Job ID = 6458558 SRX = SRX5343093 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:41:15 prefetch.2.10.7: 1) Downloading 'SRR8540870'... 2020-06-21T12:41:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:43:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:43:33 prefetch.2.10.7: 1) 'SRR8540870' was downloaded successfully 2020-06-21T12:43:33 prefetch.2.10.7: 'SRR8540870' has 0 unresolved dependencies Read 22310526 spots for SRR8540870/SRR8540870.sra Written 22310526 spots for SRR8540870/SRR8540870.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: 00:08:13 22310526 reads; of these: 22310526 (100.00%) were unpaired; of these: 1182824 (5.30%) aligned 0 times 14655039 (65.69%) aligned exactly 1 time 6472663 (29.01%) aligned >1 times 94.70% overall alignment rate Time searching: 00:08:13 Overall time: 00:08:13 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] 3075714 / 21127702 = 0.1456 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 21:59:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.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 21:59:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:38: 1000000 INFO @ Sun, 21 Jun 2020 21:59:44: 2000000 INFO @ Sun, 21 Jun 2020 21:59:51: 3000000 INFO @ Sun, 21 Jun 2020 21:59:57: 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 22:00:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.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 22:00:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:00:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:00:04: 5000000 INFO @ Sun, 21 Jun 2020 22:00:07: 1000000 INFO @ Sun, 21 Jun 2020 22:00:11: 6000000 INFO @ Sun, 21 Jun 2020 22:00:13: 2000000 INFO @ Sun, 21 Jun 2020 22:00:17: 7000000 INFO @ Sun, 21 Jun 2020 22:00:18: 3000000 INFO @ Sun, 21 Jun 2020 22:00:24: 8000000 INFO @ Sun, 21 Jun 2020 22:00:24: 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 22:00:30: 5000000 INFO @ Sun, 21 Jun 2020 22:00:31: 9000000 INFO @ Sun, 21 Jun 2020 22:00:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.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 22:00:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:00:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:00:36: 6000000 INFO @ Sun, 21 Jun 2020 22:00:37: 1000000 INFO @ Sun, 21 Jun 2020 22:00:37: 10000000 INFO @ Sun, 21 Jun 2020 22:00:42: 7000000 INFO @ Sun, 21 Jun 2020 22:00:43: 2000000 INFO @ Sun, 21 Jun 2020 22:00:44: 11000000 INFO @ Sun, 21 Jun 2020 22:00:48: 8000000 INFO @ Sun, 21 Jun 2020 22:00:49: 3000000 INFO @ Sun, 21 Jun 2020 22:00:51: 12000000 INFO @ Sun, 21 Jun 2020 22:00:54: 9000000 INFO @ Sun, 21 Jun 2020 22:00:55: 4000000 INFO @ Sun, 21 Jun 2020 22:00:58: 13000000 INFO @ Sun, 21 Jun 2020 22:01:00: 10000000 INFO @ Sun, 21 Jun 2020 22:01:01: 5000000 INFO @ Sun, 21 Jun 2020 22:01:05: 14000000 INFO @ Sun, 21 Jun 2020 22:01:07: 11000000 INFO @ Sun, 21 Jun 2020 22:01:07: 6000000 INFO @ Sun, 21 Jun 2020 22:01:12: 15000000 INFO @ Sun, 21 Jun 2020 22:01:12: 12000000 INFO @ Sun, 21 Jun 2020 22:01:13: 7000000 INFO @ Sun, 21 Jun 2020 22:01:18: 13000000 INFO @ Sun, 21 Jun 2020 22:01:19: 8000000 INFO @ Sun, 21 Jun 2020 22:01:19: 16000000 INFO @ Sun, 21 Jun 2020 22:01:24: 14000000 INFO @ Sun, 21 Jun 2020 22:01:25: 9000000 INFO @ Sun, 21 Jun 2020 22:01:26: 17000000 INFO @ Sun, 21 Jun 2020 22:01:31: 15000000 INFO @ Sun, 21 Jun 2020 22:01:31: 10000000 INFO @ Sun, 21 Jun 2020 22:01:34: 18000000 INFO @ Sun, 21 Jun 2020 22:01:34: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 22:01:34: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 22:01:34: #1 total tags in treatment: 18051988 INFO @ Sun, 21 Jun 2020 22:01:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:01:34: #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 22:01:35: #1 tags after filtering in treatment: 18051988 INFO @ Sun, 21 Jun 2020 22:01:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:01:35: #1 finished! INFO @ Sun, 21 Jun 2020 22:01:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:01:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:01:36: #2 number of paired peaks: 274 WARNING @ Sun, 21 Jun 2020 22:01:36: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Sun, 21 Jun 2020 22:01:36: start model_add_line... INFO @ Sun, 21 Jun 2020 22:01:36: start X-correlation... INFO @ Sun, 21 Jun 2020 22:01:36: end of X-cor INFO @ Sun, 21 Jun 2020 22:01:36: #2 finished! INFO @ Sun, 21 Jun 2020 22:01:36: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 22:01:36: #2 alternative fragment length(s) may be 3,46 bps INFO @ Sun, 21 Jun 2020 22:01:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.05_model.r WARNING @ Sun, 21 Jun 2020 22:01:36: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:01:36: #2 You may need to consider one of the other alternative d(s): 3,46 WARNING @ Sun, 21 Jun 2020 22:01:36: #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 22:01:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:01:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:01:37: 11000000 INFO @ Sun, 21 Jun 2020 22:01:37: 16000000 INFO @ Sun, 21 Jun 2020 22:01:42: 12000000 INFO @ Sun, 21 Jun 2020 22:01:43: 17000000 INFO @ Sun, 21 Jun 2020 22:01:48: 13000000 INFO @ Sun, 21 Jun 2020 22:01:49: 18000000 INFO @ Sun, 21 Jun 2020 22:01:50: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 22:01:50: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 22:01:50: #1 total tags in treatment: 18051988 INFO @ Sun, 21 Jun 2020 22:01:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:01:50: #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 22:01:50: #1 tags after filtering in treatment: 18051988 INFO @ Sun, 21 Jun 2020 22:01:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:01:50: #1 finished! INFO @ Sun, 21 Jun 2020 22:01:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:01:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:01:52: #2 number of paired peaks: 274 WARNING @ Sun, 21 Jun 2020 22:01:52: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Sun, 21 Jun 2020 22:01:52: start model_add_line... INFO @ Sun, 21 Jun 2020 22:01:52: start X-correlation... INFO @ Sun, 21 Jun 2020 22:01:52: end of X-cor INFO @ Sun, 21 Jun 2020 22:01:52: #2 finished! INFO @ Sun, 21 Jun 2020 22:01:52: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 22:01:52: #2 alternative fragment length(s) may be 3,46 bps INFO @ Sun, 21 Jun 2020 22:01:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.10_model.r WARNING @ Sun, 21 Jun 2020 22:01:52: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:01:52: #2 You may need to consider one of the other alternative d(s): 3,46 WARNING @ Sun, 21 Jun 2020 22:01:52: #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 22:01:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:01:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:01:54: 14000000 INFO @ Sun, 21 Jun 2020 22:02:00: 15000000 INFO @ Sun, 21 Jun 2020 22:02:06: 16000000 INFO @ Sun, 21 Jun 2020 22:02:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:02:12: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:02:18: 18000000 INFO @ Sun, 21 Jun 2020 22:02:18: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 22:02:18: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 22:02:18: #1 total tags in treatment: 18051988 INFO @ Sun, 21 Jun 2020 22:02:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:02:18: #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 22:02:19: #1 tags after filtering in treatment: 18051988 INFO @ Sun, 21 Jun 2020 22:02:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:02:19: #1 finished! INFO @ Sun, 21 Jun 2020 22:02:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:02:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:02:20: #2 number of paired peaks: 274 WARNING @ Sun, 21 Jun 2020 22:02:20: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Sun, 21 Jun 2020 22:02:20: start model_add_line... INFO @ Sun, 21 Jun 2020 22:02:20: start X-correlation... INFO @ Sun, 21 Jun 2020 22:02:20: end of X-cor INFO @ Sun, 21 Jun 2020 22:02:20: #2 finished! INFO @ Sun, 21 Jun 2020 22:02:20: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 22:02:20: #2 alternative fragment length(s) may be 3,46 bps INFO @ Sun, 21 Jun 2020 22:02:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.20_model.r WARNING @ Sun, 21 Jun 2020 22:02:20: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:02:20: #2 You may need to consider one of the other alternative d(s): 3,46 WARNING @ Sun, 21 Jun 2020 22:02:20: #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 22:02:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:02:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:02:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:02:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:02:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:02:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.05_summits.bed INFO @ Sun, 21 Jun 2020 22:02:27: Done! pass1 - making usageList (707 chroms): 1 millis pass2 - checking and writing primary data (2416 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:02:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:02:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:02:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.10_summits.bed INFO @ Sun, 21 Jun 2020 22:02:45: Done! pass1 - making usageList (539 chroms): 1 millis pass2 - checking and writing primary data (1552 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:02:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:03:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:03:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:03:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343093/SRX5343093.20_summits.bed INFO @ Sun, 21 Jun 2020 22:03:15: Done! pass1 - making usageList (275 chroms): 1 millis pass2 - checking and writing primary data (547 records, 4 fields): 11 millis CompletedMACS2peakCalling