Job ID = 6455255 SRX = SRX287596 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:58:25 prefetch.2.10.7: 1) Downloading 'SRR869739'... 2020-06-21T09:58:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:01:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:01:15 prefetch.2.10.7: 1) 'SRR869739' was downloaded successfully Read 17238699 spots for SRR869739/SRR869739.sra Written 17238699 spots for SRR869739/SRR869739.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: 00:04:44 17238699 reads; of these: 17238699 (100.00%) were unpaired; of these: 1189767 (6.90%) aligned 0 times 13347926 (77.43%) aligned exactly 1 time 2701006 (15.67%) aligned >1 times 93.10% overall alignment rate Time searching: 00:04:44 Overall time: 00:04:44 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 8 files... [bam_rmdupse_core] 7014108 / 16048932 = 0.4370 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 19:10:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.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 19:10:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:10:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:10:49: 1000000 INFO @ Sun, 21 Jun 2020 19:10:55: 2000000 INFO @ Sun, 21 Jun 2020 19:11:01: 3000000 INFO @ Sun, 21 Jun 2020 19:11:07: 4000000 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 19:11:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.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 19:11:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:11:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:11:13: 5000000 INFO @ Sun, 21 Jun 2020 19:11:20: 1000000 INFO @ Sun, 21 Jun 2020 19:11:20: 6000000 INFO @ Sun, 21 Jun 2020 19:11:26: 2000000 INFO @ Sun, 21 Jun 2020 19:11:27: 7000000 INFO @ Sun, 21 Jun 2020 19:11:33: 3000000 INFO @ Sun, 21 Jun 2020 19:11:34: 8000000 INFO @ Sun, 21 Jun 2020 19:11:40: 4000000 INFO @ Sun, 21 Jun 2020 19:11:41: 9000000 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 19:11:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:11:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:11:41: #1 total tags in treatment: 9034824 INFO @ Sun, 21 Jun 2020 19:11:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:11:41: #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 19:11:42: #1 tags after filtering in treatment: 9034809 INFO @ Sun, 21 Jun 2020 19:11:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:11:42: #1 finished! INFO @ Sun, 21 Jun 2020 19:11:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:11:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:11:43: #2 number of paired peaks: 5809 INFO @ Sun, 21 Jun 2020 19:11:43: start model_add_line... INFO @ Sun, 21 Jun 2020 19:11:43: start X-correlation... INFO @ Sun, 21 Jun 2020 19:11:43: end of X-cor INFO @ Sun, 21 Jun 2020 19:11:43: #2 finished! INFO @ Sun, 21 Jun 2020 19:11:43: #2 predicted fragment length is 198 bps INFO @ Sun, 21 Jun 2020 19:11:43: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 21 Jun 2020 19:11:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.05_model.r INFO @ Sun, 21 Jun 2020 19:11:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.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 19:11:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:11:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:11:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:11:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:11:46: 5000000 INFO @ Sun, 21 Jun 2020 19:11:50: 1000000 INFO @ Sun, 21 Jun 2020 19:11:53: 6000000 INFO @ Sun, 21 Jun 2020 19:11:57: 2000000 INFO @ Sun, 21 Jun 2020 19:12:00: 7000000 INFO @ Sun, 21 Jun 2020 19:12:03: 3000000 INFO @ Sun, 21 Jun 2020 19:12:07: 8000000 INFO @ Sun, 21 Jun 2020 19:12:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:12:10: 4000000 INFO @ Sun, 21 Jun 2020 19:12:14: 9000000 INFO @ Sun, 21 Jun 2020 19:12:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:12:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:12:14: #1 total tags in treatment: 9034824 INFO @ Sun, 21 Jun 2020 19:12:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:12:14: #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 19:12:15: #1 tags after filtering in treatment: 9034809 INFO @ Sun, 21 Jun 2020 19:12:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:12:15: #1 finished! INFO @ Sun, 21 Jun 2020 19:12:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:12:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:12:16: #2 number of paired peaks: 5809 INFO @ Sun, 21 Jun 2020 19:12:16: start model_add_line... INFO @ Sun, 21 Jun 2020 19:12:16: start X-correlation... INFO @ Sun, 21 Jun 2020 19:12:16: end of X-cor INFO @ Sun, 21 Jun 2020 19:12:16: #2 finished! INFO @ Sun, 21 Jun 2020 19:12:16: #2 predicted fragment length is 198 bps INFO @ Sun, 21 Jun 2020 19:12:16: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 21 Jun 2020 19:12:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.10_model.r INFO @ Sun, 21 Jun 2020 19:12:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:12:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:12:17: 5000000 INFO @ Sun, 21 Jun 2020 19:12:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:12:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:12:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.05_summits.bed INFO @ Sun, 21 Jun 2020 19:12:21: Done! pass1 - making usageList (558 chroms): 2 millis pass2 - checking and writing primary data (10107 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:12:23: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:12:29: 7000000 INFO @ Sun, 21 Jun 2020 19:12:36: 8000000 INFO @ Sun, 21 Jun 2020 19:12:42: 9000000 INFO @ Sun, 21 Jun 2020 19:12:42: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:12:42: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:12:42: #1 total tags in treatment: 9034824 INFO @ Sun, 21 Jun 2020 19:12:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:12:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:12:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:12:43: #1 tags after filtering in treatment: 9034809 INFO @ Sun, 21 Jun 2020 19:12:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:12:43: #1 finished! INFO @ Sun, 21 Jun 2020 19:12:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:12:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:12:44: #2 number of paired peaks: 5809 INFO @ Sun, 21 Jun 2020 19:12:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:12:44: start X-correlation... INFO @ Sun, 21 Jun 2020 19:12:44: end of X-cor INFO @ Sun, 21 Jun 2020 19:12:44: #2 finished! INFO @ Sun, 21 Jun 2020 19:12:44: #2 predicted fragment length is 198 bps INFO @ Sun, 21 Jun 2020 19:12:44: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 21 Jun 2020 19:12:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.20_model.r INFO @ Sun, 21 Jun 2020 19:12:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:12:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:12:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:12:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:12:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.10_summits.bed INFO @ Sun, 21 Jun 2020 19:12:53: Done! pass1 - making usageList (471 chroms): 2 millis pass2 - checking and writing primary data (8490 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:13:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:13:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:13:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:13:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287596/SRX287596.20_summits.bed INFO @ Sun, 21 Jun 2020 19:13:21: Done! pass1 - making usageList (236 chroms): 2 millis pass2 - checking and writing primary data (6365 records, 4 fields): 14 millis CompletedMACS2peakCalling