Job ID = 6455675 SRX = SRX287979 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:11:06 prefetch.2.10.7: 1) Downloading 'SRR870168'... 2020-06-21T10:11:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:14:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:14:06 prefetch.2.10.7: 'SRR870168' is valid 2020-06-21T10:14:06 prefetch.2.10.7: 1) 'SRR870168' was downloaded successfully Read 13809114 spots for SRR870168/SRR870168.sra Written 13809114 spots for SRR870168/SRR870168.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:10 13809114 reads; of these: 13809114 (100.00%) were unpaired; of these: 756600 (5.48%) aligned 0 times 9039976 (65.46%) aligned exactly 1 time 4012538 (29.06%) aligned >1 times 94.52% overall alignment rate Time searching: 00:04:11 Overall time: 00:04:11 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 8 files... [bam_rmdupse_core] 2216794 / 13052514 = 0.1698 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 19:22:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.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 19:22:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:22:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:22:34: 1000000 INFO @ Sun, 21 Jun 2020 19:22:40: 2000000 INFO @ Sun, 21 Jun 2020 19:22:45: 3000000 INFO @ Sun, 21 Jun 2020 19:22:51: 4000000 INFO @ Sun, 21 Jun 2020 19:22:57: 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 @ Sun, 21 Jun 2020 19:22:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.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 19:22:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:22:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:03: 6000000 INFO @ Sun, 21 Jun 2020 19:23:05: 1000000 INFO @ Sun, 21 Jun 2020 19:23:09: 7000000 INFO @ Sun, 21 Jun 2020 19:23:11: 2000000 INFO @ Sun, 21 Jun 2020 19:23:15: 8000000 INFO @ Sun, 21 Jun 2020 19:23:18: 3000000 INFO @ Sun, 21 Jun 2020 19:23:22: 9000000 INFO @ Sun, 21 Jun 2020 19:23:24: 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 19:23:28: 10000000 INFO @ Sun, 21 Jun 2020 19:23:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.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 19:23:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:23:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:30: 5000000 INFO @ Sun, 21 Jun 2020 19:23:34: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:23:34: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:23:34: #1 total tags in treatment: 10835720 INFO @ Sun, 21 Jun 2020 19:23:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:23:34: #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 19:23:34: #1 tags after filtering in treatment: 10835720 INFO @ Sun, 21 Jun 2020 19:23:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:23:34: #1 finished! INFO @ Sun, 21 Jun 2020 19:23:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:23:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:23:35: 1000000 INFO @ Sun, 21 Jun 2020 19:23:35: #2 number of paired peaks: 693 WARNING @ Sun, 21 Jun 2020 19:23:35: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Sun, 21 Jun 2020 19:23:35: start model_add_line... INFO @ Sun, 21 Jun 2020 19:23:35: start X-correlation... INFO @ Sun, 21 Jun 2020 19:23:35: end of X-cor INFO @ Sun, 21 Jun 2020 19:23:35: #2 finished! INFO @ Sun, 21 Jun 2020 19:23:35: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:23:35: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 19:23:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.05_model.r WARNING @ Sun, 21 Jun 2020 19:23:35: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:23:35: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 19:23:35: #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 19:23:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:23:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:23:37: 6000000 INFO @ Sun, 21 Jun 2020 19:23:41: 2000000 INFO @ Sun, 21 Jun 2020 19:23:43: 7000000 INFO @ Sun, 21 Jun 2020 19:23:48: 3000000 INFO @ Sun, 21 Jun 2020 19:23:49: 8000000 INFO @ Sun, 21 Jun 2020 19:23:54: 4000000 INFO @ Sun, 21 Jun 2020 19:23:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:23:56: 9000000 INFO @ Sun, 21 Jun 2020 19:24:00: 5000000 INFO @ Sun, 21 Jun 2020 19:24:03: 10000000 INFO @ Sun, 21 Jun 2020 19:24:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:24:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:24:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.05_summits.bed INFO @ Sun, 21 Jun 2020 19:24:06: Done! INFO @ Sun, 21 Jun 2020 19:24:07: 6000000 pass1 - making usageList (582 chroms): 1 millis pass2 - checking and writing primary data (2272 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:24:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:24:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:24:08: #1 total tags in treatment: 10835720 INFO @ Sun, 21 Jun 2020 19:24:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:24:08: #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 19:24:09: #1 tags after filtering in treatment: 10835720 INFO @ Sun, 21 Jun 2020 19:24:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:24:09: #1 finished! INFO @ Sun, 21 Jun 2020 19:24:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:24:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:24:10: #2 number of paired peaks: 693 WARNING @ Sun, 21 Jun 2020 19:24:10: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Sun, 21 Jun 2020 19:24:10: start model_add_line... INFO @ Sun, 21 Jun 2020 19:24:10: start X-correlation... INFO @ Sun, 21 Jun 2020 19:24:10: end of X-cor INFO @ Sun, 21 Jun 2020 19:24:10: #2 finished! INFO @ Sun, 21 Jun 2020 19:24:10: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:24:10: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 19:24:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.10_model.r WARNING @ Sun, 21 Jun 2020 19:24:10: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:24:10: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 19:24:10: #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 19:24:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:24:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:24:13: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:24:19: 8000000 INFO @ Sun, 21 Jun 2020 19:24:25: 9000000 INFO @ Sun, 21 Jun 2020 19:24:30: 10000000 INFO @ Sun, 21 Jun 2020 19:24:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:24:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:24:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:24:35: #1 total tags in treatment: 10835720 INFO @ Sun, 21 Jun 2020 19:24:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:24:35: #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 19:24:36: #1 tags after filtering in treatment: 10835720 INFO @ Sun, 21 Jun 2020 19:24:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:24:36: #1 finished! INFO @ Sun, 21 Jun 2020 19:24:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:24:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:24:37: #2 number of paired peaks: 693 WARNING @ Sun, 21 Jun 2020 19:24:37: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Sun, 21 Jun 2020 19:24:37: start model_add_line... INFO @ Sun, 21 Jun 2020 19:24:37: start X-correlation... INFO @ Sun, 21 Jun 2020 19:24:37: end of X-cor INFO @ Sun, 21 Jun 2020 19:24:37: #2 finished! INFO @ Sun, 21 Jun 2020 19:24:37: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:24:37: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 19:24:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.20_model.r WARNING @ Sun, 21 Jun 2020 19:24:37: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:24:37: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 19:24:37: #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 19:24:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:24:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:24:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:24:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:24:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.10_summits.bed INFO @ Sun, 21 Jun 2020 19:24:42: Done! pass1 - making usageList (495 chroms): 1 millis pass2 - checking and writing primary data (1830 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:24:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:25:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:25:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:25:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287979/SRX287979.20_summits.bed INFO @ Sun, 21 Jun 2020 19:25:09: Done! pass1 - making usageList (319 chroms): 1 millis pass2 - checking and writing primary data (676 records, 4 fields): 10 millis CompletedMACS2peakCalling