Job ID = 6456065 SRX = SRX3167244 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:30:36 prefetch.2.10.7: 1) Downloading 'SRR6014247'... 2020-06-21T10:30:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:39:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:39:24 prefetch.2.10.7: 1) 'SRR6014247' was downloaded successfully Read 47702706 spots for SRR6014247/SRR6014247.sra Written 47702706 spots for SRR6014247/SRR6014247.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: 00:11:59 47702706 reads; of these: 47702706 (100.00%) were unpaired; of these: 2965808 (6.22%) aligned 0 times 35023111 (73.42%) aligned exactly 1 time 9713787 (20.36%) aligned >1 times 93.78% overall alignment rate Time searching: 00:12:00 Overall time: 00:12:00 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 20 files... [bam_rmdupse_core] 35473078 / 44736898 = 0.7929 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 20:01:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.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 20:01:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:01:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:01:23: 1000000 INFO @ Sun, 21 Jun 2020 20:01:28: 2000000 INFO @ Sun, 21 Jun 2020 20:01:33: 3000000 INFO @ Sun, 21 Jun 2020 20:01:38: 4000000 INFO @ Sun, 21 Jun 2020 20:01:43: 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 20:01:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.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 20:01:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:01:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:01:48: 6000000 INFO @ Sun, 21 Jun 2020 20:01:53: 1000000 INFO @ Sun, 21 Jun 2020 20:01:53: 7000000 INFO @ Sun, 21 Jun 2020 20:01:58: 2000000 INFO @ Sun, 21 Jun 2020 20:01:59: 8000000 INFO @ Sun, 21 Jun 2020 20:02:03: 3000000 INFO @ Sun, 21 Jun 2020 20:02:04: 9000000 INFO @ Sun, 21 Jun 2020 20:02:06: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:02:06: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:02:06: #1 total tags in treatment: 9263820 INFO @ Sun, 21 Jun 2020 20:02:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:02:06: #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 20:02:06: #1 tags after filtering in treatment: 9263751 INFO @ Sun, 21 Jun 2020 20:02:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:02:06: #1 finished! INFO @ Sun, 21 Jun 2020 20:02:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:02:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:02:07: #2 number of paired peaks: 3818 INFO @ Sun, 21 Jun 2020 20:02:07: start model_add_line... INFO @ Sun, 21 Jun 2020 20:02:07: start X-correlation... INFO @ Sun, 21 Jun 2020 20:02:07: end of X-cor INFO @ Sun, 21 Jun 2020 20:02:07: #2 finished! INFO @ Sun, 21 Jun 2020 20:02:07: #2 predicted fragment length is 125 bps INFO @ Sun, 21 Jun 2020 20:02:07: #2 alternative fragment length(s) may be 4,125 bps INFO @ Sun, 21 Jun 2020 20:02:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.05_model.r INFO @ Sun, 21 Jun 2020 20:02:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:02:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:02:09: 4000000 INFO @ Sun, 21 Jun 2020 20:02:14: 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 20:02:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.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 20:02:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:02:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:02:19: 6000000 INFO @ Sun, 21 Jun 2020 20:02:23: 1000000 INFO @ Sun, 21 Jun 2020 20:02:25: 7000000 INFO @ Sun, 21 Jun 2020 20:02:28: 2000000 INFO @ Sun, 21 Jun 2020 20:02:30: 8000000 INFO @ Sun, 21 Jun 2020 20:02:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:02:33: 3000000 INFO @ Sun, 21 Jun 2020 20:02:35: 9000000 INFO @ Sun, 21 Jun 2020 20:02:37: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:02:37: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:02:37: #1 total tags in treatment: 9263820 INFO @ Sun, 21 Jun 2020 20:02:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:02:37: #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 20:02:37: #1 tags after filtering in treatment: 9263751 INFO @ Sun, 21 Jun 2020 20:02:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:02:37: #1 finished! INFO @ Sun, 21 Jun 2020 20:02:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:02:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:02:38: #2 number of paired peaks: 3818 INFO @ Sun, 21 Jun 2020 20:02:38: start model_add_line... INFO @ Sun, 21 Jun 2020 20:02:38: start X-correlation... INFO @ Sun, 21 Jun 2020 20:02:38: end of X-cor INFO @ Sun, 21 Jun 2020 20:02:38: #2 finished! INFO @ Sun, 21 Jun 2020 20:02:38: #2 predicted fragment length is 125 bps INFO @ Sun, 21 Jun 2020 20:02:38: #2 alternative fragment length(s) may be 4,125 bps INFO @ Sun, 21 Jun 2020 20:02:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.10_model.r INFO @ Sun, 21 Jun 2020 20:02:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:02:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:02:39: 4000000 INFO @ Sun, 21 Jun 2020 20:02:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:02:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:02:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.05_summits.bed INFO @ Sun, 21 Jun 2020 20:02:41: Done! pass1 - making usageList (907 chroms): 2 millis pass2 - checking and writing primary data (4868 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:02:44: 5000000 INFO @ Sun, 21 Jun 2020 20:02:49: 6000000 INFO @ Sun, 21 Jun 2020 20:02:54: 7000000 INFO @ Sun, 21 Jun 2020 20:03:00: 8000000 INFO @ Sun, 21 Jun 2020 20:03:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:03:05: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:03:06: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:03:06: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:03:06: #1 total tags in treatment: 9263820 INFO @ Sun, 21 Jun 2020 20:03:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:03:06: #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 20:03:07: #1 tags after filtering in treatment: 9263751 INFO @ Sun, 21 Jun 2020 20:03:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:03:07: #1 finished! INFO @ Sun, 21 Jun 2020 20:03:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:03:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:03:08: #2 number of paired peaks: 3818 INFO @ Sun, 21 Jun 2020 20:03:08: start model_add_line... INFO @ Sun, 21 Jun 2020 20:03:08: start X-correlation... INFO @ Sun, 21 Jun 2020 20:03:08: end of X-cor INFO @ Sun, 21 Jun 2020 20:03:08: #2 finished! INFO @ Sun, 21 Jun 2020 20:03:08: #2 predicted fragment length is 125 bps INFO @ Sun, 21 Jun 2020 20:03:08: #2 alternative fragment length(s) may be 4,125 bps INFO @ Sun, 21 Jun 2020 20:03:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.20_model.r INFO @ Sun, 21 Jun 2020 20:03:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:03:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:03:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:03:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:03:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.10_summits.bed INFO @ Sun, 21 Jun 2020 20:03:10: Done! pass1 - making usageList (784 chroms): 2 millis pass2 - checking and writing primary data (2999 records, 4 fields): 22 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:03:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:03:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:03:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:03:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167244/SRX3167244.20_summits.bed INFO @ Sun, 21 Jun 2020 20:03:40: Done! pass1 - making usageList (652 chroms): 1 millis pass2 - checking and writing primary data (1763 records, 4 fields): 18 millis CompletedMACS2peakCalling