Job ID = 6459044 SRX = SRX6386725 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:51:37 prefetch.2.10.7: 1) Downloading 'SRR9624457'... 2020-06-21T12:51:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:59:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:59:46 prefetch.2.10.7: 1) 'SRR9624457' was downloaded successfully Read 31504881 spots for SRR9624457/SRR9624457.sra Written 31504881 spots for SRR9624457/SRR9624457.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: 00:06:51 31504881 reads; of these: 31504881 (100.00%) were unpaired; of these: 8868268 (28.15%) aligned 0 times 16801907 (53.33%) aligned exactly 1 time 5834706 (18.52%) aligned >1 times 71.85% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 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] 8247048 / 22636613 = 0.3643 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 22:13:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.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 22:13:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:13:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:13:55: 1000000 INFO @ Sun, 21 Jun 2020 22:14:01: 2000000 INFO @ Sun, 21 Jun 2020 22:14:06: 3000000 INFO @ Sun, 21 Jun 2020 22:14:12: 4000000 INFO @ Sun, 21 Jun 2020 22:14:17: 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 22:14:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.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 22:14:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:14:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:14:23: 6000000 INFO @ Sun, 21 Jun 2020 22:14:26: 1000000 INFO @ Sun, 21 Jun 2020 22:14:29: 7000000 INFO @ Sun, 21 Jun 2020 22:14:32: 2000000 INFO @ Sun, 21 Jun 2020 22:14:35: 8000000 INFO @ Sun, 21 Jun 2020 22:14:38: 3000000 INFO @ Sun, 21 Jun 2020 22:14:41: 9000000 INFO @ Sun, 21 Jun 2020 22:14:44: 4000000 INFO @ Sun, 21 Jun 2020 22:14:46: 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 22:14:50: 5000000 INFO @ Sun, 21 Jun 2020 22:14:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.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 22:14:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:14:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:14:53: 11000000 INFO @ Sun, 21 Jun 2020 22:14:56: 6000000 INFO @ Sun, 21 Jun 2020 22:14:56: 1000000 INFO @ Sun, 21 Jun 2020 22:14:59: 12000000 INFO @ Sun, 21 Jun 2020 22:15:02: 7000000 INFO @ Sun, 21 Jun 2020 22:15:02: 2000000 INFO @ Sun, 21 Jun 2020 22:15:05: 13000000 INFO @ Sun, 21 Jun 2020 22:15:08: 8000000 INFO @ Sun, 21 Jun 2020 22:15:08: 3000000 INFO @ Sun, 21 Jun 2020 22:15:11: 14000000 INFO @ Sun, 21 Jun 2020 22:15:13: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:15:13: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:15:13: #1 total tags in treatment: 14389565 INFO @ Sun, 21 Jun 2020 22:15:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:15:13: #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 22:15:14: 9000000 INFO @ Sun, 21 Jun 2020 22:15:14: #1 tags after filtering in treatment: 14389537 INFO @ Sun, 21 Jun 2020 22:15:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:15:14: #1 finished! INFO @ Sun, 21 Jun 2020 22:15:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:15:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:15:14: 4000000 INFO @ Sun, 21 Jun 2020 22:15:15: #2 number of paired peaks: 1377 INFO @ Sun, 21 Jun 2020 22:15:15: start model_add_line... INFO @ Sun, 21 Jun 2020 22:15:15: start X-correlation... INFO @ Sun, 21 Jun 2020 22:15:15: end of X-cor INFO @ Sun, 21 Jun 2020 22:15:15: #2 finished! INFO @ Sun, 21 Jun 2020 22:15:15: #2 predicted fragment length is 134 bps INFO @ Sun, 21 Jun 2020 22:15:15: #2 alternative fragment length(s) may be 134 bps INFO @ Sun, 21 Jun 2020 22:15:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.05_model.r INFO @ Sun, 21 Jun 2020 22:15:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:15:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:15:20: 10000000 INFO @ Sun, 21 Jun 2020 22:15:20: 5000000 INFO @ Sun, 21 Jun 2020 22:15:26: 11000000 INFO @ Sun, 21 Jun 2020 22:15:26: 6000000 INFO @ Sun, 21 Jun 2020 22:15:32: 12000000 INFO @ Sun, 21 Jun 2020 22:15:32: 7000000 INFO @ Sun, 21 Jun 2020 22:15:38: 13000000 INFO @ Sun, 21 Jun 2020 22:15:39: 8000000 INFO @ Sun, 21 Jun 2020 22:15:44: 14000000 INFO @ Sun, 21 Jun 2020 22:15:45: 9000000 INFO @ Sun, 21 Jun 2020 22:15:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:15:47: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:15:47: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:15:47: #1 total tags in treatment: 14389565 INFO @ Sun, 21 Jun 2020 22:15:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:15:47: #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 22:15:47: #1 tags after filtering in treatment: 14389537 INFO @ Sun, 21 Jun 2020 22:15:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:15:47: #1 finished! INFO @ Sun, 21 Jun 2020 22:15:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:15:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:15:48: #2 number of paired peaks: 1377 INFO @ Sun, 21 Jun 2020 22:15:48: start model_add_line... INFO @ Sun, 21 Jun 2020 22:15:49: start X-correlation... INFO @ Sun, 21 Jun 2020 22:15:49: end of X-cor INFO @ Sun, 21 Jun 2020 22:15:49: #2 finished! INFO @ Sun, 21 Jun 2020 22:15:49: #2 predicted fragment length is 134 bps INFO @ Sun, 21 Jun 2020 22:15:49: #2 alternative fragment length(s) may be 134 bps INFO @ Sun, 21 Jun 2020 22:15:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.10_model.r INFO @ Sun, 21 Jun 2020 22:15:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:15:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:15:51: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:15:57: 11000000 INFO @ Sun, 21 Jun 2020 22:16:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:16:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:16:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.05_summits.bed INFO @ Sun, 21 Jun 2020 22:16:01: Done! pass1 - making usageList (730 chroms): 1 millis pass2 - checking and writing primary data (5100 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:16:03: 12000000 INFO @ Sun, 21 Jun 2020 22:16:08: 13000000 INFO @ Sun, 21 Jun 2020 22:16:14: 14000000 INFO @ Sun, 21 Jun 2020 22:16:17: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:16:17: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:16:17: #1 total tags in treatment: 14389565 INFO @ Sun, 21 Jun 2020 22:16:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:16:17: #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 22:16:17: #1 tags after filtering in treatment: 14389537 INFO @ Sun, 21 Jun 2020 22:16:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:16:17: #1 finished! INFO @ Sun, 21 Jun 2020 22:16:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:16:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:16:18: #2 number of paired peaks: 1377 INFO @ Sun, 21 Jun 2020 22:16:18: start model_add_line... INFO @ Sun, 21 Jun 2020 22:16:18: start X-correlation... INFO @ Sun, 21 Jun 2020 22:16:18: end of X-cor INFO @ Sun, 21 Jun 2020 22:16:18: #2 finished! INFO @ Sun, 21 Jun 2020 22:16:18: #2 predicted fragment length is 134 bps INFO @ Sun, 21 Jun 2020 22:16:18: #2 alternative fragment length(s) may be 134 bps INFO @ Sun, 21 Jun 2020 22:16:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.20_model.r INFO @ Sun, 21 Jun 2020 22:16:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:16:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:16:22: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:16:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:16:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:16:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.10_summits.bed INFO @ Sun, 21 Jun 2020 22:16:36: Done! pass1 - making usageList (637 chroms): 2 millis pass2 - checking and writing primary data (3292 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:16:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:17:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:17:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:17:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386725/SRX6386725.20_summits.bed INFO @ Sun, 21 Jun 2020 22:17:03: Done! pass1 - making usageList (548 chroms): 1 millis pass2 - checking and writing primary data (2123 records, 4 fields): 16 millis CompletedMACS2peakCalling