Job ID = 6455435 SRX = SRX287786 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:21:06 prefetch.2.10.7: 1) Downloading 'SRR869975'... 2020-06-21T10:21:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:24:27 prefetch.2.10.7: 1) 'SRR869975' was downloaded successfully Read 21987706 spots for SRR869975/SRR869975.sra Written 21987706 spots for SRR869975/SRR869975.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: 00:07:05 21987706 reads; of these: 21987706 (100.00%) were unpaired; of these: 1314962 (5.98%) aligned 0 times 13883592 (63.14%) aligned exactly 1 time 6789152 (30.88%) aligned >1 times 94.02% overall alignment rate Time searching: 00:07:05 Overall time: 00:07:05 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 12 files... [bam_rmdupse_core] 3273938 / 20672744 = 0.1584 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 19:38:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.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 19:38:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:38:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:38:16: 1000000 INFO @ Sun, 21 Jun 2020 19:38:21: 2000000 INFO @ Sun, 21 Jun 2020 19:38:27: 3000000 INFO @ Sun, 21 Jun 2020 19:38:32: 4000000 INFO @ Sun, 21 Jun 2020 19:38:38: 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 19:38:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.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 19:38:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:38:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:38:44: 6000000 INFO @ Sun, 21 Jun 2020 19:38:47: 1000000 INFO @ Sun, 21 Jun 2020 19:38:50: 7000000 INFO @ Sun, 21 Jun 2020 19:38:54: 2000000 INFO @ Sun, 21 Jun 2020 19:38:57: 8000000 INFO @ Sun, 21 Jun 2020 19:39:01: 3000000 INFO @ Sun, 21 Jun 2020 19:39:03: 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 19:39:08: 4000000 INFO @ Sun, 21 Jun 2020 19:39:10: 10000000 INFO @ Sun, 21 Jun 2020 19:39:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.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 19:39:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:39:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:39:16: 5000000 INFO @ Sun, 21 Jun 2020 19:39:17: 11000000 INFO @ Sun, 21 Jun 2020 19:39:18: 1000000 INFO @ Sun, 21 Jun 2020 19:39:23: 12000000 INFO @ Sun, 21 Jun 2020 19:39:24: 6000000 INFO @ Sun, 21 Jun 2020 19:39:25: 2000000 INFO @ Sun, 21 Jun 2020 19:39:30: 13000000 INFO @ Sun, 21 Jun 2020 19:39:31: 7000000 INFO @ Sun, 21 Jun 2020 19:39:33: 3000000 INFO @ Sun, 21 Jun 2020 19:39:37: 14000000 INFO @ Sun, 21 Jun 2020 19:39:39: 8000000 INFO @ Sun, 21 Jun 2020 19:39:40: 4000000 INFO @ Sun, 21 Jun 2020 19:39:43: 15000000 INFO @ Sun, 21 Jun 2020 19:39:46: 9000000 INFO @ Sun, 21 Jun 2020 19:39:47: 5000000 INFO @ Sun, 21 Jun 2020 19:39:50: 16000000 INFO @ Sun, 21 Jun 2020 19:39:53: 10000000 INFO @ Sun, 21 Jun 2020 19:39:55: 6000000 INFO @ Sun, 21 Jun 2020 19:39:57: 17000000 INFO @ Sun, 21 Jun 2020 19:40:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:40:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:40:00: #1 total tags in treatment: 17398806 INFO @ Sun, 21 Jun 2020 19:40:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:40:00: #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 19:40:00: #1 tags after filtering in treatment: 17398806 INFO @ Sun, 21 Jun 2020 19:40:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:40:00: #1 finished! INFO @ Sun, 21 Jun 2020 19:40:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:40:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:40:01: 11000000 INFO @ Sun, 21 Jun 2020 19:40:01: #2 number of paired peaks: 717 WARNING @ Sun, 21 Jun 2020 19:40:01: Fewer paired peaks (717) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 717 pairs to build model! INFO @ Sun, 21 Jun 2020 19:40:01: start model_add_line... INFO @ Sun, 21 Jun 2020 19:40:01: start X-correlation... INFO @ Sun, 21 Jun 2020 19:40:01: end of X-cor INFO @ Sun, 21 Jun 2020 19:40:01: #2 finished! INFO @ Sun, 21 Jun 2020 19:40:01: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 19:40:01: #2 alternative fragment length(s) may be 2,40,598 bps INFO @ Sun, 21 Jun 2020 19:40:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.05_model.r WARNING @ Sun, 21 Jun 2020 19:40:01: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:40:01: #2 You may need to consider one of the other alternative d(s): 2,40,598 WARNING @ Sun, 21 Jun 2020 19:40:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:40:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:40:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:40:02: 7000000 INFO @ Sun, 21 Jun 2020 19:40:08: 12000000 INFO @ Sun, 21 Jun 2020 19:40:09: 8000000 INFO @ Sun, 21 Jun 2020 19:40:15: 13000000 INFO @ Sun, 21 Jun 2020 19:40:17: 9000000 INFO @ Sun, 21 Jun 2020 19:40:23: 14000000 INFO @ Sun, 21 Jun 2020 19:40:24: 10000000 INFO @ Sun, 21 Jun 2020 19:40:30: 15000000 INFO @ Sun, 21 Jun 2020 19:40:31: 11000000 INFO @ Sun, 21 Jun 2020 19:40:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:40:38: 16000000 INFO @ Sun, 21 Jun 2020 19:40:38: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:40:45: 13000000 INFO @ Sun, 21 Jun 2020 19:40:45: 17000000 INFO @ Sun, 21 Jun 2020 19:40:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:40:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:40:48: #1 total tags in treatment: 17398806 INFO @ Sun, 21 Jun 2020 19:40:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:40:48: #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 19:40:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:40:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:40:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.05_summits.bed INFO @ Sun, 21 Jun 2020 19:40:48: Done! INFO @ Sun, 21 Jun 2020 19:40:49: #1 tags after filtering in treatment: 17398806 INFO @ Sun, 21 Jun 2020 19:40:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:40:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:40:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:40:49: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (699 chroms): 2 millis pass2 - checking and writing primary data (2629 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:40:50: #2 number of paired peaks: 717 WARNING @ Sun, 21 Jun 2020 19:40:50: Fewer paired peaks (717) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 717 pairs to build model! INFO @ Sun, 21 Jun 2020 19:40:50: start model_add_line... INFO @ Sun, 21 Jun 2020 19:40:50: start X-correlation... INFO @ Sun, 21 Jun 2020 19:40:50: end of X-cor INFO @ Sun, 21 Jun 2020 19:40:50: #2 finished! INFO @ Sun, 21 Jun 2020 19:40:50: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 19:40:50: #2 alternative fragment length(s) may be 2,40,598 bps INFO @ Sun, 21 Jun 2020 19:40:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.10_model.r WARNING @ Sun, 21 Jun 2020 19:40:50: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:40:50: #2 You may need to consider one of the other alternative d(s): 2,40,598 WARNING @ Sun, 21 Jun 2020 19:40:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:40:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:40:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:40:52: 14000000 INFO @ Sun, 21 Jun 2020 19:40:59: 15000000 INFO @ Sun, 21 Jun 2020 19:41:05: 16000000 INFO @ Sun, 21 Jun 2020 19:41:12: 17000000 INFO @ Sun, 21 Jun 2020 19:41:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:41:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:41:15: #1 total tags in treatment: 17398806 INFO @ Sun, 21 Jun 2020 19:41:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:41:15: #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 19:41:16: #1 tags after filtering in treatment: 17398806 INFO @ Sun, 21 Jun 2020 19:41:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:41:16: #1 finished! INFO @ Sun, 21 Jun 2020 19:41:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:41:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:41:17: #2 number of paired peaks: 717 WARNING @ Sun, 21 Jun 2020 19:41:17: Fewer paired peaks (717) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 717 pairs to build model! INFO @ Sun, 21 Jun 2020 19:41:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:41:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:41:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:41:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:41:17: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 19:41:17: #2 alternative fragment length(s) may be 2,40,598 bps INFO @ Sun, 21 Jun 2020 19:41:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.20_model.r WARNING @ Sun, 21 Jun 2020 19:41:17: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:41:17: #2 You may need to consider one of the other alternative d(s): 2,40,598 WARNING @ Sun, 21 Jun 2020 19:41:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:41:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:41:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:41:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:41:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:41:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:41:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.10_summits.bed INFO @ Sun, 21 Jun 2020 19:41:38: Done! pass1 - making usageList (578 chroms): 1 millis pass2 - checking and writing primary data (2133 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:41:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:42:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:42:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:42:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287786/SRX287786.20_summits.bed INFO @ Sun, 21 Jun 2020 19:42:04: Done! pass1 - making usageList (439 chroms): 1 millis pass2 - checking and writing primary data (1398 records, 4 fields): 14 millis CompletedMACS2peakCalling