Job ID = 6458352 SRX = SRX5011093 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:38:26 prefetch.2.10.7: 1) Downloading 'SRR8191542'... 2020-06-21T12:38:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:41:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:41:56 prefetch.2.10.7: 1) 'SRR8191542' was downloaded successfully 2020-06-21T12:41:56 prefetch.2.10.7: 'SRR8191542' has 0 unresolved dependencies Read 38180841 spots for SRR8191542/SRR8191542.sra Written 38180841 spots for SRR8191542/SRR8191542.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: 00:08:47 38180841 reads; of these: 38180841 (100.00%) were unpaired; of these: 6631474 (17.37%) aligned 0 times 24134717 (63.21%) aligned exactly 1 time 7414650 (19.42%) aligned >1 times 82.63% overall alignment rate Time searching: 00:08:47 Overall time: 00:08:47 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 16 files... [bam_rmdupse_core] 21721926 / 31549367 = 0.6885 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 21:56:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.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 21:56:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:56:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:57:04: 1000000 INFO @ Sun, 21 Jun 2020 21:57:09: 2000000 INFO @ Sun, 21 Jun 2020 21:57:15: 3000000 INFO @ Sun, 21 Jun 2020 21:57:20: 4000000 INFO @ Sun, 21 Jun 2020 21:57:26: 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 21:57:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.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 21:57:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:57:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:57:31: 6000000 INFO @ Sun, 21 Jun 2020 21:57:34: 1000000 INFO @ Sun, 21 Jun 2020 21:57:37: 7000000 INFO @ Sun, 21 Jun 2020 21:57:39: 2000000 INFO @ Sun, 21 Jun 2020 21:57:43: 8000000 INFO @ Sun, 21 Jun 2020 21:57:44: 3000000 INFO @ Sun, 21 Jun 2020 21:57:48: 9000000 INFO @ Sun, 21 Jun 2020 21:57:48: 4000000 INFO @ Sun, 21 Jun 2020 21:57:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:57:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:57:53: #1 total tags in treatment: 9827441 INFO @ Sun, 21 Jun 2020 21:57:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:57:53: #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 21:57:53: 5000000 INFO @ Sun, 21 Jun 2020 21:57:54: #1 tags after filtering in treatment: 9827375 INFO @ Sun, 21 Jun 2020 21:57:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:57:54: #1 finished! INFO @ Sun, 21 Jun 2020 21:57:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:57:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:57:55: #2 number of paired peaks: 4150 INFO @ Sun, 21 Jun 2020 21:57:55: start model_add_line... INFO @ Sun, 21 Jun 2020 21:57:55: start X-correlation... INFO @ Sun, 21 Jun 2020 21:57:55: end of X-cor INFO @ Sun, 21 Jun 2020 21:57:55: #2 finished! INFO @ Sun, 21 Jun 2020 21:57:55: #2 predicted fragment length is 185 bps INFO @ Sun, 21 Jun 2020 21:57:55: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 21 Jun 2020 21:57:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.05_model.r INFO @ Sun, 21 Jun 2020 21:57:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:57:55: #3 Pre-compute pvalue-qvalue table... 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 21:57:58: 6000000 INFO @ Sun, 21 Jun 2020 21:57:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.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 21:57:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:57:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:58:03: 7000000 INFO @ Sun, 21 Jun 2020 21:58:03: 1000000 INFO @ Sun, 21 Jun 2020 21:58:08: 2000000 INFO @ Sun, 21 Jun 2020 21:58:09: 8000000 INFO @ Sun, 21 Jun 2020 21:58:13: 3000000 INFO @ Sun, 21 Jun 2020 21:58:14: 9000000 INFO @ Sun, 21 Jun 2020 21:58:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:58:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:58:18: #1 total tags in treatment: 9827441 INFO @ Sun, 21 Jun 2020 21:58:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:58:18: #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 21:58:18: 4000000 INFO @ Sun, 21 Jun 2020 21:58:18: #1 tags after filtering in treatment: 9827375 INFO @ Sun, 21 Jun 2020 21:58:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:58:18: #1 finished! INFO @ Sun, 21 Jun 2020 21:58:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:58:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:58:19: #2 number of paired peaks: 4150 INFO @ Sun, 21 Jun 2020 21:58:19: start model_add_line... INFO @ Sun, 21 Jun 2020 21:58:19: start X-correlation... INFO @ Sun, 21 Jun 2020 21:58:19: end of X-cor INFO @ Sun, 21 Jun 2020 21:58:19: #2 finished! INFO @ Sun, 21 Jun 2020 21:58:19: #2 predicted fragment length is 185 bps INFO @ Sun, 21 Jun 2020 21:58:19: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 21 Jun 2020 21:58:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.10_model.r INFO @ Sun, 21 Jun 2020 21:58:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:58:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:58:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:58:23: 5000000 INFO @ Sun, 21 Jun 2020 21:58:28: 6000000 INFO @ Sun, 21 Jun 2020 21:58:32: 7000000 INFO @ Sun, 21 Jun 2020 21:58:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:58:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:58:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.05_summits.bed INFO @ Sun, 21 Jun 2020 21:58:33: Done! pass1 - making usageList (818 chroms): 1 millis pass2 - checking and writing primary data (7563 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:58:38: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:58:42: 9000000 INFO @ Sun, 21 Jun 2020 21:58:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:58:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:58:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:58:47: #1 total tags in treatment: 9827441 INFO @ Sun, 21 Jun 2020 21:58:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:58:47: #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 21:58:47: #1 tags after filtering in treatment: 9827375 INFO @ Sun, 21 Jun 2020 21:58:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:58:47: #1 finished! INFO @ Sun, 21 Jun 2020 21:58:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:58:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:58:48: #2 number of paired peaks: 4150 INFO @ Sun, 21 Jun 2020 21:58:48: start model_add_line... INFO @ Sun, 21 Jun 2020 21:58:48: start X-correlation... INFO @ Sun, 21 Jun 2020 21:58:48: end of X-cor INFO @ Sun, 21 Jun 2020 21:58:48: #2 finished! INFO @ Sun, 21 Jun 2020 21:58:48: #2 predicted fragment length is 185 bps INFO @ Sun, 21 Jun 2020 21:58:48: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 21 Jun 2020 21:58:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.20_model.r INFO @ Sun, 21 Jun 2020 21:58:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:58:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:58:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:58:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:58:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.10_summits.bed INFO @ Sun, 21 Jun 2020 21:58:56: Done! pass1 - making usageList (728 chroms): 2 millis pass2 - checking and writing primary data (5262 records, 4 fields): 25 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:59:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:59:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:59:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:59:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011093/SRX5011093.20_summits.bed INFO @ Sun, 21 Jun 2020 21:59:25: Done! pass1 - making usageList (611 chroms): 1 millis pass2 - checking and writing primary data (3480 records, 4 fields): 19 millis CompletedMACS2peakCalling