Job ID = 6452637 SRX = SRX020697 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:59:53 prefetch.2.10.7: 1) Downloading 'SRR060775'... 2020-06-21T07:59:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:03:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:03:40 prefetch.2.10.7: 1) 'SRR060775' was downloaded successfully Read 18869507 spots for SRR060775/SRR060775.sra Written 18869507 spots for SRR060775/SRR060775.sra 2020-06-21T08:04:45 prefetch.2.10.7: 1) Downloading 'SRR060776'... 2020-06-21T08:04:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:06:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:06:24 prefetch.2.10.7: 'SRR060776' is valid 2020-06-21T08:06:24 prefetch.2.10.7: 1) 'SRR060776' was downloaded successfully Read 10207389 spots for SRR060776/SRR060776.sra Written 10207389 spots for SRR060776/SRR060776.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: 00:03:52 29076896 reads; of these: 29076896 (100.00%) were unpaired; of these: 14943605 (51.39%) aligned 0 times 11410782 (39.24%) aligned exactly 1 time 2722509 (9.36%) aligned >1 times 48.61% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 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_rmdupse_core] 3460106 / 14133291 = 0.2448 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 17:14:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.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 17:14:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:14:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:14:09: 1000000 INFO @ Sun, 21 Jun 2020 17:14:13: 2000000 INFO @ Sun, 21 Jun 2020 17:14:18: 3000000 INFO @ Sun, 21 Jun 2020 17:14:22: 4000000 INFO @ Sun, 21 Jun 2020 17:14:27: 5000000 INFO @ Sun, 21 Jun 2020 17:14:31: 6000000 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 17:14:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.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 17:14:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:14:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:14:36: 7000000 INFO @ Sun, 21 Jun 2020 17:14:38: 1000000 INFO @ Sun, 21 Jun 2020 17:14:40: 8000000 INFO @ Sun, 21 Jun 2020 17:14:43: 2000000 INFO @ Sun, 21 Jun 2020 17:14:45: 9000000 INFO @ Sun, 21 Jun 2020 17:14:47: 3000000 INFO @ Sun, 21 Jun 2020 17:14:49: 10000000 INFO @ Sun, 21 Jun 2020 17:14:52: 4000000 INFO @ Sun, 21 Jun 2020 17:14:53: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:14:53: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:14:53: #1 total tags in treatment: 10673185 INFO @ Sun, 21 Jun 2020 17:14:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:14:53: #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 17:14:53: #1 tags after filtering in treatment: 10673180 INFO @ Sun, 21 Jun 2020 17:14:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:14:53: #1 finished! INFO @ Sun, 21 Jun 2020 17:14:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:14:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:14:54: #2 number of paired peaks: 1700 INFO @ Sun, 21 Jun 2020 17:14:54: start model_add_line... INFO @ Sun, 21 Jun 2020 17:14:54: start X-correlation... INFO @ Sun, 21 Jun 2020 17:14:54: end of X-cor INFO @ Sun, 21 Jun 2020 17:14:54: #2 finished! INFO @ Sun, 21 Jun 2020 17:14:54: #2 predicted fragment length is 68 bps INFO @ Sun, 21 Jun 2020 17:14:54: #2 alternative fragment length(s) may be 68 bps INFO @ Sun, 21 Jun 2020 17:14:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.05_model.r WARNING @ Sun, 21 Jun 2020 17:14:54: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:14:54: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sun, 21 Jun 2020 17:14:54: #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 17:14:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:14:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:14:56: 5000000 INFO @ Sun, 21 Jun 2020 17:15:01: 6000000 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 17:15:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.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 17:15:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:15:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:15:06: 7000000 INFO @ Sun, 21 Jun 2020 17:15:08: 1000000 INFO @ Sun, 21 Jun 2020 17:15:10: 8000000 INFO @ Sun, 21 Jun 2020 17:15:13: 2000000 INFO @ Sun, 21 Jun 2020 17:15:15: 9000000 INFO @ Sun, 21 Jun 2020 17:15:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:15:18: 3000000 INFO @ Sun, 21 Jun 2020 17:15:20: 10000000 INFO @ Sun, 21 Jun 2020 17:15:22: 4000000 INFO @ Sun, 21 Jun 2020 17:15:24: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:15:24: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:15:24: #1 total tags in treatment: 10673185 INFO @ Sun, 21 Jun 2020 17:15:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:15:24: #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 17:15:24: #1 tags after filtering in treatment: 10673180 INFO @ Sun, 21 Jun 2020 17:15:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:15:24: #1 finished! INFO @ Sun, 21 Jun 2020 17:15:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:15:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:15:25: #2 number of paired peaks: 1700 INFO @ Sun, 21 Jun 2020 17:15:25: start model_add_line... INFO @ Sun, 21 Jun 2020 17:15:25: start X-correlation... INFO @ Sun, 21 Jun 2020 17:15:25: end of X-cor INFO @ Sun, 21 Jun 2020 17:15:25: #2 finished! INFO @ Sun, 21 Jun 2020 17:15:25: #2 predicted fragment length is 68 bps INFO @ Sun, 21 Jun 2020 17:15:25: #2 alternative fragment length(s) may be 68 bps INFO @ Sun, 21 Jun 2020 17:15:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.10_model.r WARNING @ Sun, 21 Jun 2020 17:15:25: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:15:25: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sun, 21 Jun 2020 17:15:25: #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 17:15:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:15:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:15:27: 5000000 INFO @ Sun, 21 Jun 2020 17:15:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:15:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:15:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.05_summits.bed INFO @ Sun, 21 Jun 2020 17:15:29: Done! pass1 - making usageList (330 chroms): 2 millis pass2 - checking and writing primary data (9013 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:15:31: 6000000 INFO @ Sun, 21 Jun 2020 17:15:36: 7000000 INFO @ Sun, 21 Jun 2020 17:15:40: 8000000 INFO @ Sun, 21 Jun 2020 17:15:45: 9000000 INFO @ Sun, 21 Jun 2020 17:15:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:15:49: 10000000 INFO @ Sun, 21 Jun 2020 17:15:53: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:15:53: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:15:53: #1 total tags in treatment: 10673185 INFO @ Sun, 21 Jun 2020 17:15:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:15:53: #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 17:15:53: #1 tags after filtering in treatment: 10673180 INFO @ Sun, 21 Jun 2020 17:15:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:15:53: #1 finished! INFO @ Sun, 21 Jun 2020 17:15:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:15:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:15:54: #2 number of paired peaks: 1700 INFO @ Sun, 21 Jun 2020 17:15:54: start model_add_line... INFO @ Sun, 21 Jun 2020 17:15:54: start X-correlation... INFO @ Sun, 21 Jun 2020 17:15:54: end of X-cor INFO @ Sun, 21 Jun 2020 17:15:54: #2 finished! INFO @ Sun, 21 Jun 2020 17:15:54: #2 predicted fragment length is 68 bps INFO @ Sun, 21 Jun 2020 17:15:54: #2 alternative fragment length(s) may be 68 bps INFO @ Sun, 21 Jun 2020 17:15:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.20_model.r WARNING @ Sun, 21 Jun 2020 17:15:54: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:15:54: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sun, 21 Jun 2020 17:15:54: #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 17:15:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:15:54: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:16:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:16:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:16:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.10_summits.bed INFO @ Sun, 21 Jun 2020 17:16:01: Done! pass1 - making usageList (141 chroms): 2 millis pass2 - checking and writing primary data (4954 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:16:16: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:16:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:16:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:16:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX020697/SRX020697.20_summits.bed INFO @ Sun, 21 Jun 2020 17:16:27: Done! pass1 - making usageList (108 chroms): 1 millis pass2 - checking and writing primary data (1795 records, 4 fields): 6 millis CompletedMACS2peakCalling