Job ID = 6627565 SRX = SRX8521403 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T03:00:52 prefetch.2.10.7: 1) Downloading 'SRR11978354'... 2020-07-14T03:00:52 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:02:39 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:02:40 prefetch.2.10.7: 'SRR11978354' is valid 2020-07-14T03:02:40 prefetch.2.10.7: 1) 'SRR11978354' was downloaded successfully 2020-07-14T03:02:40 prefetch.2.10.7: 'SRR11978354' has 0 unresolved dependencies Read 13704762 spots for SRR11978354/SRR11978354.sra Written 13704762 spots for SRR11978354/SRR11978354.sra 2020-07-14T03:03:39 prefetch.2.10.7: 1) Downloading 'SRR11978355'... 2020-07-14T03:03:39 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:05:28 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:05:29 prefetch.2.10.7: 'SRR11978355' is valid 2020-07-14T03:05:29 prefetch.2.10.7: 1) 'SRR11978355' was downloaded successfully 2020-07-14T03:05:29 prefetch.2.10.7: 'SRR11978355' has 0 unresolved dependencies Read 13454562 spots for SRR11978355/SRR11978355.sra Written 13454562 spots for SRR11978355/SRR11978355.sra 2020-07-14T03:06:27 prefetch.2.10.7: 1) Downloading 'SRR11978356'... 2020-07-14T03:06:27 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:08:19 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:08:20 prefetch.2.10.7: 'SRR11978356' is valid 2020-07-14T03:08:20 prefetch.2.10.7: 1) 'SRR11978356' was downloaded successfully 2020-07-14T03:08:20 prefetch.2.10.7: 'SRR11978356' has 0 unresolved dependencies Read 13376188 spots for SRR11978356/SRR11978356.sra Written 13376188 spots for SRR11978356/SRR11978356.sra 2020-07-14T03:09:19 prefetch.2.10.7: 1) Downloading 'SRR11978357'... 2020-07-14T03:09:19 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:10:34 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:10:34 prefetch.2.10.7: 'SRR11978357' is valid 2020-07-14T03:10:34 prefetch.2.10.7: 1) 'SRR11978357' was downloaded successfully 2020-07-14T03:10:34 prefetch.2.10.7: 'SRR11978357' has 0 unresolved dependencies Read 13637100 spots for SRR11978357/SRR11978357.sra Written 13637100 spots for SRR11978357/SRR11978357.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627756 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:07:46 54172612 reads; of these: 54172612 (100.00%) were unpaired; of these: 47970572 (88.55%) aligned 0 times 4653307 (8.59%) aligned exactly 1 time 1548733 (2.86%) aligned >1 times 11.45% overall alignment rate Time searching: 00:07:47 Overall time: 00:07:47 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 1080522 / 6202040 = 0.1742 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 @ Tue, 14 Jul 2020 12:21:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.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 @ Tue, 14 Jul 2020 12:21:37: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:21:37: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:21:42: 1000000 INFO @ Tue, 14 Jul 2020 12:21:47: 2000000 INFO @ Tue, 14 Jul 2020 12:21:52: 3000000 INFO @ Tue, 14 Jul 2020 12:21:56: 4000000 INFO @ Tue, 14 Jul 2020 12:22:01: 5000000 INFO @ Tue, 14 Jul 2020 12:22:02: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:22:02: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:22:02: #1 total tags in treatment: 5121518 INFO @ Tue, 14 Jul 2020 12:22:02: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:22:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:22:02: #1 tags after filtering in treatment: 5121518 INFO @ Tue, 14 Jul 2020 12:22:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:22:02: #1 finished! INFO @ Tue, 14 Jul 2020 12:22:02: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:22:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:22:03: #2 number of paired peaks: 489 WARNING @ Tue, 14 Jul 2020 12:22:03: Fewer paired peaks (489) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 489 pairs to build model! INFO @ Tue, 14 Jul 2020 12:22:03: start model_add_line... INFO @ Tue, 14 Jul 2020 12:22:03: start X-correlation... INFO @ Tue, 14 Jul 2020 12:22:03: end of X-cor INFO @ Tue, 14 Jul 2020 12:22:03: #2 finished! INFO @ Tue, 14 Jul 2020 12:22:03: #2 predicted fragment length is 55 bps INFO @ Tue, 14 Jul 2020 12:22:03: #2 alternative fragment length(s) may be 55 bps INFO @ Tue, 14 Jul 2020 12:22:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.05_model.r WARNING @ Tue, 14 Jul 2020 12:22:03: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:22:03: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Tue, 14 Jul 2020 12:22:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:22:03: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:22:03: #3 Pre-compute pvalue-qvalue table... 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 @ Tue, 14 Jul 2020 12:22:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.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 @ Tue, 14 Jul 2020 12:22:07: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:22:07: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:22:12: 1000000 INFO @ Tue, 14 Jul 2020 12:22:13: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:22:17: 2000000 INFO @ Tue, 14 Jul 2020 12:22:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:22:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:22:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.05_summits.bed INFO @ Tue, 14 Jul 2020 12:22:19: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1769 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:22:23: 3000000 INFO @ Tue, 14 Jul 2020 12:22:28: 4000000 INFO @ Tue, 14 Jul 2020 12:22:33: 5000000 INFO @ Tue, 14 Jul 2020 12:22:34: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:22:34: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:22:34: #1 total tags in treatment: 5121518 INFO @ Tue, 14 Jul 2020 12:22:34: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:22:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:22:34: #1 tags after filtering in treatment: 5121518 INFO @ Tue, 14 Jul 2020 12:22:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:22:34: #1 finished! INFO @ Tue, 14 Jul 2020 12:22:34: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:22:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:22:34: #2 number of paired peaks: 489 WARNING @ Tue, 14 Jul 2020 12:22:34: Fewer paired peaks (489) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 489 pairs to build model! INFO @ Tue, 14 Jul 2020 12:22:34: start model_add_line... INFO @ Tue, 14 Jul 2020 12:22:34: start X-correlation... INFO @ Tue, 14 Jul 2020 12:22:34: end of X-cor INFO @ Tue, 14 Jul 2020 12:22:34: #2 finished! INFO @ Tue, 14 Jul 2020 12:22:34: #2 predicted fragment length is 55 bps INFO @ Tue, 14 Jul 2020 12:22:34: #2 alternative fragment length(s) may be 55 bps INFO @ Tue, 14 Jul 2020 12:22:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.10_model.r WARNING @ Tue, 14 Jul 2020 12:22:34: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:22:34: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Tue, 14 Jul 2020 12:22:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:22:34: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:22:34: #3 Pre-compute pvalue-qvalue table... 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 @ Tue, 14 Jul 2020 12:22:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.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 @ Tue, 14 Jul 2020 12:22:37: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:22:37: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:22:42: 1000000 INFO @ Tue, 14 Jul 2020 12:22:45: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:22:49: 2000000 INFO @ Tue, 14 Jul 2020 12:22:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:22:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:22:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.10_summits.bed INFO @ Tue, 14 Jul 2020 12:22:50: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (738 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:22:54: 3000000 INFO @ Tue, 14 Jul 2020 12:23:00: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:23:06: 5000000 INFO @ Tue, 14 Jul 2020 12:23:07: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:23:07: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:23:07: #1 total tags in treatment: 5121518 INFO @ Tue, 14 Jul 2020 12:23:07: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:23:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:23:07: #1 tags after filtering in treatment: 5121518 INFO @ Tue, 14 Jul 2020 12:23:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:23:07: #1 finished! INFO @ Tue, 14 Jul 2020 12:23:07: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:23:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:23:07: #2 number of paired peaks: 489 WARNING @ Tue, 14 Jul 2020 12:23:07: Fewer paired peaks (489) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 489 pairs to build model! INFO @ Tue, 14 Jul 2020 12:23:07: start model_add_line... INFO @ Tue, 14 Jul 2020 12:23:08: start X-correlation... INFO @ Tue, 14 Jul 2020 12:23:08: end of X-cor INFO @ Tue, 14 Jul 2020 12:23:08: #2 finished! INFO @ Tue, 14 Jul 2020 12:23:08: #2 predicted fragment length is 55 bps INFO @ Tue, 14 Jul 2020 12:23:08: #2 alternative fragment length(s) may be 55 bps INFO @ Tue, 14 Jul 2020 12:23:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.20_model.r WARNING @ Tue, 14 Jul 2020 12:23:08: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:23:08: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Tue, 14 Jul 2020 12:23:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:23:08: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:23:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:23:18: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:23:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:23:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:23:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521403/SRX8521403.20_summits.bed INFO @ Tue, 14 Jul 2020 12:23:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (149 records, 4 fields): 1 millis CompletedMACS2peakCalling