Job ID = 6455331 SRX = SRX287700 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:07:36 prefetch.2.10.7: 1) Downloading 'SRR869888'... 2020-06-21T10:07:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:10:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:10:30 prefetch.2.10.7: 1) 'SRR869888' was downloaded successfully Read 18291400 spots for SRR869888/SRR869888.sra Written 18291400 spots for SRR869888/SRR869888.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: 00:04:04 18291400 reads; of these: 18291400 (100.00%) were unpaired; of these: 1410413 (7.71%) aligned 0 times 15575889 (85.15%) aligned exactly 1 time 1305098 (7.14%) aligned >1 times 92.29% overall alignment rate Time searching: 00:04:04 Overall time: 00:04:04 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] 4233465 / 16880987 = 0.2508 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 19:19:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.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 19:19:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:19:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:19:47: 1000000 INFO @ Sun, 21 Jun 2020 19:19:52: 2000000 INFO @ Sun, 21 Jun 2020 19:19:57: 3000000 INFO @ Sun, 21 Jun 2020 19:20:02: 4000000 INFO @ Sun, 21 Jun 2020 19:20:07: 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 19:20:12: 6000000 INFO @ Sun, 21 Jun 2020 19:20:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.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 19:20:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:20:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:20:17: 7000000 INFO @ Sun, 21 Jun 2020 19:20:18: 1000000 INFO @ Sun, 21 Jun 2020 19:20:22: 8000000 INFO @ Sun, 21 Jun 2020 19:20:23: 2000000 INFO @ Sun, 21 Jun 2020 19:20:27: 9000000 INFO @ Sun, 21 Jun 2020 19:20:29: 3000000 INFO @ Sun, 21 Jun 2020 19:20:33: 10000000 INFO @ Sun, 21 Jun 2020 19:20:35: 4000000 INFO @ Sun, 21 Jun 2020 19:20:38: 11000000 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 19:20:40: 5000000 INFO @ Sun, 21 Jun 2020 19:20:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.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 19:20:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:20:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:20:43: 12000000 INFO @ Sun, 21 Jun 2020 19:20:46: 6000000 INFO @ Sun, 21 Jun 2020 19:20:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:20:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:20:47: #1 total tags in treatment: 12647522 INFO @ Sun, 21 Jun 2020 19:20:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:20:47: #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 19:20:47: 1000000 INFO @ Sun, 21 Jun 2020 19:20:48: #1 tags after filtering in treatment: 12647487 INFO @ Sun, 21 Jun 2020 19:20:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:20:48: #1 finished! INFO @ Sun, 21 Jun 2020 19:20:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:20:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:20:48: #2 number of paired peaks: 554 WARNING @ Sun, 21 Jun 2020 19:20:48: Fewer paired peaks (554) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 554 pairs to build model! INFO @ Sun, 21 Jun 2020 19:20:48: start model_add_line... INFO @ Sun, 21 Jun 2020 19:20:49: start X-correlation... INFO @ Sun, 21 Jun 2020 19:20:49: end of X-cor INFO @ Sun, 21 Jun 2020 19:20:49: #2 finished! INFO @ Sun, 21 Jun 2020 19:20:49: #2 predicted fragment length is 217 bps INFO @ Sun, 21 Jun 2020 19:20:49: #2 alternative fragment length(s) may be 217 bps INFO @ Sun, 21 Jun 2020 19:20:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.05_model.r INFO @ Sun, 21 Jun 2020 19:20:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:20:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:20:52: 7000000 INFO @ Sun, 21 Jun 2020 19:20:53: 2000000 INFO @ Sun, 21 Jun 2020 19:20:58: 8000000 INFO @ Sun, 21 Jun 2020 19:20:58: 3000000 INFO @ Sun, 21 Jun 2020 19:21:03: 4000000 INFO @ Sun, 21 Jun 2020 19:21:03: 9000000 INFO @ Sun, 21 Jun 2020 19:21:08: 5000000 INFO @ Sun, 21 Jun 2020 19:21:09: 10000000 INFO @ Sun, 21 Jun 2020 19:21:14: 6000000 INFO @ Sun, 21 Jun 2020 19:21:16: 11000000 INFO @ Sun, 21 Jun 2020 19:21:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:21:19: 7000000 INFO @ Sun, 21 Jun 2020 19:21:21: 12000000 INFO @ Sun, 21 Jun 2020 19:21:24: 8000000 INFO @ Sun, 21 Jun 2020 19:21:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:21:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:21:25: #1 total tags in treatment: 12647522 INFO @ Sun, 21 Jun 2020 19:21:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:21:25: #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 19:21:26: #1 tags after filtering in treatment: 12647487 INFO @ Sun, 21 Jun 2020 19:21:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:21:26: #1 finished! INFO @ Sun, 21 Jun 2020 19:21:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:21:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:21:27: #2 number of paired peaks: 554 WARNING @ Sun, 21 Jun 2020 19:21:27: Fewer paired peaks (554) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 554 pairs to build model! INFO @ Sun, 21 Jun 2020 19:21:27: start model_add_line... INFO @ Sun, 21 Jun 2020 19:21:27: start X-correlation... INFO @ Sun, 21 Jun 2020 19:21:27: end of X-cor INFO @ Sun, 21 Jun 2020 19:21:27: #2 finished! INFO @ Sun, 21 Jun 2020 19:21:27: #2 predicted fragment length is 217 bps INFO @ Sun, 21 Jun 2020 19:21:27: #2 alternative fragment length(s) may be 217 bps INFO @ Sun, 21 Jun 2020 19:21:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.10_model.r INFO @ Sun, 21 Jun 2020 19:21:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:21:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:21:29: 9000000 INFO @ Sun, 21 Jun 2020 19:21:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:21:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:21:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.05_summits.bed INFO @ Sun, 21 Jun 2020 19:21:33: Done! pass1 - making usageList (100 chroms): 1 millis pass2 - checking and writing primary data (4625 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:21:34: 10000000 INFO @ Sun, 21 Jun 2020 19:21:39: 11000000 INFO @ Sun, 21 Jun 2020 19:21:44: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:21:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:21:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:21:48: #1 total tags in treatment: 12647522 INFO @ Sun, 21 Jun 2020 19:21:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:21:48: #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 19:21:48: #1 tags after filtering in treatment: 12647487 INFO @ Sun, 21 Jun 2020 19:21:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:21:48: #1 finished! INFO @ Sun, 21 Jun 2020 19:21:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:21:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:21:49: #2 number of paired peaks: 554 WARNING @ Sun, 21 Jun 2020 19:21:49: Fewer paired peaks (554) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 554 pairs to build model! INFO @ Sun, 21 Jun 2020 19:21:49: start model_add_line... INFO @ Sun, 21 Jun 2020 19:21:49: start X-correlation... INFO @ Sun, 21 Jun 2020 19:21:49: end of X-cor INFO @ Sun, 21 Jun 2020 19:21:49: #2 finished! INFO @ Sun, 21 Jun 2020 19:21:49: #2 predicted fragment length is 217 bps INFO @ Sun, 21 Jun 2020 19:21:49: #2 alternative fragment length(s) may be 217 bps INFO @ Sun, 21 Jun 2020 19:21:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.20_model.r INFO @ Sun, 21 Jun 2020 19:21:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:21:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:21:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:22:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:22:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:22:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.10_summits.bed INFO @ Sun, 21 Jun 2020 19:22:13: Done! pass1 - making usageList (77 chroms): 1 millis pass2 - checking and writing primary data (2207 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:22:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:22:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:22:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:22:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287700/SRX287700.20_summits.bed INFO @ Sun, 21 Jun 2020 19:22:35: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (734 records, 4 fields): 4 millis CompletedMACS2peakCalling