Job ID = 6455416 SRX = SRX287770 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:02:40 prefetch.2.10.7: 1) Downloading 'SRR869959'... 2020-06-21T10:02:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:04:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:04:57 prefetch.2.10.7: 1) 'SRR869959' was downloaded successfully Read 17667108 spots for SRR869959/SRR869959.sra Written 17667108 spots for SRR869959/SRR869959.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: 00:05:36 17667108 reads; of these: 17667108 (100.00%) were unpaired; of these: 989039 (5.60%) aligned 0 times 11539930 (65.32%) aligned exactly 1 time 5138139 (29.08%) aligned >1 times 94.40% overall alignment rate Time searching: 00:05:36 Overall time: 00:05:36 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] 2391920 / 16678069 = 0.1434 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 19:16:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.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 19:16:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:16:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:16:06: 1000000 INFO @ Sun, 21 Jun 2020 19:16:12: 2000000 INFO @ Sun, 21 Jun 2020 19:16:18: 3000000 INFO @ Sun, 21 Jun 2020 19:16:24: 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 19:16:29: 5000000 INFO @ Sun, 21 Jun 2020 19:16:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.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 19:16:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:16:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:16:36: 6000000 INFO @ Sun, 21 Jun 2020 19:16:38: 1000000 INFO @ Sun, 21 Jun 2020 19:16:43: 7000000 INFO @ Sun, 21 Jun 2020 19:16:46: 2000000 INFO @ Sun, 21 Jun 2020 19:16:51: 8000000 INFO @ Sun, 21 Jun 2020 19:16:54: 3000000 INFO @ Sun, 21 Jun 2020 19:16:58: 9000000 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 19:17:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.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 19:17:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:17:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:17:01: 4000000 INFO @ Sun, 21 Jun 2020 19:17:05: 10000000 INFO @ Sun, 21 Jun 2020 19:17:08: 1000000 INFO @ Sun, 21 Jun 2020 19:17:09: 5000000 INFO @ Sun, 21 Jun 2020 19:17:12: 11000000 INFO @ Sun, 21 Jun 2020 19:17:15: 2000000 INFO @ Sun, 21 Jun 2020 19:17:17: 6000000 INFO @ Sun, 21 Jun 2020 19:17:20: 12000000 INFO @ Sun, 21 Jun 2020 19:17:22: 3000000 INFO @ Sun, 21 Jun 2020 19:17:25: 7000000 INFO @ Sun, 21 Jun 2020 19:17:28: 13000000 INFO @ Sun, 21 Jun 2020 19:17:30: 4000000 INFO @ Sun, 21 Jun 2020 19:17:33: 8000000 INFO @ Sun, 21 Jun 2020 19:17:36: 14000000 INFO @ Sun, 21 Jun 2020 19:17:37: 5000000 INFO @ Sun, 21 Jun 2020 19:17:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:17:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:17:38: #1 total tags in treatment: 14286149 INFO @ Sun, 21 Jun 2020 19:17:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:17:38: #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 19:17:38: #1 tags after filtering in treatment: 14286149 INFO @ Sun, 21 Jun 2020 19:17:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:17:38: #1 finished! INFO @ Sun, 21 Jun 2020 19:17:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:17:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:17:39: #2 number of paired peaks: 449 WARNING @ Sun, 21 Jun 2020 19:17:39: Fewer paired peaks (449) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 449 pairs to build model! INFO @ Sun, 21 Jun 2020 19:17:39: start model_add_line... INFO @ Sun, 21 Jun 2020 19:17:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:17:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:17:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:17:39: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:17:39: #2 alternative fragment length(s) may be 4,42 bps INFO @ Sun, 21 Jun 2020 19:17:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.05_model.r WARNING @ Sun, 21 Jun 2020 19:17:39: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:17:39: #2 You may need to consider one of the other alternative d(s): 4,42 WARNING @ Sun, 21 Jun 2020 19:17:39: #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 19:17:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:17:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:17:42: 9000000 INFO @ Sun, 21 Jun 2020 19:17:44: 6000000 INFO @ Sun, 21 Jun 2020 19:17:50: 10000000 INFO @ Sun, 21 Jun 2020 19:17:52: 7000000 INFO @ Sun, 21 Jun 2020 19:17:58: 11000000 INFO @ Sun, 21 Jun 2020 19:17:59: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:18:06: 12000000 INFO @ Sun, 21 Jun 2020 19:18:07: 9000000 INFO @ Sun, 21 Jun 2020 19:18:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:18:14: 10000000 INFO @ Sun, 21 Jun 2020 19:18:15: 13000000 INFO @ Sun, 21 Jun 2020 19:18:21: 11000000 INFO @ Sun, 21 Jun 2020 19:18:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:18:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:18:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.05_summits.bed INFO @ Sun, 21 Jun 2020 19:18:22: Done! pass1 - making usageList (617 chroms): 1 millis pass2 - checking and writing primary data (2379 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:18:23: 14000000 INFO @ Sun, 21 Jun 2020 19:18:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:18:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:18:26: #1 total tags in treatment: 14286149 INFO @ Sun, 21 Jun 2020 19:18:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:18:26: #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 19:18:26: #1 tags after filtering in treatment: 14286149 INFO @ Sun, 21 Jun 2020 19:18:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:18:26: #1 finished! INFO @ Sun, 21 Jun 2020 19:18:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:18:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:18:27: #2 number of paired peaks: 449 WARNING @ Sun, 21 Jun 2020 19:18:27: Fewer paired peaks (449) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 449 pairs to build model! INFO @ Sun, 21 Jun 2020 19:18:27: start model_add_line... INFO @ Sun, 21 Jun 2020 19:18:27: start X-correlation... INFO @ Sun, 21 Jun 2020 19:18:27: end of X-cor INFO @ Sun, 21 Jun 2020 19:18:27: #2 finished! INFO @ Sun, 21 Jun 2020 19:18:27: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:18:27: #2 alternative fragment length(s) may be 4,42 bps INFO @ Sun, 21 Jun 2020 19:18:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.10_model.r WARNING @ Sun, 21 Jun 2020 19:18:27: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:18:27: #2 You may need to consider one of the other alternative d(s): 4,42 WARNING @ Sun, 21 Jun 2020 19:18:27: #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 19:18:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:18:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:18:29: 12000000 INFO @ Sun, 21 Jun 2020 19:18:35: 13000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:18:41: 14000000 INFO @ Sun, 21 Jun 2020 19:18:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:18:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:18:43: #1 total tags in treatment: 14286149 INFO @ Sun, 21 Jun 2020 19:18:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:18:43: #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 19:18:44: #1 tags after filtering in treatment: 14286149 INFO @ Sun, 21 Jun 2020 19:18:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:18:44: #1 finished! INFO @ Sun, 21 Jun 2020 19:18:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:18:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:18:45: #2 number of paired peaks: 449 WARNING @ Sun, 21 Jun 2020 19:18:45: Fewer paired peaks (449) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 449 pairs to build model! INFO @ Sun, 21 Jun 2020 19:18:45: start model_add_line... INFO @ Sun, 21 Jun 2020 19:18:45: start X-correlation... INFO @ Sun, 21 Jun 2020 19:18:45: end of X-cor INFO @ Sun, 21 Jun 2020 19:18:45: #2 finished! INFO @ Sun, 21 Jun 2020 19:18:45: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:18:45: #2 alternative fragment length(s) may be 4,42 bps INFO @ Sun, 21 Jun 2020 19:18:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.20_model.r WARNING @ Sun, 21 Jun 2020 19:18:45: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:18:45: #2 You may need to consider one of the other alternative d(s): 4,42 WARNING @ Sun, 21 Jun 2020 19:18:45: #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 19:18:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:18:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:18:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:19:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:19:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:19:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.10_summits.bed INFO @ Sun, 21 Jun 2020 19:19:09: Done! pass1 - making usageList (508 chroms): 1 millis pass2 - checking and writing primary data (1854 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:19:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:19:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:19:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:19:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287770/SRX287770.20_summits.bed INFO @ Sun, 21 Jun 2020 19:19:27: Done! pass1 - making usageList (282 chroms): 1 millis pass2 - checking and writing primary data (577 records, 4 fields): 10 millis CompletedMACS2peakCalling