Job ID = 6458547 SRX = SRX5343085 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:30:07 prefetch.2.10.7: 1) Downloading 'SRR8540862'... 2020-06-21T12:30:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:32:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:32:42 prefetch.2.10.7: 1) 'SRR8540862' was downloaded successfully 2020-06-21T12:32:42 prefetch.2.10.7: 'SRR8540862' has 0 unresolved dependencies Read 22310529 spots for SRR8540862/SRR8540862.sra Written 22310529 spots for SRR8540862/SRR8540862.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: 00:08:10 22310529 reads; of these: 22310529 (100.00%) were unpaired; of these: 1182793 (5.30%) aligned 0 times 14655124 (65.69%) aligned exactly 1 time 6472612 (29.01%) aligned >1 times 94.70% overall alignment rate Time searching: 00:08:10 Overall time: 00:08:10 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] 3075569 / 21127736 = 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 21:48:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.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 21:48:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:48:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:48:45: 1000000 INFO @ Sun, 21 Jun 2020 21:48:51: 2000000 INFO @ Sun, 21 Jun 2020 21:48:57: 3000000 INFO @ Sun, 21 Jun 2020 21:49:02: 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 21:49:08: 5000000 INFO @ Sun, 21 Jun 2020 21:49:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.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 21:49:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:49:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:49:14: 6000000 INFO @ Sun, 21 Jun 2020 21:49:16: 1000000 INFO @ Sun, 21 Jun 2020 21:49:20: 7000000 INFO @ Sun, 21 Jun 2020 21:49:23: 2000000 INFO @ Sun, 21 Jun 2020 21:49:26: 8000000 INFO @ Sun, 21 Jun 2020 21:49:30: 3000000 INFO @ Sun, 21 Jun 2020 21:49:32: 9000000 INFO @ Sun, 21 Jun 2020 21:49:37: 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 21:49:38: 10000000 INFO @ Sun, 21 Jun 2020 21:49:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.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 21:49:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:49:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:49:43: 5000000 INFO @ Sun, 21 Jun 2020 21:49:44: 11000000 INFO @ Sun, 21 Jun 2020 21:49:47: 1000000 INFO @ Sun, 21 Jun 2020 21:49:50: 6000000 INFO @ Sun, 21 Jun 2020 21:49:51: 12000000 INFO @ Sun, 21 Jun 2020 21:49:54: 2000000 INFO @ Sun, 21 Jun 2020 21:49:57: 13000000 INFO @ Sun, 21 Jun 2020 21:49:57: 7000000 INFO @ Sun, 21 Jun 2020 21:50:01: 3000000 INFO @ Sun, 21 Jun 2020 21:50:03: 14000000 INFO @ Sun, 21 Jun 2020 21:50:04: 8000000 INFO @ Sun, 21 Jun 2020 21:50:08: 4000000 INFO @ Sun, 21 Jun 2020 21:50:10: 15000000 INFO @ Sun, 21 Jun 2020 21:50:11: 9000000 INFO @ Sun, 21 Jun 2020 21:50:15: 5000000 INFO @ Sun, 21 Jun 2020 21:50:16: 16000000 INFO @ Sun, 21 Jun 2020 21:50:18: 10000000 INFO @ Sun, 21 Jun 2020 21:50:22: 6000000 INFO @ Sun, 21 Jun 2020 21:50:22: 17000000 INFO @ Sun, 21 Jun 2020 21:50:26: 11000000 INFO @ Sun, 21 Jun 2020 21:50:29: 7000000 INFO @ Sun, 21 Jun 2020 21:50:29: 18000000 INFO @ Sun, 21 Jun 2020 21:50:30: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:50:30: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:50:30: #1 total tags in treatment: 18052167 INFO @ Sun, 21 Jun 2020 21:50:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:50:30: #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 21:50:30: #1 tags after filtering in treatment: 18052167 INFO @ Sun, 21 Jun 2020 21:50:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:50:30: #1 finished! INFO @ Sun, 21 Jun 2020 21:50:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:50:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:50:31: #2 number of paired peaks: 272 WARNING @ Sun, 21 Jun 2020 21:50:31: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Sun, 21 Jun 2020 21:50:31: start model_add_line... INFO @ Sun, 21 Jun 2020 21:50:31: start X-correlation... INFO @ Sun, 21 Jun 2020 21:50:32: end of X-cor INFO @ Sun, 21 Jun 2020 21:50:32: #2 finished! INFO @ Sun, 21 Jun 2020 21:50:32: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 21:50:32: #2 alternative fragment length(s) may be 3,54 bps INFO @ Sun, 21 Jun 2020 21:50:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.05_model.r WARNING @ Sun, 21 Jun 2020 21:50:32: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:50:32: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Sun, 21 Jun 2020 21:50:32: #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 21:50:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:50:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:50:33: 12000000 INFO @ Sun, 21 Jun 2020 21:50:35: 8000000 INFO @ Sun, 21 Jun 2020 21:50:40: 13000000 INFO @ Sun, 21 Jun 2020 21:50:42: 9000000 INFO @ Sun, 21 Jun 2020 21:50:48: 14000000 INFO @ Sun, 21 Jun 2020 21:50:49: 10000000 INFO @ Sun, 21 Jun 2020 21:50:55: 15000000 INFO @ Sun, 21 Jun 2020 21:50:56: 11000000 INFO @ Sun, 21 Jun 2020 21:51:02: 16000000 INFO @ Sun, 21 Jun 2020 21:51:03: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:51:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:51:09: 17000000 INFO @ Sun, 21 Jun 2020 21:51:10: 13000000 INFO @ Sun, 21 Jun 2020 21:51:17: 18000000 INFO @ Sun, 21 Jun 2020 21:51:17: 14000000 INFO @ Sun, 21 Jun 2020 21:51:17: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:51:17: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:51:17: #1 total tags in treatment: 18052167 INFO @ Sun, 21 Jun 2020 21:51:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:51:17: #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 21:51:18: #1 tags after filtering in treatment: 18052167 INFO @ Sun, 21 Jun 2020 21:51:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:51:18: #1 finished! INFO @ Sun, 21 Jun 2020 21:51:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:51:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:51:19: #2 number of paired peaks: 272 WARNING @ Sun, 21 Jun 2020 21:51:19: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Sun, 21 Jun 2020 21:51:19: start model_add_line... INFO @ Sun, 21 Jun 2020 21:51:19: start X-correlation... INFO @ Sun, 21 Jun 2020 21:51:19: end of X-cor INFO @ Sun, 21 Jun 2020 21:51:19: #2 finished! INFO @ Sun, 21 Jun 2020 21:51:19: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 21:51:19: #2 alternative fragment length(s) may be 3,54 bps INFO @ Sun, 21 Jun 2020 21:51:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.10_model.r WARNING @ Sun, 21 Jun 2020 21:51:19: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:51:19: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Sun, 21 Jun 2020 21:51:19: #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 21:51:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:51:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:51:24: 15000000 INFO @ Sun, 21 Jun 2020 21:51:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:51:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:51:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.05_summits.bed INFO @ Sun, 21 Jun 2020 21:51:24: Done! pass1 - making usageList (709 chroms): 1 millis pass2 - checking and writing primary data (2369 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:51:31: 16000000 INFO @ Sun, 21 Jun 2020 21:51:38: 17000000 INFO @ Sun, 21 Jun 2020 21:51:45: 18000000 INFO @ Sun, 21 Jun 2020 21:51:46: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:51:46: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:51:46: #1 total tags in treatment: 18052167 INFO @ Sun, 21 Jun 2020 21:51:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:51:46: #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 21:51:46: #1 tags after filtering in treatment: 18052167 INFO @ Sun, 21 Jun 2020 21:51:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:51:46: #1 finished! INFO @ Sun, 21 Jun 2020 21:51:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:51:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:51:48: #2 number of paired peaks: 272 WARNING @ Sun, 21 Jun 2020 21:51:48: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Sun, 21 Jun 2020 21:51:48: start model_add_line... INFO @ Sun, 21 Jun 2020 21:51:48: start X-correlation... INFO @ Sun, 21 Jun 2020 21:51:48: end of X-cor INFO @ Sun, 21 Jun 2020 21:51:48: #2 finished! INFO @ Sun, 21 Jun 2020 21:51:48: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 21:51:48: #2 alternative fragment length(s) may be 3,54 bps INFO @ Sun, 21 Jun 2020 21:51:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.20_model.r WARNING @ Sun, 21 Jun 2020 21:51:48: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:51:48: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Sun, 21 Jun 2020 21:51:48: #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 21:51:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:51:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:51:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:52:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.10_summits.bed INFO @ Sun, 21 Jun 2020 21:52:12: Done! pass1 - making usageList (542 chroms): 2 millis pass2 - checking and writing primary data (1583 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:52:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:52:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343085/SRX5343085.20_summits.bed INFO @ Sun, 21 Jun 2020 21:52:41: Done! pass1 - making usageList (331 chroms): 1 millis pass2 - checking and writing primary data (655 records, 4 fields): 11 millis CompletedMACS2peakCalling