Job ID = 6455461 SRX = SRX287806 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:06:25 prefetch.2.10.7: 1) Downloading 'SRR869995'... 2020-06-21T10:06:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:11:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:11:30 prefetch.2.10.7: 1) 'SRR869995' was downloaded successfully Read 21559305 spots for SRR869995/SRR869995.sra Written 21559305 spots for SRR869995/SRR869995.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: 00:05:56 21559305 reads; of these: 21559305 (100.00%) were unpaired; of these: 1516113 (7.03%) aligned 0 times 15525199 (72.01%) aligned exactly 1 time 4517993 (20.96%) aligned >1 times 92.97% overall alignment rate Time searching: 00:05:56 Overall time: 00:05:56 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 12 files... [bam_rmdupse_core] 2295213 / 20043192 = 0.1145 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 19:23:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.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 19:23:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:23:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:50: 1000000 INFO @ Sun, 21 Jun 2020 19:23:55: 2000000 INFO @ Sun, 21 Jun 2020 19:23:59: 3000000 INFO @ Sun, 21 Jun 2020 19:24:04: 4000000 INFO @ Sun, 21 Jun 2020 19:24:09: 5000000 INFO @ Sun, 21 Jun 2020 19:24:13: 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 19:24:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.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 19:24:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:24:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:24:18: 7000000 INFO @ Sun, 21 Jun 2020 19:24:20: 1000000 INFO @ Sun, 21 Jun 2020 19:24:23: 8000000 INFO @ Sun, 21 Jun 2020 19:24:25: 2000000 INFO @ Sun, 21 Jun 2020 19:24:28: 9000000 INFO @ Sun, 21 Jun 2020 19:24:30: 3000000 INFO @ Sun, 21 Jun 2020 19:24:32: 10000000 INFO @ Sun, 21 Jun 2020 19:24:34: 4000000 INFO @ Sun, 21 Jun 2020 19:24:37: 11000000 INFO @ Sun, 21 Jun 2020 19:24:39: 5000000 INFO @ Sun, 21 Jun 2020 19:24:42: 12000000 INFO @ Sun, 21 Jun 2020 19:24:44: 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 19:24:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.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 19:24:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:24:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:24:47: 13000000 INFO @ Sun, 21 Jun 2020 19:24:49: 7000000 INFO @ Sun, 21 Jun 2020 19:24:51: 1000000 INFO @ Sun, 21 Jun 2020 19:24:52: 14000000 INFO @ Sun, 21 Jun 2020 19:24:53: 8000000 INFO @ Sun, 21 Jun 2020 19:24:55: 2000000 INFO @ Sun, 21 Jun 2020 19:24:57: 15000000 INFO @ Sun, 21 Jun 2020 19:24:58: 9000000 INFO @ Sun, 21 Jun 2020 19:25:00: 3000000 INFO @ Sun, 21 Jun 2020 19:25:02: 16000000 INFO @ Sun, 21 Jun 2020 19:25:03: 10000000 INFO @ Sun, 21 Jun 2020 19:25:05: 4000000 INFO @ Sun, 21 Jun 2020 19:25:07: 17000000 INFO @ Sun, 21 Jun 2020 19:25:08: 11000000 INFO @ Sun, 21 Jun 2020 19:25:10: 5000000 INFO @ Sun, 21 Jun 2020 19:25:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:25:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:25:11: #1 total tags in treatment: 17747979 INFO @ Sun, 21 Jun 2020 19:25:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:25:11: #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 19:25:12: #1 tags after filtering in treatment: 17747979 INFO @ Sun, 21 Jun 2020 19:25:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:25:12: #1 finished! INFO @ Sun, 21 Jun 2020 19:25:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:25:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:25:13: #2 number of paired peaks: 243 WARNING @ Sun, 21 Jun 2020 19:25:13: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Sun, 21 Jun 2020 19:25:13: start model_add_line... INFO @ Sun, 21 Jun 2020 19:25:13: start X-correlation... INFO @ Sun, 21 Jun 2020 19:25:13: end of X-cor INFO @ Sun, 21 Jun 2020 19:25:13: #2 finished! INFO @ Sun, 21 Jun 2020 19:25:13: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:25:13: #2 alternative fragment length(s) may be 3,41 bps INFO @ Sun, 21 Jun 2020 19:25:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.05_model.r WARNING @ Sun, 21 Jun 2020 19:25:13: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:25:13: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Sun, 21 Jun 2020 19:25:13: #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 19:25:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:25:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:25:13: 12000000 INFO @ Sun, 21 Jun 2020 19:25:15: 6000000 INFO @ Sun, 21 Jun 2020 19:25:18: 13000000 INFO @ Sun, 21 Jun 2020 19:25:20: 7000000 INFO @ Sun, 21 Jun 2020 19:25:23: 14000000 INFO @ Sun, 21 Jun 2020 19:25:25: 8000000 INFO @ Sun, 21 Jun 2020 19:25:28: 15000000 INFO @ Sun, 21 Jun 2020 19:25:30: 9000000 INFO @ Sun, 21 Jun 2020 19:25:33: 16000000 INFO @ Sun, 21 Jun 2020 19:25:35: 10000000 INFO @ Sun, 21 Jun 2020 19:25:38: 17000000 INFO @ Sun, 21 Jun 2020 19:25:40: 11000000 INFO @ Sun, 21 Jun 2020 19:25:42: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:25:42: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:25:42: #1 total tags in treatment: 17747979 INFO @ Sun, 21 Jun 2020 19:25:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:25:42: #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 19:25:43: #1 tags after filtering in treatment: 17747979 INFO @ Sun, 21 Jun 2020 19:25:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:25:43: #1 finished! INFO @ Sun, 21 Jun 2020 19:25:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:25:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:25:44: #2 number of paired peaks: 243 WARNING @ Sun, 21 Jun 2020 19:25:44: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Sun, 21 Jun 2020 19:25:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:25:44: start X-correlation... INFO @ Sun, 21 Jun 2020 19:25:44: end of X-cor INFO @ Sun, 21 Jun 2020 19:25:44: #2 finished! INFO @ Sun, 21 Jun 2020 19:25:44: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:25:44: #2 alternative fragment length(s) may be 3,41 bps INFO @ Sun, 21 Jun 2020 19:25:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.10_model.r WARNING @ Sun, 21 Jun 2020 19:25:44: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:25:44: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Sun, 21 Jun 2020 19:25:44: #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 19:25:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:25:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:25:45: 12000000 INFO @ Sun, 21 Jun 2020 19:25:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:25:50: 13000000 INFO @ Sun, 21 Jun 2020 19:25:55: 14000000 INFO @ Sun, 21 Jun 2020 19:26:00: 15000000 INFO @ Sun, 21 Jun 2020 19:26:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:26:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:26:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.05_summits.bed INFO @ Sun, 21 Jun 2020 19:26:03: Done! pass1 - making usageList (510 chroms): 1 millis pass2 - checking and writing primary data (2172 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:26:06: 16000000 INFO @ Sun, 21 Jun 2020 19:26:11: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:26:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:26:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:26:15: #1 total tags in treatment: 17747979 INFO @ Sun, 21 Jun 2020 19:26:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:26:15: #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 19:26:15: #1 tags after filtering in treatment: 17747979 INFO @ Sun, 21 Jun 2020 19:26:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:26:15: #1 finished! INFO @ Sun, 21 Jun 2020 19:26:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:26:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:26:17: #2 number of paired peaks: 243 WARNING @ Sun, 21 Jun 2020 19:26:17: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Sun, 21 Jun 2020 19:26:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:26:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:26:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:26:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:26:17: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:26:17: #2 alternative fragment length(s) may be 3,41 bps INFO @ Sun, 21 Jun 2020 19:26:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.20_model.r WARNING @ Sun, 21 Jun 2020 19:26:17: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:26:17: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Sun, 21 Jun 2020 19:26:17: #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 19:26:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:26:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:26:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:26:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:26:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:26:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.10_summits.bed INFO @ Sun, 21 Jun 2020 19:26:35: Done! pass1 - making usageList (434 chroms): 1 millis pass2 - checking and writing primary data (1422 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:26:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:27:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:27:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:27:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287806/SRX287806.20_summits.bed INFO @ Sun, 21 Jun 2020 19:27:08: Done! pass1 - making usageList (211 chroms): 1 millis pass2 - checking and writing primary data (449 records, 4 fields): 9 millis CompletedMACS2peakCalling