Job ID = 6455359 SRX = SRX287724 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:51:55 prefetch.2.10.7: 1) Downloading 'SRR869913'... 2020-06-21T09:51:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:55:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:55:00 prefetch.2.10.7: 1) 'SRR869913' was downloaded successfully Read 17992996 spots for SRR869913/SRR869913.sra Written 17992996 spots for SRR869913/SRR869913.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: 00:04:08 17992996 reads; of these: 17992996 (100.00%) were unpaired; of these: 1224168 (6.80%) aligned 0 times 13898152 (77.24%) aligned exactly 1 time 2870676 (15.95%) aligned >1 times 93.20% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:08 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] 1440083 / 16768828 = 0.0859 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 19:04:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.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 19:04:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:04:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:04:54: 1000000 INFO @ Sun, 21 Jun 2020 19:05:01: 2000000 INFO @ Sun, 21 Jun 2020 19:05:08: 3000000 INFO @ Sun, 21 Jun 2020 19:05:14: 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 19:05:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.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 19:05:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:05:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:05:21: 5000000 INFO @ Sun, 21 Jun 2020 19:05:24: 1000000 INFO @ Sun, 21 Jun 2020 19:05:28: 6000000 INFO @ Sun, 21 Jun 2020 19:05:31: 2000000 INFO @ Sun, 21 Jun 2020 19:05:35: 7000000 INFO @ Sun, 21 Jun 2020 19:05:37: 3000000 INFO @ Sun, 21 Jun 2020 19:05:42: 8000000 INFO @ Sun, 21 Jun 2020 19:05:43: 4000000 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 19:05:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.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 19:05:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:05:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:05:49: 9000000 INFO @ Sun, 21 Jun 2020 19:05:49: 5000000 INFO @ Sun, 21 Jun 2020 19:05:54: 1000000 INFO @ Sun, 21 Jun 2020 19:05:55: 6000000 INFO @ Sun, 21 Jun 2020 19:05:56: 10000000 INFO @ Sun, 21 Jun 2020 19:06:00: 2000000 INFO @ Sun, 21 Jun 2020 19:06:02: 7000000 INFO @ Sun, 21 Jun 2020 19:06:03: 11000000 INFO @ Sun, 21 Jun 2020 19:06:06: 3000000 INFO @ Sun, 21 Jun 2020 19:06:08: 8000000 INFO @ Sun, 21 Jun 2020 19:06:10: 12000000 INFO @ Sun, 21 Jun 2020 19:06:13: 4000000 INFO @ Sun, 21 Jun 2020 19:06:14: 9000000 INFO @ Sun, 21 Jun 2020 19:06:18: 13000000 INFO @ Sun, 21 Jun 2020 19:06:19: 5000000 INFO @ Sun, 21 Jun 2020 19:06:20: 10000000 INFO @ Sun, 21 Jun 2020 19:06:25: 6000000 INFO @ Sun, 21 Jun 2020 19:06:25: 14000000 INFO @ Sun, 21 Jun 2020 19:06:26: 11000000 INFO @ Sun, 21 Jun 2020 19:06:31: 7000000 INFO @ Sun, 21 Jun 2020 19:06:32: 15000000 INFO @ Sun, 21 Jun 2020 19:06:33: 12000000 INFO @ Sun, 21 Jun 2020 19:06:34: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:06:34: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:06:34: #1 total tags in treatment: 15328745 INFO @ Sun, 21 Jun 2020 19:06:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:06:34: #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 19:06:35: #1 tags after filtering in treatment: 15328743 INFO @ Sun, 21 Jun 2020 19:06:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:06:35: #1 finished! INFO @ Sun, 21 Jun 2020 19:06:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:06:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:06:36: #2 number of paired peaks: 491 WARNING @ Sun, 21 Jun 2020 19:06:36: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Sun, 21 Jun 2020 19:06:36: start model_add_line... INFO @ Sun, 21 Jun 2020 19:06:36: start X-correlation... INFO @ Sun, 21 Jun 2020 19:06:36: end of X-cor INFO @ Sun, 21 Jun 2020 19:06:36: #2 finished! INFO @ Sun, 21 Jun 2020 19:06:36: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 19:06:36: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 19:06:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.05_model.r INFO @ Sun, 21 Jun 2020 19:06:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:06:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:06:37: 8000000 INFO @ Sun, 21 Jun 2020 19:06:39: 13000000 INFO @ Sun, 21 Jun 2020 19:06:43: 9000000 INFO @ Sun, 21 Jun 2020 19:06:45: 14000000 INFO @ Sun, 21 Jun 2020 19:06:49: 10000000 INFO @ Sun, 21 Jun 2020 19:06:51: 15000000 INFO @ Sun, 21 Jun 2020 19:06:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:06:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:06:53: #1 total tags in treatment: 15328745 INFO @ Sun, 21 Jun 2020 19:06:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:06:53: #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 19:06:54: #1 tags after filtering in treatment: 15328743 INFO @ Sun, 21 Jun 2020 19:06:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:06:54: #1 finished! INFO @ Sun, 21 Jun 2020 19:06:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:06:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:06:55: #2 number of paired peaks: 491 WARNING @ Sun, 21 Jun 2020 19:06:55: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Sun, 21 Jun 2020 19:06:55: start model_add_line... INFO @ Sun, 21 Jun 2020 19:06:55: start X-correlation... INFO @ Sun, 21 Jun 2020 19:06:55: end of X-cor INFO @ Sun, 21 Jun 2020 19:06:55: #2 finished! INFO @ Sun, 21 Jun 2020 19:06:55: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 19:06:55: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 19:06:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.10_model.r INFO @ Sun, 21 Jun 2020 19:06:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:06:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:06:55: 11000000 INFO @ Sun, 21 Jun 2020 19:07:01: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:07:07: 13000000 INFO @ Sun, 21 Jun 2020 19:07:12: 14000000 INFO @ Sun, 21 Jun 2020 19:07:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:07:18: 15000000 INFO @ Sun, 21 Jun 2020 19:07:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:07:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:07:20: #1 total tags in treatment: 15328745 INFO @ Sun, 21 Jun 2020 19:07:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:07:20: #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 19:07:21: #1 tags after filtering in treatment: 15328743 INFO @ Sun, 21 Jun 2020 19:07:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:07:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:07:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:07:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:07:22: #2 number of paired peaks: 491 WARNING @ Sun, 21 Jun 2020 19:07:22: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Sun, 21 Jun 2020 19:07:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:07:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:07:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:07:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:07:22: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 19:07:22: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 19:07:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.20_model.r INFO @ Sun, 21 Jun 2020 19:07:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:07:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:07:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:07:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:07:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:07:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.05_summits.bed INFO @ Sun, 21 Jun 2020 19:07:32: Done! pass1 - making usageList (238 chroms): 2 millis pass2 - checking and writing primary data (6386 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:07:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:07:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:07:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.10_summits.bed INFO @ Sun, 21 Jun 2020 19:07:49: Done! pass1 - making usageList (139 chroms): 1 millis pass2 - checking and writing primary data (3462 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:07:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:08:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:08:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:08:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287724/SRX287724.20_summits.bed INFO @ Sun, 21 Jun 2020 19:08:16: Done! pass1 - making usageList (87 chroms): 1 millis pass2 - checking and writing primary data (872 records, 4 fields): 5 millis CompletedMACS2peakCalling