 17000000 INFO @ Sun, 21 Jun 2020 19:26:42: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:26:42: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:26:42: #1 total tags in treatment: 17183110 INFO @ Sun, 21 Jun 2020 19:26:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:26:42: #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 19:26:42: #1 tags after filtering in treatment: 17183007 INFO @ Sun, 21 Jun 2020 19:26:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:26:42: #1 finished! INFO @ Sun, 21 Jun 2020 19:26:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:26:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:26:44: #2 number of paired peaks: 4875 INFO @ Sun, 21 Jun 2020 19:26:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:26:44: start X-correlation... INFO @ Sun, 21 Jun 2020 19:26:44: end of X-cor INFO @ Sun, 21 Jun 2020 19:26:44: #2 finished! INFO @ Sun, 21 Jun 2020 19:26:44: #2 predicted fragment length is 204 bps INFO @ Sun, 21 Jun 2020 19:26:44: #2 alternative fragment length(s) may be 204 bps INFO @ Sun, 21 Jun 2020 19:26:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.10_model.r INFO @ Sun, 21 Jun 2020 19:26:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:26:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:26:44: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:26:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:26:49: 15000000 INFO @ Sun, 21 Jun 2020 19:26:54: 16000000 INFO @ Sun, 21 Jun 2020 19:26:59: 17000000 INFO @ Sun, 21 Jun 2020 19:27:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:27:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:27:00: #1 total tags in treatment: 17183110 INFO @ Sun, 21 Jun 2020 19:27:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:27:00: #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 19:27:00: #1 tags after filtering in treatment: 17183007 INFO @ Sun, 21 Jun 2020 19:27:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:27:00: #1 finished! INFO @ Sun, 21 Jun 2020 19:27:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:27:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:27:02: #2 number of paired peaks: 4875 INFO @ Sun, 21 Jun 2020 19:27:02: start model_add_line... INFO @ Sun, 21 Jun 2020 19:27:02: start X-correlation... INFO @ Sun, 21 Jun 2020 19:27:02: end of X-cor INFO @ Sun, 21 Jun 2020 19:27:02: #2 finished! INFO @ Sun, 21 Jun 2020 19:27:02: #2 predicted fragment length is 204 bps INFO @ Sun, 21 Jun 2020 19:27:02: #2 alternative fragment length(s) may be 204 bps INFO @ Sun, 21 Jun 2020 19:27:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.20_model.r INFO @ Sun, 21 Jun 2020 19:27:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:27:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:27:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:27:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:27:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.05_summits.bed INFO @ Sun, 21 Jun 2020 19:27:08: Done! pass1 - making usageList (62 chroms): 2 millis pass2 - checking and writing primary data (11434 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:27:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:27:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:27:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:27:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:27:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.10_summits.bed INFO @ Sun, 21 Jun 2020 19:27:53: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (7102 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:28:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:28:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:28:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288001/SRX288001.20_summits.bed INFO @ Sun, 21 Jun 2020 19:28:08: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (3527 records, 4 fields): 5 millis CompletedMACS2peakCalling