Job ID = 6452672 SRX = SRX025478 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:37:56 prefetch.2.10.7: 1) Downloading 'SRR063878'... 2020-06-21T07:37:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:41:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:41:49 prefetch.2.10.7: 'SRR063878' is valid 2020-06-21T07:41:49 prefetch.2.10.7: 1) 'SRR063878' was downloaded successfully Read 26376652 spots for SRR063878/SRR063878.sra Written 26376652 spots for SRR063878/SRR063878.sra 2020-06-21T07:43:06 prefetch.2.10.7: 1) Downloading 'SRR063879'... 2020-06-21T07:43:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:48:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:48:48 prefetch.2.10.7: 'SRR063879' is valid 2020-06-21T07:48:48 prefetch.2.10.7: 1) 'SRR063879' was downloaded successfully Read 23787659 spots for SRR063879/SRR063879.sra Written 23787659 spots for SRR063879/SRR063879.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: 00:11:29 50164311 reads; of these: 50164311 (100.00%) were unpaired; of these: 914057 (1.82%) aligned 0 times 39961686 (79.66%) aligned exactly 1 time 9288568 (18.52%) aligned >1 times 98.18% overall alignment rate Time searching: 00:11:29 Overall time: 00:11:29 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 16 files... [bam_rmdupse_core] 35977311 / 49250254 = 0.7305 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 17:08:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.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 17:08:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:08:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:08:12: 1000000 INFO @ Sun, 21 Jun 2020 17:08:17: 2000000 INFO @ Sun, 21 Jun 2020 17:08:22: 3000000 INFO @ Sun, 21 Jun 2020 17:08:27: 4000000 INFO @ Sun, 21 Jun 2020 17:08:32: 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 17:08:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.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 17:08:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:08:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:08:38: 6000000 INFO @ Sun, 21 Jun 2020 17:08:42: 1000000 INFO @ Sun, 21 Jun 2020 17:08:43: 7000000 INFO @ Sun, 21 Jun 2020 17:08:47: 2000000 INFO @ Sun, 21 Jun 2020 17:08:48: 8000000 INFO @ Sun, 21 Jun 2020 17:08:52: 3000000 INFO @ Sun, 21 Jun 2020 17:08:54: 9000000 INFO @ Sun, 21 Jun 2020 17:08:58: 4000000 INFO @ Sun, 21 Jun 2020 17:08:59: 10000000 INFO @ Sun, 21 Jun 2020 17:09:03: 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 17:09:05: 11000000 INFO @ Sun, 21 Jun 2020 17:09:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.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 17:09:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:09:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:09:09: 6000000 INFO @ Sun, 21 Jun 2020 17:09:10: 12000000 INFO @ Sun, 21 Jun 2020 17:09:12: 1000000 INFO @ Sun, 21 Jun 2020 17:09:14: 7000000 INFO @ Sun, 21 Jun 2020 17:09:15: 13000000 INFO @ Sun, 21 Jun 2020 17:09:17: 2000000 INFO @ Sun, 21 Jun 2020 17:09:17: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:09:17: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:09:17: #1 total tags in treatment: 13272943 INFO @ Sun, 21 Jun 2020 17:09:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:09:17: #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 17:09:18: #1 tags after filtering in treatment: 13272942 INFO @ Sun, 21 Jun 2020 17:09:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:09:18: #1 finished! INFO @ Sun, 21 Jun 2020 17:09:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:09:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:09:19: #2 number of paired peaks: 4176 INFO @ Sun, 21 Jun 2020 17:09:19: start model_add_line... INFO @ Sun, 21 Jun 2020 17:09:19: start X-correlation... INFO @ Sun, 21 Jun 2020 17:09:19: end of X-cor INFO @ Sun, 21 Jun 2020 17:09:19: #2 finished! INFO @ Sun, 21 Jun 2020 17:09:19: #2 predicted fragment length is 275 bps INFO @ Sun, 21 Jun 2020 17:09:19: #2 alternative fragment length(s) may be 275 bps INFO @ Sun, 21 Jun 2020 17:09:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.05_model.r INFO @ Sun, 21 Jun 2020 17:09:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:09:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:09:19: 8000000 INFO @ Sun, 21 Jun 2020 17:09:22: 3000000 INFO @ Sun, 21 Jun 2020 17:09:25: 9000000 INFO @ Sun, 21 Jun 2020 17:09:27: 4000000 INFO @ Sun, 21 Jun 2020 17:09:30: 10000000 INFO @ Sun, 21 Jun 2020 17:09:33: 5000000 INFO @ Sun, 21 Jun 2020 17:09:36: 11000000 INFO @ Sun, 21 Jun 2020 17:09:38: 6000000 INFO @ Sun, 21 Jun 2020 17:09:41: 12000000 INFO @ Sun, 21 Jun 2020 17:09:43: 7000000 INFO @ Sun, 21 Jun 2020 17:09:47: 13000000 INFO @ Sun, 21 Jun 2020 17:09:48: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:09:48: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:09:48: #1 total tags in treatment: 13272943 INFO @ Sun, 21 Jun 2020 17:09:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:09:48: #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 17:09:49: 8000000 INFO @ Sun, 21 Jun 2020 17:09:49: #1 tags after filtering in treatment: 13272942 INFO @ Sun, 21 Jun 2020 17:09:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:09:49: #1 finished! INFO @ Sun, 21 Jun 2020 17:09:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:09:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:09:50: #2 number of paired peaks: 4176 INFO @ Sun, 21 Jun 2020 17:09:50: start model_add_line... INFO @ Sun, 21 Jun 2020 17:09:50: start X-correlation... INFO @ Sun, 21 Jun 2020 17:09:50: end of X-cor INFO @ Sun, 21 Jun 2020 17:09:50: #2 finished! INFO @ Sun, 21 Jun 2020 17:09:50: #2 predicted fragment length is 275 bps INFO @ Sun, 21 Jun 2020 17:09:50: #2 alternative fragment length(s) may be 275 bps INFO @ Sun, 21 Jun 2020 17:09:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.10_model.r INFO @ Sun, 21 Jun 2020 17:09:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:09:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:09:54: 9000000 INFO @ Sun, 21 Jun 2020 17:09:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:09:59: 10000000 INFO @ Sun, 21 Jun 2020 17:10:05: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:10:10: 12000000 INFO @ Sun, 21 Jun 2020 17:10:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:10:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:10:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.05_summits.bed INFO @ Sun, 21 Jun 2020 17:10:12: Done! pass1 - making usageList (725 chroms): 2 millis pass2 - checking and writing primary data (7580 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:10:15: 13000000 INFO @ Sun, 21 Jun 2020 17:10:17: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:10:17: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:10:17: #1 total tags in treatment: 13272943 INFO @ Sun, 21 Jun 2020 17:10:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:10:17: #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 17:10:17: #1 tags after filtering in treatment: 13272942 INFO @ Sun, 21 Jun 2020 17:10:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:10:17: #1 finished! INFO @ Sun, 21 Jun 2020 17:10:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:10:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:10:18: #2 number of paired peaks: 4176 INFO @ Sun, 21 Jun 2020 17:10:18: start model_add_line... INFO @ Sun, 21 Jun 2020 17:10:19: start X-correlation... INFO @ Sun, 21 Jun 2020 17:10:19: end of X-cor INFO @ Sun, 21 Jun 2020 17:10:19: #2 finished! INFO @ Sun, 21 Jun 2020 17:10:19: #2 predicted fragment length is 275 bps INFO @ Sun, 21 Jun 2020 17:10:19: #2 alternative fragment length(s) may be 275 bps INFO @ Sun, 21 Jun 2020 17:10:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.20_model.r INFO @ Sun, 21 Jun 2020 17:10:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:10:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:10:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:10:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:10:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:10:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.10_summits.bed INFO @ Sun, 21 Jun 2020 17:10:42: Done! pass1 - making usageList (650 chroms): 1 millis pass2 - checking and writing primary data (6331 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:10:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:11:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:11:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:11:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025478/SRX025478.20_summits.bed INFO @ Sun, 21 Jun 2020 17:11:09: Done! pass1 - making usageList (549 chroms): 2 millis pass2 - checking and writing primary data (5131 records, 4 fields): 18 millis CompletedMACS2peakCalling