Job ID = 6459076 SRX = SRX6386753 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:55:25 prefetch.2.10.7: 1) Downloading 'SRR9624485'... 2020-06-21T12:55:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:00:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:00:22 prefetch.2.10.7: 1) 'SRR9624485' was downloaded successfully Read 27925816 spots for SRR9624485/SRR9624485.sra Written 27925816 spots for SRR9624485/SRR9624485.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: 00:06:56 27925816 reads; of these: 27925816 (100.00%) were unpaired; of these: 3972401 (14.22%) aligned 0 times 17747252 (63.55%) aligned exactly 1 time 6206163 (22.22%) aligned >1 times 85.78% overall alignment rate Time searching: 00:06:56 Overall time: 00:06:56 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] 10893734 / 23953415 = 0.4548 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 22:14:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.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 22:14:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:14:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:14:06: 1000000 INFO @ Sun, 21 Jun 2020 22:14:11: 2000000 INFO @ Sun, 21 Jun 2020 22:14:16: 3000000 INFO @ Sun, 21 Jun 2020 22:14:21: 4000000 INFO @ Sun, 21 Jun 2020 22:14:26: 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 22:14:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.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 22:14:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:14:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:14:31: 6000000 INFO @ Sun, 21 Jun 2020 22:14:36: 1000000 INFO @ Sun, 21 Jun 2020 22:14:36: 7000000 INFO @ Sun, 21 Jun 2020 22:14:41: 2000000 INFO @ Sun, 21 Jun 2020 22:14:42: 8000000 INFO @ Sun, 21 Jun 2020 22:14:47: 3000000 INFO @ Sun, 21 Jun 2020 22:14:47: 9000000 INFO @ Sun, 21 Jun 2020 22:14:52: 4000000 INFO @ Sun, 21 Jun 2020 22:14:53: 10000000 INFO @ Sun, 21 Jun 2020 22:14:57: 5000000 INFO @ Sun, 21 Jun 2020 22:14:58: 11000000 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 22:15:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.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 22:15:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:15:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:15:03: 6000000 INFO @ Sun, 21 Jun 2020 22:15:04: 12000000 INFO @ Sun, 21 Jun 2020 22:15:08: 7000000 INFO @ Sun, 21 Jun 2020 22:15:09: 1000000 INFO @ Sun, 21 Jun 2020 22:15:10: 13000000 INFO @ Sun, 21 Jun 2020 22:15:10: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:15:10: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:15:10: #1 total tags in treatment: 13059681 INFO @ Sun, 21 Jun 2020 22:15:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:15:10: #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 22:15:11: #1 tags after filtering in treatment: 13059669 INFO @ Sun, 21 Jun 2020 22:15:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:15:11: #1 finished! INFO @ Sun, 21 Jun 2020 22:15:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:15:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:15:12: #2 number of paired peaks: 1435 INFO @ Sun, 21 Jun 2020 22:15:12: start model_add_line... INFO @ Sun, 21 Jun 2020 22:15:12: start X-correlation... INFO @ Sun, 21 Jun 2020 22:15:12: end of X-cor INFO @ Sun, 21 Jun 2020 22:15:12: #2 finished! INFO @ Sun, 21 Jun 2020 22:15:12: #2 predicted fragment length is 114 bps INFO @ Sun, 21 Jun 2020 22:15:12: #2 alternative fragment length(s) may be 4,114 bps INFO @ Sun, 21 Jun 2020 22:15:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.05_model.r INFO @ Sun, 21 Jun 2020 22:15:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:15:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:15:14: 8000000 INFO @ Sun, 21 Jun 2020 22:15:15: 2000000 INFO @ Sun, 21 Jun 2020 22:15:19: 9000000 INFO @ Sun, 21 Jun 2020 22:15:22: 3000000 INFO @ Sun, 21 Jun 2020 22:15:25: 10000000 INFO @ Sun, 21 Jun 2020 22:15:29: 4000000 INFO @ Sun, 21 Jun 2020 22:15:31: 11000000 INFO @ Sun, 21 Jun 2020 22:15:36: 5000000 INFO @ Sun, 21 Jun 2020 22:15:36: 12000000 INFO @ Sun, 21 Jun 2020 22:15:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:15:42: 13000000 INFO @ Sun, 21 Jun 2020 22:15:42: 6000000 INFO @ Sun, 21 Jun 2020 22:15:43: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:15:43: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:15:43: #1 total tags in treatment: 13059681 INFO @ Sun, 21 Jun 2020 22:15:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:15:43: #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 22:15:43: #1 tags after filtering in treatment: 13059669 INFO @ Sun, 21 Jun 2020 22:15:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:15:43: #1 finished! INFO @ Sun, 21 Jun 2020 22:15:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:15:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:15:44: #2 number of paired peaks: 1435 INFO @ Sun, 21 Jun 2020 22:15:44: start model_add_line... INFO @ Sun, 21 Jun 2020 22:15:44: start X-correlation... INFO @ Sun, 21 Jun 2020 22:15:44: end of X-cor INFO @ Sun, 21 Jun 2020 22:15:44: #2 finished! INFO @ Sun, 21 Jun 2020 22:15:44: #2 predicted fragment length is 114 bps INFO @ Sun, 21 Jun 2020 22:15:44: #2 alternative fragment length(s) may be 4,114 bps INFO @ Sun, 21 Jun 2020 22:15:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.10_model.r INFO @ Sun, 21 Jun 2020 22:15:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:15:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:15:49: 7000000 INFO @ Sun, 21 Jun 2020 22:15:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:15:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:15:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.05_summits.bed INFO @ Sun, 21 Jun 2020 22:15:55: Done! INFO @ Sun, 21 Jun 2020 22:15:55: 8000000 pass1 - making usageList (764 chroms): 2 millis pass2 - checking and writing primary data (4451 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:16:02: 9000000 INFO @ Sun, 21 Jun 2020 22:16:08: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:16:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:16:15: 11000000 INFO @ Sun, 21 Jun 2020 22:16:21: 12000000 INFO @ Sun, 21 Jun 2020 22:16:28: 13000000 INFO @ Sun, 21 Jun 2020 22:16:28: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:16:28: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:16:28: #1 total tags in treatment: 13059681 INFO @ Sun, 21 Jun 2020 22:16:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:16:28: #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 22:16:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:16:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:16:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.10_summits.bed INFO @ Sun, 21 Jun 2020 22:16:28: Done! pass1 - making usageList (647 chroms): 1 millis pass2 - checking and writing primary data (2832 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:16:29: #1 tags after filtering in treatment: 13059669 INFO @ Sun, 21 Jun 2020 22:16:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:16:29: #1 finished! INFO @ Sun, 21 Jun 2020 22:16:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:16:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:16:30: #2 number of paired peaks: 1435 INFO @ Sun, 21 Jun 2020 22:16:30: start model_add_line... INFO @ Sun, 21 Jun 2020 22:16:30: start X-correlation... INFO @ Sun, 21 Jun 2020 22:16:30: end of X-cor INFO @ Sun, 21 Jun 2020 22:16:30: #2 finished! INFO @ Sun, 21 Jun 2020 22:16:30: #2 predicted fragment length is 114 bps INFO @ Sun, 21 Jun 2020 22:16:30: #2 alternative fragment length(s) may be 4,114 bps INFO @ Sun, 21 Jun 2020 22:16:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.20_model.r INFO @ Sun, 21 Jun 2020 22:16:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:16:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:17:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:17:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:17:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:17:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386753/SRX6386753.20_summits.bed INFO @ Sun, 21 Jun 2020 22:17:15: Done! pass1 - making usageList (546 chroms): 2 millis pass2 - checking and writing primary data (1847 records, 4 fields): 17 millis CompletedMACS2peakCalling