Job ID = 6455561 SRX = SRX287887 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:35:29 prefetch.2.10.7: 1) Downloading 'SRR870076'... 2020-06-21T10:35:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:37:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:37:50 prefetch.2.10.7: 1) 'SRR870076' was downloaded successfully Read 18826306 spots for SRR870076/SRR870076.sra Written 18826306 spots for SRR870076/SRR870076.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: 00:05:00 18826306 reads; of these: 18826306 (100.00%) were unpaired; of these: 1021917 (5.43%) aligned 0 times 13330600 (70.81%) aligned exactly 1 time 4473789 (23.76%) aligned >1 times 94.57% overall alignment rate Time searching: 00:05:00 Overall time: 00:05:00 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] 2303566 / 17804389 = 0.1294 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 19:48:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.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 19:48:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:48:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:48:29: 1000000 INFO @ Sun, 21 Jun 2020 19:48:36: 2000000 INFO @ Sun, 21 Jun 2020 19:48:42: 3000000 INFO @ Sun, 21 Jun 2020 19:48:48: 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 19:48:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.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 19:48:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:48:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:48:55: 5000000 INFO @ Sun, 21 Jun 2020 19:49:00: 1000000 INFO @ Sun, 21 Jun 2020 19:49:01: 6000000 INFO @ Sun, 21 Jun 2020 19:49:07: 2000000 INFO @ Sun, 21 Jun 2020 19:49:08: 7000000 INFO @ Sun, 21 Jun 2020 19:49:13: 3000000 INFO @ Sun, 21 Jun 2020 19:49:15: 8000000 INFO @ Sun, 21 Jun 2020 19:49:20: 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 19:49:22: 9000000 INFO @ Sun, 21 Jun 2020 19:49:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.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 19:49:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:49:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:49:27: 5000000 INFO @ Sun, 21 Jun 2020 19:49:28: 10000000 INFO @ Sun, 21 Jun 2020 19:49:29: 1000000 INFO @ Sun, 21 Jun 2020 19:49:34: 6000000 INFO @ Sun, 21 Jun 2020 19:49:35: 11000000 INFO @ Sun, 21 Jun 2020 19:49:36: 2000000 INFO @ Sun, 21 Jun 2020 19:49:41: 7000000 INFO @ Sun, 21 Jun 2020 19:49:42: 3000000 INFO @ Sun, 21 Jun 2020 19:49:42: 12000000 INFO @ Sun, 21 Jun 2020 19:49:48: 8000000 INFO @ Sun, 21 Jun 2020 19:49:49: 4000000 INFO @ Sun, 21 Jun 2020 19:49:50: 13000000 INFO @ Sun, 21 Jun 2020 19:49:55: 9000000 INFO @ Sun, 21 Jun 2020 19:49:55: 5000000 INFO @ Sun, 21 Jun 2020 19:49:57: 14000000 INFO @ Sun, 21 Jun 2020 19:50:02: 10000000 INFO @ Sun, 21 Jun 2020 19:50:02: 6000000 INFO @ Sun, 21 Jun 2020 19:50:04: 15000000 INFO @ Sun, 21 Jun 2020 19:50:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:50:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:50:07: #1 total tags in treatment: 15500823 INFO @ Sun, 21 Jun 2020 19:50:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:07: #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 19:50:08: #1 tags after filtering in treatment: 15500823 INFO @ Sun, 21 Jun 2020 19:50:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:08: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:08: 7000000 INFO @ Sun, 21 Jun 2020 19:50:09: 11000000 INFO @ Sun, 21 Jun 2020 19:50:09: #2 number of paired peaks: 740 WARNING @ Sun, 21 Jun 2020 19:50:09: Fewer paired peaks (740) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 740 pairs to build model! INFO @ Sun, 21 Jun 2020 19:50:09: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:09: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:09: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:09: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:09: #2 predicted fragment length is 136 bps INFO @ Sun, 21 Jun 2020 19:50:09: #2 alternative fragment length(s) may be 136 bps INFO @ Sun, 21 Jun 2020 19:50:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.05_model.r INFO @ Sun, 21 Jun 2020 19:50:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:50:14: 8000000 INFO @ Sun, 21 Jun 2020 19:50:16: 12000000 INFO @ Sun, 21 Jun 2020 19:50:21: 9000000 INFO @ Sun, 21 Jun 2020 19:50:23: 13000000 INFO @ Sun, 21 Jun 2020 19:50:27: 10000000 INFO @ Sun, 21 Jun 2020 19:50:30: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:50:33: 11000000 INFO @ Sun, 21 Jun 2020 19:50:37: 15000000 INFO @ Sun, 21 Jun 2020 19:50:40: 12000000 INFO @ Sun, 21 Jun 2020 19:50:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:50:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:50:40: #1 total tags in treatment: 15500823 INFO @ Sun, 21 Jun 2020 19:50:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:40: #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 19:50:41: #1 tags after filtering in treatment: 15500823 INFO @ Sun, 21 Jun 2020 19:50:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:41: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:50:42: #2 number of paired peaks: 740 WARNING @ Sun, 21 Jun 2020 19:50:42: Fewer paired peaks (740) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 740 pairs to build model! INFO @ Sun, 21 Jun 2020 19:50:42: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:42: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:42: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:42: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:42: #2 predicted fragment length is 136 bps INFO @ Sun, 21 Jun 2020 19:50:42: #2 alternative fragment length(s) may be 136 bps INFO @ Sun, 21 Jun 2020 19:50:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.10_model.r INFO @ Sun, 21 Jun 2020 19:50:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:50:46: 13000000 INFO @ Sun, 21 Jun 2020 19:50:51: 14000000 INFO @ Sun, 21 Jun 2020 19:50:57: 15000000 INFO @ Sun, 21 Jun 2020 19:50:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:50:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:50:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.05_summits.bed INFO @ Sun, 21 Jun 2020 19:50:58: Done! pass1 - making usageList (619 chroms): 2 millis pass2 - checking and writing primary data (6115 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:51:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:51:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:51:00: #1 total tags in treatment: 15500823 INFO @ Sun, 21 Jun 2020 19:51:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:51:00: #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 19:51:00: #1 tags after filtering in treatment: 15500823 INFO @ Sun, 21 Jun 2020 19:51:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:51:00: #1 finished! INFO @ Sun, 21 Jun 2020 19:51:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:51:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:51:01: #2 number of paired peaks: 740 WARNING @ Sun, 21 Jun 2020 19:51:01: Fewer paired peaks (740) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 740 pairs to build model! INFO @ Sun, 21 Jun 2020 19:51:01: start model_add_line... INFO @ Sun, 21 Jun 2020 19:51:02: start X-correlation... INFO @ Sun, 21 Jun 2020 19:51:02: end of X-cor INFO @ Sun, 21 Jun 2020 19:51:02: #2 finished! INFO @ Sun, 21 Jun 2020 19:51:02: #2 predicted fragment length is 136 bps INFO @ Sun, 21 Jun 2020 19:51:02: #2 alternative fragment length(s) may be 136 bps INFO @ Sun, 21 Jun 2020 19:51:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.20_model.r INFO @ Sun, 21 Jun 2020 19:51:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:51:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:51:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:51:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.10_summits.bed INFO @ Sun, 21 Jun 2020 19:51:29: Done! pass1 - making usageList (521 chroms): 2 millis pass2 - checking and writing primary data (4107 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:51:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:51:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287887/SRX287887.20_summits.bed INFO @ Sun, 21 Jun 2020 19:51:49: Done! pass1 - making usageList (426 chroms): 1 millis pass2 - checking and writing primary data (2211 records, 4 fields): 13 millis CompletedMACS2peakCalling