Job ID = 6455101 SRX = SRX2692976 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:47:10 prefetch.2.10.7: 1) Downloading 'SRR5398175'... 2020-06-21T09:47:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:57:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:57:57 prefetch.2.10.7: 1) 'SRR5398175' was downloaded successfully 2020-06-21T09:57:57 prefetch.2.10.7: 'SRR5398175' has 0 unresolved dependencies Read 87596775 spots for SRR5398175/SRR5398175.sra Written 87596775 spots for SRR5398175/SRR5398175.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:58:47 87596775 reads; of these: 87596775 (100.00%) were unpaired; of these: 19733123 (22.53%) aligned 0 times 12224433 (13.96%) aligned exactly 1 time 55639219 (63.52%) aligned >1 times 77.47% overall alignment rate Time searching: 00:58:48 Overall time: 00:58:48 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 28 files... [bam_rmdupse_core] 50690477 / 67863652 = 0.7469 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 20:14:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.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 20:14:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:14:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:14:22: 1000000 INFO @ Sun, 21 Jun 2020 20:14:28: 2000000 INFO @ Sun, 21 Jun 2020 20:14:34: 3000000 INFO @ Sun, 21 Jun 2020 20:14:41: 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 20:14:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.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 20:14:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:14:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:14:47: 5000000 INFO @ Sun, 21 Jun 2020 20:14:52: 1000000 INFO @ Sun, 21 Jun 2020 20:14:54: 6000000 INFO @ Sun, 21 Jun 2020 20:14:59: 2000000 INFO @ Sun, 21 Jun 2020 20:15:01: 7000000 INFO @ Sun, 21 Jun 2020 20:15:06: 3000000 INFO @ Sun, 21 Jun 2020 20:15:08: 8000000 INFO @ Sun, 21 Jun 2020 20:15:13: 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 20:15:15: 9000000 INFO @ Sun, 21 Jun 2020 20:15:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.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 20:15:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:15:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:15:20: 5000000 INFO @ Sun, 21 Jun 2020 20:15:22: 10000000 INFO @ Sun, 21 Jun 2020 20:15:23: 1000000 INFO @ Sun, 21 Jun 2020 20:15:27: 6000000 INFO @ Sun, 21 Jun 2020 20:15:29: 11000000 INFO @ Sun, 21 Jun 2020 20:15:30: 2000000 INFO @ Sun, 21 Jun 2020 20:15:35: 7000000 INFO @ Sun, 21 Jun 2020 20:15:36: 12000000 INFO @ Sun, 21 Jun 2020 20:15:38: 3000000 INFO @ Sun, 21 Jun 2020 20:15:42: 8000000 INFO @ Sun, 21 Jun 2020 20:15:44: 13000000 INFO @ Sun, 21 Jun 2020 20:15:45: 4000000 INFO @ Sun, 21 Jun 2020 20:15:49: 9000000 INFO @ Sun, 21 Jun 2020 20:15:51: 14000000 INFO @ Sun, 21 Jun 2020 20:15:52: 5000000 INFO @ Sun, 21 Jun 2020 20:15:56: 10000000 INFO @ Sun, 21 Jun 2020 20:15:58: 15000000 INFO @ Sun, 21 Jun 2020 20:15:59: 6000000 INFO @ Sun, 21 Jun 2020 20:16:03: 11000000 INFO @ Sun, 21 Jun 2020 20:16:05: 16000000 INFO @ Sun, 21 Jun 2020 20:16:06: 7000000 INFO @ Sun, 21 Jun 2020 20:16:10: 12000000 INFO @ Sun, 21 Jun 2020 20:16:12: 17000000 INFO @ Sun, 21 Jun 2020 20:16:13: 8000000 INFO @ Sun, 21 Jun 2020 20:16:14: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 20:16:14: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 20:16:14: #1 total tags in treatment: 17173175 INFO @ Sun, 21 Jun 2020 20:16:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:16:14: #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 20:16:14: #1 tags after filtering in treatment: 17173169 INFO @ Sun, 21 Jun 2020 20:16:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:16:14: #1 finished! INFO @ Sun, 21 Jun 2020 20:16:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:16:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:16:16: #2 number of paired peaks: 3188 INFO @ Sun, 21 Jun 2020 20:16:16: start model_add_line... INFO @ Sun, 21 Jun 2020 20:16:16: start X-correlation... INFO @ Sun, 21 Jun 2020 20:16:16: end of X-cor INFO @ Sun, 21 Jun 2020 20:16:16: #2 finished! INFO @ Sun, 21 Jun 2020 20:16:16: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 20:16:16: #2 alternative fragment length(s) may be 3,77 bps INFO @ Sun, 21 Jun 2020 20:16:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.05_model.r WARNING @ Sun, 21 Jun 2020 20:16:16: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:16:16: #2 You may need to consider one of the other alternative d(s): 3,77 WARNING @ Sun, 21 Jun 2020 20:16:16: #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 20:16:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:16:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:16:18: 13000000 INFO @ Sun, 21 Jun 2020 20:16:21: 9000000 INFO @ Sun, 21 Jun 2020 20:16:25: 14000000 INFO @ Sun, 21 Jun 2020 20:16:28: 10000000 INFO @ Sun, 21 Jun 2020 20:16:32: 15000000 INFO @ Sun, 21 Jun 2020 20:16:35: 11000000 INFO @ Sun, 21 Jun 2020 20:16:39: 16000000 INFO @ Sun, 21 Jun 2020 20:16:42: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:16:46: 17000000 INFO @ Sun, 21 Jun 2020 20:16:48: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 20:16:48: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 20:16:48: #1 total tags in treatment: 17173175 INFO @ Sun, 21 Jun 2020 20:16:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:16:48: #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 20:16:48: #1 tags after filtering in treatment: 17173169 INFO @ Sun, 21 Jun 2020 20:16:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:16:48: #1 finished! INFO @ Sun, 21 Jun 2020 20:16:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:16:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:16:49: 13000000 INFO @ Sun, 21 Jun 2020 20:16:50: #2 number of paired peaks: 3188 INFO @ Sun, 21 Jun 2020 20:16:50: start model_add_line... INFO @ Sun, 21 Jun 2020 20:16:50: start X-correlation... INFO @ Sun, 21 Jun 2020 20:16:50: end of X-cor INFO @ Sun, 21 Jun 2020 20:16:50: #2 finished! INFO @ Sun, 21 Jun 2020 20:16:50: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 20:16:50: #2 alternative fragment length(s) may be 3,77 bps INFO @ Sun, 21 Jun 2020 20:16:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.10_model.r WARNING @ Sun, 21 Jun 2020 20:16:50: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:16:50: #2 You may need to consider one of the other alternative d(s): 3,77 WARNING @ Sun, 21 Jun 2020 20:16:50: #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 20:16:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:16:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:16:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:16:56: 14000000 INFO @ Sun, 21 Jun 2020 20:17:02: 15000000 INFO @ Sun, 21 Jun 2020 20:17:08: 16000000 INFO @ Sun, 21 Jun 2020 20:17:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:17:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:17:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.05_summits.bed INFO @ Sun, 21 Jun 2020 20:17:13: Done! pass1 - making usageList (964 chroms): 2 millis pass2 - checking and writing primary data (7127 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:17:15: 17000000 INFO @ Sun, 21 Jun 2020 20:17:16: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 20:17:16: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 20:17:16: #1 total tags in treatment: 17173175 INFO @ Sun, 21 Jun 2020 20:17:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:17:16: #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 20:17:17: #1 tags after filtering in treatment: 17173169 INFO @ Sun, 21 Jun 2020 20:17:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:17:17: #1 finished! INFO @ Sun, 21 Jun 2020 20:17:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:17:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:17:18: #2 number of paired peaks: 3188 INFO @ Sun, 21 Jun 2020 20:17:18: start model_add_line... INFO @ Sun, 21 Jun 2020 20:17:18: start X-correlation... INFO @ Sun, 21 Jun 2020 20:17:18: end of X-cor INFO @ Sun, 21 Jun 2020 20:17:18: #2 finished! INFO @ Sun, 21 Jun 2020 20:17:18: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 20:17:18: #2 alternative fragment length(s) may be 3,77 bps INFO @ Sun, 21 Jun 2020 20:17:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.20_model.r WARNING @ Sun, 21 Jun 2020 20:17:18: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:17:18: #2 You may need to consider one of the other alternative d(s): 3,77 WARNING @ Sun, 21 Jun 2020 20:17:18: #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 20:17:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:17:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:17:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:17:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:17:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:17:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.10_summits.bed INFO @ Sun, 21 Jun 2020 20:17:45: Done! pass1 - making usageList (848 chroms): 2 millis pass2 - checking and writing primary data (3921 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:17:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:18:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:18:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:18:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2692976/SRX2692976.20_summits.bed INFO @ Sun, 21 Jun 2020 20:18:15: Done! pass1 - making usageList (754 chroms): 1 millis pass2 - checking and writing primary data (2176 records, 4 fields): 24 millis CompletedMACS2peakCalling