Job ID = 14167131 SRX = SRX11016835 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2021-12-10T01:16:45 prefetch.2.10.7: 1) Downloading 'SRR14678415'... 2021-12-10T01:16:45 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T01:16:53 prefetch.2.10.7: HTTPS download succeed 2021-12-10T01:16:53 prefetch.2.10.7: 1) 'SRR14678415' was downloaded successfully 2021-12-10T01:16:53 prefetch.2.10.7: 'SRR14678415' has 0 unresolved dependencies Read 22858127 spots for SRR14678415/SRR14678415.sra Written 22858127 spots for SRR14678415/SRR14678415.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167588 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:06 22858127 reads; of these: 22858127 (100.00%) were unpaired; of these: 1461978 (6.40%) aligned 0 times 18780918 (82.16%) aligned exactly 1 time 2615231 (11.44%) aligned >1 times 93.60% overall alignment rate Time searching: 00:07:06 Overall time: 00:07:06 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 12238415 / 21396149 = 0.5720 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 10:29:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.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 @ Fri, 10 Dec 2021 10:29:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:29:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:29:30: 1000000 INFO @ Fri, 10 Dec 2021 10:29:35: 2000000 INFO @ Fri, 10 Dec 2021 10:29:39: 3000000 INFO @ Fri, 10 Dec 2021 10:29:44: 4000000 INFO @ Fri, 10 Dec 2021 10:29:49: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 10:29:54: 6000000 INFO @ Fri, 10 Dec 2021 10:29:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.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 @ Fri, 10 Dec 2021 10:29:55: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:29:55: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:29:59: 7000000 INFO @ Fri, 10 Dec 2021 10:29:59: 1000000 INFO @ Fri, 10 Dec 2021 10:30:04: 8000000 INFO @ Fri, 10 Dec 2021 10:30:04: 2000000 INFO @ Fri, 10 Dec 2021 10:30:08: 9000000 INFO @ Fri, 10 Dec 2021 10:30:09: #1 tag size is determined as 76 bps INFO @ Fri, 10 Dec 2021 10:30:09: #1 tag size = 76 INFO @ Fri, 10 Dec 2021 10:30:09: #1 total tags in treatment: 9157734 INFO @ Fri, 10 Dec 2021 10:30:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:30:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:30:09: 3000000 INFO @ Fri, 10 Dec 2021 10:30:09: #1 tags after filtering in treatment: 9157734 INFO @ Fri, 10 Dec 2021 10:30:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:30:09: #1 finished! INFO @ Fri, 10 Dec 2021 10:30:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:30:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:30:10: #2 number of paired peaks: 2950 INFO @ Fri, 10 Dec 2021 10:30:10: start model_add_line... INFO @ Fri, 10 Dec 2021 10:30:10: start X-correlation... INFO @ Fri, 10 Dec 2021 10:30:10: end of X-cor INFO @ Fri, 10 Dec 2021 10:30:10: #2 finished! INFO @ Fri, 10 Dec 2021 10:30:10: #2 predicted fragment length is 223 bps INFO @ Fri, 10 Dec 2021 10:30:10: #2 alternative fragment length(s) may be 223 bps INFO @ Fri, 10 Dec 2021 10:30:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.05_model.r INFO @ Fri, 10 Dec 2021 10:30:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:30:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:30:14: 4000000 INFO @ Fri, 10 Dec 2021 10:30:19: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 10:30:23: 6000000 INFO @ Fri, 10 Dec 2021 10:30:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.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 @ Fri, 10 Dec 2021 10:30:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:30:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:30:28: 7000000 INFO @ Fri, 10 Dec 2021 10:30:30: 1000000 INFO @ Fri, 10 Dec 2021 10:30:33: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:30:33: 8000000 INFO @ Fri, 10 Dec 2021 10:30:36: 2000000 INFO @ Fri, 10 Dec 2021 10:30:38: 9000000 INFO @ Fri, 10 Dec 2021 10:30:39: #1 tag size is determined as 76 bps INFO @ Fri, 10 Dec 2021 10:30:39: #1 tag size = 76 INFO @ Fri, 10 Dec 2021 10:30:39: #1 total tags in treatment: 9157734 INFO @ Fri, 10 Dec 2021 10:30:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:30:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:30:39: #1 tags after filtering in treatment: 9157734 INFO @ Fri, 10 Dec 2021 10:30:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:30:39: #1 finished! INFO @ Fri, 10 Dec 2021 10:30:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:30:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:30:40: #2 number of paired peaks: 2950 INFO @ Fri, 10 Dec 2021 10:30:40: start model_add_line... INFO @ Fri, 10 Dec 2021 10:30:40: start X-correlation... INFO @ Fri, 10 Dec 2021 10:30:40: end of X-cor INFO @ Fri, 10 Dec 2021 10:30:40: #2 finished! INFO @ Fri, 10 Dec 2021 10:30:40: #2 predicted fragment length is 223 bps INFO @ Fri, 10 Dec 2021 10:30:40: #2 alternative fragment length(s) may be 223 bps INFO @ Fri, 10 Dec 2021 10:30:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.10_model.r INFO @ Fri, 10 Dec 2021 10:30:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:30:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:30:42: 3000000 INFO @ Fri, 10 Dec 2021 10:30:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:30:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:30:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.05_summits.bed INFO @ Fri, 10 Dec 2021 10:30:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7285 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:30:47: 4000000 INFO @ Fri, 10 Dec 2021 10:30:53: 5000000 INFO @ Fri, 10 Dec 2021 10:30:58: 6000000 INFO @ Fri, 10 Dec 2021 10:31:02: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:31:04: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:31:09: 8000000 INFO @ Fri, 10 Dec 2021 10:31:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:31:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:31:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.10_summits.bed INFO @ Fri, 10 Dec 2021 10:31:12: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4758 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:31:15: 9000000 INFO @ Fri, 10 Dec 2021 10:31:16: #1 tag size is determined as 76 bps INFO @ Fri, 10 Dec 2021 10:31:16: #1 tag size = 76 INFO @ Fri, 10 Dec 2021 10:31:16: #1 total tags in treatment: 9157734 INFO @ Fri, 10 Dec 2021 10:31:16: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:31:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:31:16: #1 tags after filtering in treatment: 9157734 INFO @ Fri, 10 Dec 2021 10:31:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:31:16: #1 finished! INFO @ Fri, 10 Dec 2021 10:31:16: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:31:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:31:17: #2 number of paired peaks: 2950 INFO @ Fri, 10 Dec 2021 10:31:17: start model_add_line... INFO @ Fri, 10 Dec 2021 10:31:17: start X-correlation... INFO @ Fri, 10 Dec 2021 10:31:17: end of X-cor INFO @ Fri, 10 Dec 2021 10:31:17: #2 finished! INFO @ Fri, 10 Dec 2021 10:31:17: #2 predicted fragment length is 223 bps INFO @ Fri, 10 Dec 2021 10:31:17: #2 alternative fragment length(s) may be 223 bps INFO @ Fri, 10 Dec 2021 10:31:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.20_model.r INFO @ Fri, 10 Dec 2021 10:31:17: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:31:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:31:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:31:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:31:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:31:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11016835/SRX11016835.20_summits.bed INFO @ Fri, 10 Dec 2021 10:31:50: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2387 records, 4 fields): 4 millis CompletedMACS2peakCalling