Job ID = 6527792 SRX = SRX287603 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:44:00 prefetch.2.10.7: 1) Downloading 'SRR869746'... 2020-06-29T13:44:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:47:54 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:47:54 prefetch.2.10.7: 1) 'SRR869746' was downloaded successfully Read 23008083 spots for SRR869746/SRR869746.sra Written 23008083 spots for SRR869746/SRR869746.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: 00:08:50 23008083 reads; of these: 23008083 (100.00%) were unpaired; of these: 1291622 (5.61%) aligned 0 times 14514810 (63.09%) aligned exactly 1 time 7201651 (31.30%) aligned >1 times 94.39% overall alignment rate Time searching: 00:08:50 Overall time: 00:08:50 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_sort_core] merging from 12 files... [bam_rmdupse_core] 3391686 / 21716461 = 0.1562 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 @ Mon, 29 Jun 2020 23:08:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.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 @ Mon, 29 Jun 2020 23:08:10: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:08:10: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:08:16: 1000000 INFO @ Mon, 29 Jun 2020 23:08:21: 2000000 INFO @ Mon, 29 Jun 2020 23:08:26: 3000000 INFO @ Mon, 29 Jun 2020 23:08:31: 4000000 INFO @ Mon, 29 Jun 2020 23:08:36: 5000000 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 @ Mon, 29 Jun 2020 23:08:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.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 @ Mon, 29 Jun 2020 23:08:40: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:08:40: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:08:42: 6000000 INFO @ Mon, 29 Jun 2020 23:08:46: 1000000 INFO @ Mon, 29 Jun 2020 23:08:47: 7000000 INFO @ Mon, 29 Jun 2020 23:08:52: 2000000 INFO @ Mon, 29 Jun 2020 23:08:53: 8000000 INFO @ Mon, 29 Jun 2020 23:08:57: 3000000 INFO @ Mon, 29 Jun 2020 23:08:58: 9000000 INFO @ Mon, 29 Jun 2020 23:09:03: 4000000 INFO @ Mon, 29 Jun 2020 23:09:04: 10000000 INFO @ Mon, 29 Jun 2020 23:09:08: 5000000 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 @ Mon, 29 Jun 2020 23:09:09: 11000000 INFO @ Mon, 29 Jun 2020 23:09:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.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 @ Mon, 29 Jun 2020 23:09:10: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:09:10: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:09:14: 6000000 INFO @ Mon, 29 Jun 2020 23:09:14: 12000000 INFO @ Mon, 29 Jun 2020 23:09:15: 1000000 INFO @ Mon, 29 Jun 2020 23:09:19: 7000000 INFO @ Mon, 29 Jun 2020 23:09:20: 2000000 INFO @ Mon, 29 Jun 2020 23:09:20: 13000000 INFO @ Mon, 29 Jun 2020 23:09:24: 8000000 INFO @ Mon, 29 Jun 2020 23:09:24: 3000000 INFO @ Mon, 29 Jun 2020 23:09:25: 14000000 INFO @ Mon, 29 Jun 2020 23:09:29: 4000000 INFO @ Mon, 29 Jun 2020 23:09:29: 9000000 INFO @ Mon, 29 Jun 2020 23:09:30: 15000000 INFO @ Mon, 29 Jun 2020 23:09:34: 5000000 INFO @ Mon, 29 Jun 2020 23:09:35: 10000000 INFO @ Mon, 29 Jun 2020 23:09:36: 16000000 INFO @ Mon, 29 Jun 2020 23:09:38: 6000000 INFO @ Mon, 29 Jun 2020 23:09:40: 11000000 INFO @ Mon, 29 Jun 2020 23:09:41: 17000000 INFO @ Mon, 29 Jun 2020 23:09:43: 7000000 INFO @ Mon, 29 Jun 2020 23:09:45: 12000000 INFO @ Mon, 29 Jun 2020 23:09:46: 18000000 INFO @ Mon, 29 Jun 2020 23:09:48: 8000000 INFO @ Mon, 29 Jun 2020 23:09:48: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:09:48: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:09:48: #1 total tags in treatment: 18324775 INFO @ Mon, 29 Jun 2020 23:09:48: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:09:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:09:48: #1 tags after filtering in treatment: 18324775 INFO @ Mon, 29 Jun 2020 23:09:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:09:48: #1 finished! INFO @ Mon, 29 Jun 2020 23:09:48: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:09:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:09:49: #2 number of paired peaks: 144 WARNING @ Mon, 29 Jun 2020 23:09:49: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Mon, 29 Jun 2020 23:09:49: start model_add_line... INFO @ Mon, 29 Jun 2020 23:09:50: start X-correlation... INFO @ Mon, 29 Jun 2020 23:09:50: end of X-cor INFO @ Mon, 29 Jun 2020 23:09:50: #2 finished! INFO @ Mon, 29 Jun 2020 23:09:50: #2 predicted fragment length is 45 bps INFO @ Mon, 29 Jun 2020 23:09:50: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 29 Jun 2020 23:09:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.05_model.r WARNING @ Mon, 29 Jun 2020 23:09:50: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:09:50: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 29 Jun 2020 23:09:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:09:50: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:09:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:09:50: 13000000 INFO @ Mon, 29 Jun 2020 23:09:53: 9000000 INFO @ Mon, 29 Jun 2020 23:09:56: 14000000 INFO @ Mon, 29 Jun 2020 23:09:58: 10000000 INFO @ Mon, 29 Jun 2020 23:10:01: 15000000 INFO @ Mon, 29 Jun 2020 23:10:03: 11000000 INFO @ Mon, 29 Jun 2020 23:10:06: 16000000 INFO @ Mon, 29 Jun 2020 23:10:07: 12000000 INFO @ Mon, 29 Jun 2020 23:10:11: 17000000 INFO @ Mon, 29 Jun 2020 23:10:12: 13000000 INFO @ Mon, 29 Jun 2020 23:10:16: 18000000 INFO @ Mon, 29 Jun 2020 23:10:16: 14000000 INFO @ Mon, 29 Jun 2020 23:10:18: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:10:18: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:10:18: #1 total tags in treatment: 18324775 INFO @ Mon, 29 Jun 2020 23:10:18: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:10:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:10:18: #1 tags after filtering in treatment: 18324775 INFO @ Mon, 29 Jun 2020 23:10:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:10:18: #1 finished! INFO @ Mon, 29 Jun 2020 23:10:18: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:10:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:10:19: #2 number of paired peaks: 144 WARNING @ Mon, 29 Jun 2020 23:10:19: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Mon, 29 Jun 2020 23:10:19: start model_add_line... INFO @ Mon, 29 Jun 2020 23:10:19: start X-correlation... INFO @ Mon, 29 Jun 2020 23:10:19: end of X-cor INFO @ Mon, 29 Jun 2020 23:10:19: #2 finished! INFO @ Mon, 29 Jun 2020 23:10:19: #2 predicted fragment length is 45 bps INFO @ Mon, 29 Jun 2020 23:10:19: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 29 Jun 2020 23:10:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.10_model.r WARNING @ Mon, 29 Jun 2020 23:10:19: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:10:19: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 29 Jun 2020 23:10:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:10:19: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:10:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:10:21: 15000000 INFO @ Mon, 29 Jun 2020 23:10:23: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:10:25: 16000000 INFO @ Mon, 29 Jun 2020 23:10:30: 17000000 INFO @ Mon, 29 Jun 2020 23:10:35: 18000000 INFO @ Mon, 29 Jun 2020 23:10:36: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:10:36: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:10:36: #1 total tags in treatment: 18324775 INFO @ Mon, 29 Jun 2020 23:10:36: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:10:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:10:36: #1 tags after filtering in treatment: 18324775 INFO @ Mon, 29 Jun 2020 23:10:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:10:36: #1 finished! INFO @ Mon, 29 Jun 2020 23:10:36: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:10:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:10:38: #2 number of paired peaks: 144 WARNING @ Mon, 29 Jun 2020 23:10:38: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Mon, 29 Jun 2020 23:10:38: start model_add_line... INFO @ Mon, 29 Jun 2020 23:10:38: start X-correlation... INFO @ Mon, 29 Jun 2020 23:10:38: end of X-cor INFO @ Mon, 29 Jun 2020 23:10:38: #2 finished! INFO @ Mon, 29 Jun 2020 23:10:38: #2 predicted fragment length is 45 bps INFO @ Mon, 29 Jun 2020 23:10:38: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 29 Jun 2020 23:10:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.20_model.r WARNING @ Mon, 29 Jun 2020 23:10:38: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:10:38: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 29 Jun 2020 23:10:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:10:38: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:10:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:10:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:10:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:10:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.05_summits.bed INFO @ Mon, 29 Jun 2020 23:10:40: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2175 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:10:52: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:11:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:11:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:11:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.10_summits.bed INFO @ Mon, 29 Jun 2020 23:11:09: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1805 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:11:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:11:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:11:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:11:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287603/SRX287603.20_summits.bed INFO @ Mon, 29 Jun 2020 23:11:28: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1349 records, 4 fields): 3 millis CompletedMACS2peakCalling