Job ID = 6458307 SRX = SRX5011060 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:28:07 prefetch.2.10.7: 1) Downloading 'SRR8191509'... 2020-06-21T12:28:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:31:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:31:16 prefetch.2.10.7: 1) 'SRR8191509' was downloaded successfully 2020-06-21T12:31:16 prefetch.2.10.7: 'SRR8191509' has 0 unresolved dependencies Read 35673391 spots for SRR8191509/SRR8191509.sra Written 35673391 spots for SRR8191509/SRR8191509.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: 00:07:31 35673391 reads; of these: 35673391 (100.00%) were unpaired; of these: 5407567 (15.16%) aligned 0 times 25748507 (72.18%) aligned exactly 1 time 4517317 (12.66%) aligned >1 times 84.84% overall alignment rate Time searching: 00:07:31 Overall time: 00:07:31 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] 15700233 / 30265824 = 0.5187 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 21:45:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.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 21:45:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:45:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:45:16: 1000000 INFO @ Sun, 21 Jun 2020 21:45:22: 2000000 INFO @ Sun, 21 Jun 2020 21:45:29: 3000000 INFO @ Sun, 21 Jun 2020 21:45:35: 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 21:45:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.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 21:45:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:45:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:45:41: 5000000 INFO @ Sun, 21 Jun 2020 21:45:47: 1000000 INFO @ Sun, 21 Jun 2020 21:45:48: 6000000 INFO @ Sun, 21 Jun 2020 21:45:54: 2000000 INFO @ Sun, 21 Jun 2020 21:45:55: 7000000 INFO @ Sun, 21 Jun 2020 21:46:01: 3000000 INFO @ Sun, 21 Jun 2020 21:46:01: 8000000 INFO @ Sun, 21 Jun 2020 21:46:08: 4000000 INFO @ Sun, 21 Jun 2020 21:46:08: 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 21:46:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.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 21:46:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:46:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:46:15: 10000000 INFO @ Sun, 21 Jun 2020 21:46:15: 5000000 INFO @ Sun, 21 Jun 2020 21:46:17: 1000000 INFO @ Sun, 21 Jun 2020 21:46:21: 11000000 INFO @ Sun, 21 Jun 2020 21:46:22: 6000000 INFO @ Sun, 21 Jun 2020 21:46:24: 2000000 INFO @ Sun, 21 Jun 2020 21:46:28: 12000000 INFO @ Sun, 21 Jun 2020 21:46:29: 7000000 INFO @ Sun, 21 Jun 2020 21:46:30: 3000000 INFO @ Sun, 21 Jun 2020 21:46:35: 13000000 INFO @ Sun, 21 Jun 2020 21:46:36: 8000000 INFO @ Sun, 21 Jun 2020 21:46:37: 4000000 INFO @ Sun, 21 Jun 2020 21:46:42: 14000000 INFO @ Sun, 21 Jun 2020 21:46:43: 9000000 INFO @ Sun, 21 Jun 2020 21:46:44: 5000000 INFO @ Sun, 21 Jun 2020 21:46:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:46:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:46:46: #1 total tags in treatment: 14565591 INFO @ Sun, 21 Jun 2020 21:46:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:46:46: #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 21:46:46: #1 tags after filtering in treatment: 14565479 INFO @ Sun, 21 Jun 2020 21:46:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:46:46: #1 finished! INFO @ Sun, 21 Jun 2020 21:46:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:46:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:46:48: #2 number of paired peaks: 6186 INFO @ Sun, 21 Jun 2020 21:46:48: start model_add_line... INFO @ Sun, 21 Jun 2020 21:46:48: start X-correlation... INFO @ Sun, 21 Jun 2020 21:46:48: end of X-cor INFO @ Sun, 21 Jun 2020 21:46:48: #2 finished! INFO @ Sun, 21 Jun 2020 21:46:48: #2 predicted fragment length is 269 bps INFO @ Sun, 21 Jun 2020 21:46:48: #2 alternative fragment length(s) may be 269 bps INFO @ Sun, 21 Jun 2020 21:46:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.05_model.r INFO @ Sun, 21 Jun 2020 21:46:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:46:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:46:49: 10000000 INFO @ Sun, 21 Jun 2020 21:46:51: 6000000 INFO @ Sun, 21 Jun 2020 21:46:56: 11000000 INFO @ Sun, 21 Jun 2020 21:46:58: 7000000 INFO @ Sun, 21 Jun 2020 21:47:03: 12000000 INFO @ Sun, 21 Jun 2020 21:47:04: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:47:10: 13000000 INFO @ Sun, 21 Jun 2020 21:47:11: 9000000 INFO @ Sun, 21 Jun 2020 21:47:17: 14000000 INFO @ Sun, 21 Jun 2020 21:47:18: 10000000 INFO @ Sun, 21 Jun 2020 21:47:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:47:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:47:21: #1 total tags in treatment: 14565591 INFO @ Sun, 21 Jun 2020 21:47:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:47:21: #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 21:47:21: #1 tags after filtering in treatment: 14565479 INFO @ Sun, 21 Jun 2020 21:47:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:47:21: #1 finished! INFO @ Sun, 21 Jun 2020 21:47:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:47:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:47:22: #2 number of paired peaks: 6186 INFO @ Sun, 21 Jun 2020 21:47:22: start model_add_line... INFO @ Sun, 21 Jun 2020 21:47:23: start X-correlation... INFO @ Sun, 21 Jun 2020 21:47:23: end of X-cor INFO @ Sun, 21 Jun 2020 21:47:23: #2 finished! INFO @ Sun, 21 Jun 2020 21:47:23: #2 predicted fragment length is 269 bps INFO @ Sun, 21 Jun 2020 21:47:23: #2 alternative fragment length(s) may be 269 bps INFO @ Sun, 21 Jun 2020 21:47:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.10_model.r INFO @ Sun, 21 Jun 2020 21:47:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:47:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:47:24: 11000000 INFO @ Sun, 21 Jun 2020 21:47:31: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:47:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:47:37: 13000000 INFO @ Sun, 21 Jun 2020 21:47:44: 14000000 INFO @ Sun, 21 Jun 2020 21:47:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:47:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:47:47: #1 total tags in treatment: 14565591 INFO @ Sun, 21 Jun 2020 21:47:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:47:47: #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 21:47:48: #1 tags after filtering in treatment: 14565479 INFO @ Sun, 21 Jun 2020 21:47:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:47:48: #1 finished! INFO @ Sun, 21 Jun 2020 21:47:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:47:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:47:49: #2 number of paired peaks: 6186 INFO @ Sun, 21 Jun 2020 21:47:49: start model_add_line... INFO @ Sun, 21 Jun 2020 21:47:49: start X-correlation... INFO @ Sun, 21 Jun 2020 21:47:49: end of X-cor INFO @ Sun, 21 Jun 2020 21:47:49: #2 finished! INFO @ Sun, 21 Jun 2020 21:47:49: #2 predicted fragment length is 269 bps INFO @ Sun, 21 Jun 2020 21:47:49: #2 alternative fragment length(s) may be 269 bps INFO @ Sun, 21 Jun 2020 21:47:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.20_model.r INFO @ Sun, 21 Jun 2020 21:47:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:47:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:47:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:47:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:47:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.05_summits.bed INFO @ Sun, 21 Jun 2020 21:47:54: Done! pass1 - making usageList (307 chroms): 3 millis pass2 - checking and writing primary data (12528 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:48:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:48:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:48:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:48:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.10_summits.bed INFO @ Sun, 21 Jun 2020 21:48:27: Done! pass1 - making usageList (223 chroms): 2 millis pass2 - checking and writing primary data (10010 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:48:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:48:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:48:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:48:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011060/SRX5011060.20_summits.bed INFO @ Sun, 21 Jun 2020 21:48:55: Done! pass1 - making usageList (146 chroms): 1 millis pass2 - checking and writing primary data (7366 records, 4 fields): 12 millis CompletedMACS2peakCalling