Job ID = 6455158 SRX = SRX2804220 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:48:55 prefetch.2.10.7: 1) Downloading 'SRR5534648'... 2020-06-21T09:48:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:52:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:52:02 prefetch.2.10.7: 1) 'SRR5534648' was downloaded successfully 2020-06-21T09:52:02 prefetch.2.10.7: 'SRR5534648' has 0 unresolved dependencies Read 33987866 spots for SRR5534648/SRR5534648.sra Written 33987866 spots for SRR5534648/SRR5534648.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: 00:00:01 Multiseed full-index search: 00:07:33 33987866 reads; of these: 33987866 (100.00%) were unpaired; of these: 8343520 (24.55%) aligned 0 times 19252888 (56.65%) aligned exactly 1 time 6391458 (18.81%) aligned >1 times 75.45% overall alignment rate Time searching: 00:07:34 Overall time: 00:07:34 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] 8049956 / 25644346 = 0.3139 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 19:07:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.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 19:07:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:07:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:07:40: 1000000 INFO @ Sun, 21 Jun 2020 19:07:46: 2000000 INFO @ Sun, 21 Jun 2020 19:07:53: 3000000 INFO @ Sun, 21 Jun 2020 19:08:00: 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 19:08:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.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 19:08:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:07: 5000000 INFO @ Sun, 21 Jun 2020 19:08:12: 1000000 INFO @ Sun, 21 Jun 2020 19:08:15: 6000000 INFO @ Sun, 21 Jun 2020 19:08:20: 2000000 INFO @ Sun, 21 Jun 2020 19:08:22: 7000000 INFO @ Sun, 21 Jun 2020 19:08:28: 3000000 INFO @ Sun, 21 Jun 2020 19:08:30: 8000000 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 19:08:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.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 19:08:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:37: 4000000 INFO @ Sun, 21 Jun 2020 19:08:39: 9000000 INFO @ Sun, 21 Jun 2020 19:08:43: 1000000 INFO @ Sun, 21 Jun 2020 19:08:44: 5000000 INFO @ Sun, 21 Jun 2020 19:08:48: 10000000 INFO @ Sun, 21 Jun 2020 19:08:52: 2000000 INFO @ Sun, 21 Jun 2020 19:08:53: 6000000 INFO @ Sun, 21 Jun 2020 19:08:56: 11000000 INFO @ Sun, 21 Jun 2020 19:09:01: 3000000 INFO @ Sun, 21 Jun 2020 19:09:01: 7000000 INFO @ Sun, 21 Jun 2020 19:09:05: 12000000 INFO @ Sun, 21 Jun 2020 19:09:09: 4000000 INFO @ Sun, 21 Jun 2020 19:09:10: 8000000 INFO @ Sun, 21 Jun 2020 19:09:14: 13000000 INFO @ Sun, 21 Jun 2020 19:09:17: 5000000 INFO @ Sun, 21 Jun 2020 19:09:19: 9000000 INFO @ Sun, 21 Jun 2020 19:09:23: 14000000 INFO @ Sun, 21 Jun 2020 19:09:25: 6000000 INFO @ Sun, 21 Jun 2020 19:09:28: 10000000 INFO @ Sun, 21 Jun 2020 19:09:32: 15000000 INFO @ Sun, 21 Jun 2020 19:09:33: 7000000 INFO @ Sun, 21 Jun 2020 19:09:37: 11000000 INFO @ Sun, 21 Jun 2020 19:09:41: 16000000 INFO @ Sun, 21 Jun 2020 19:09:42: 8000000 INFO @ Sun, 21 Jun 2020 19:09:45: 12000000 INFO @ Sun, 21 Jun 2020 19:09:49: 17000000 INFO @ Sun, 21 Jun 2020 19:09:50: 9000000 INFO @ Sun, 21 Jun 2020 19:09:54: 13000000 INFO @ Sun, 21 Jun 2020 19:09:55: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:09:55: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:09:55: #1 total tags in treatment: 17594390 INFO @ Sun, 21 Jun 2020 19:09:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:55: #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 19:09:56: #1 tags after filtering in treatment: 17594390 INFO @ Sun, 21 Jun 2020 19:09:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:57: #2 number of paired peaks: 1035 INFO @ Sun, 21 Jun 2020 19:09:57: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:57: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:57: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:57: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:57: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 19:09:57: #2 alternative fragment length(s) may be 137 bps INFO @ Sun, 21 Jun 2020 19:09:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.05_model.r INFO @ Sun, 21 Jun 2020 19:09:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:09:59: 10000000 INFO @ Sun, 21 Jun 2020 19:10:03: 14000000 INFO @ Sun, 21 Jun 2020 19:10:06: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:10:12: 15000000 INFO @ Sun, 21 Jun 2020 19:10:13: 12000000 INFO @ Sun, 21 Jun 2020 19:10:20: 16000000 INFO @ Sun, 21 Jun 2020 19:10:21: 13000000 INFO @ Sun, 21 Jun 2020 19:10:29: 17000000 INFO @ Sun, 21 Jun 2020 19:10:29: 14000000 INFO @ Sun, 21 Jun 2020 19:10:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:10:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:10:33: #1 total tags in treatment: 17594390 INFO @ Sun, 21 Jun 2020 19:10:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:10:33: #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 19:10:34: #1 tags after filtering in treatment: 17594390 INFO @ Sun, 21 Jun 2020 19:10:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:10:34: #1 finished! INFO @ Sun, 21 Jun 2020 19:10:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:10:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:10:36: #2 number of paired peaks: 1035 INFO @ Sun, 21 Jun 2020 19:10:36: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:10:36: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:36: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:36: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:36: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 19:10:36: #2 alternative fragment length(s) may be 137 bps INFO @ Sun, 21 Jun 2020 19:10:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.10_model.r INFO @ Sun, 21 Jun 2020 19:10:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:10:38: 15000000 INFO @ Sun, 21 Jun 2020 19:10:47: 16000000 INFO @ Sun, 21 Jun 2020 19:10:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:10:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:10:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.05_summits.bed INFO @ Sun, 21 Jun 2020 19:10:54: Done! pass1 - making usageList (701 chroms): 3 millis pass2 - checking and writing primary data (9257 records, 4 fields): 49 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:10:56: 17000000 INFO @ Sun, 21 Jun 2020 19:11:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:11:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:11:01: #1 total tags in treatment: 17594390 INFO @ Sun, 21 Jun 2020 19:11:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:11:01: #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 19:11:02: #1 tags after filtering in treatment: 17594390 INFO @ Sun, 21 Jun 2020 19:11:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:11:02: #1 finished! INFO @ Sun, 21 Jun 2020 19:11:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:11:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:11:03: #2 number of paired peaks: 1035 INFO @ Sun, 21 Jun 2020 19:11:03: start model_add_line... INFO @ Sun, 21 Jun 2020 19:11:04: start X-correlation... INFO @ Sun, 21 Jun 2020 19:11:04: end of X-cor INFO @ Sun, 21 Jun 2020 19:11:04: #2 finished! INFO @ Sun, 21 Jun 2020 19:11:04: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 19:11:04: #2 alternative fragment length(s) may be 137 bps INFO @ Sun, 21 Jun 2020 19:11:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.20_model.r INFO @ Sun, 21 Jun 2020 19:11:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:11:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:11:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:11:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:11:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:11:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.10_summits.bed INFO @ Sun, 21 Jun 2020 19:11:33: Done! pass1 - making usageList (627 chroms): 2 millis pass2 - checking and writing primary data (6889 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:11:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:11:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:11:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:11:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804220/SRX2804220.20_summits.bed INFO @ Sun, 21 Jun 2020 19:11:58: Done! pass1 - making usageList (520 chroms): 2 millis pass2 - checking and writing primary data (4724 records, 4 fields): 34 millis CompletedMACS2peakCalling