Job ID = 6456824 SRX = SRX3981712 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:06:54 prefetch.2.10.7: 1) Downloading 'SRR7050543'... 2020-06-21T11:06:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:07:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:07:41 prefetch.2.10.7: 'SRR7050543' is valid 2020-06-21T11:07:41 prefetch.2.10.7: 1) 'SRR7050543' was downloaded successfully 2020-06-21T11:07:41 prefetch.2.10.7: 'SRR7050543' has 0 unresolved dependencies Read 8788980 spots for SRR7050543/SRR7050543.sra Written 8788980 spots for SRR7050543/SRR7050543.sra 2020-06-21T11:08:19 prefetch.2.10.7: 1) Downloading 'SRR7050544'... 2020-06-21T11:08:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:09:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:09:30 prefetch.2.10.7: 'SRR7050544' is valid 2020-06-21T11:09:30 prefetch.2.10.7: 1) 'SRR7050544' was downloaded successfully 2020-06-21T11:09:30 prefetch.2.10.7: 'SRR7050544' has 0 unresolved dependencies Read 8781857 spots for SRR7050544/SRR7050544.sra Written 8781857 spots for SRR7050544/SRR7050544.sra 2020-06-21T11:10:11 prefetch.2.10.7: 1) Downloading 'SRR7050545'... 2020-06-21T11:10:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:11:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:11:26 prefetch.2.10.7: 'SRR7050545' is valid 2020-06-21T11:11:26 prefetch.2.10.7: 1) 'SRR7050545' was downloaded successfully 2020-06-21T11:11:26 prefetch.2.10.7: 'SRR7050545' has 0 unresolved dependencies Read 8817725 spots for SRR7050545/SRR7050545.sra Written 8817725 spots for SRR7050545/SRR7050545.sra 2020-06-21T11:12:04 prefetch.2.10.7: 1) Downloading 'SRR7050546'... 2020-06-21T11:12:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:12:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:12:56 prefetch.2.10.7: 'SRR7050546' is valid 2020-06-21T11:12:56 prefetch.2.10.7: 1) 'SRR7050546' was downloaded successfully 2020-06-21T11:12:56 prefetch.2.10.7: 'SRR7050546' has 0 unresolved dependencies Read 8846952 spots for SRR7050546/SRR7050546.sra Written 8846952 spots for SRR7050546/SRR7050546.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: 00:09:19 35235514 reads; of these: 35235514 (100.00%) were unpaired; of these: 1279635 (3.63%) aligned 0 times 24968339 (70.86%) aligned exactly 1 time 8987540 (25.51%) aligned >1 times 96.37% overall alignment rate Time searching: 00:09:19 Overall time: 00:09:19 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 16 files... [bam_rmdupse_core] 5531575 / 33955879 = 0.1629 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 20:29:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.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 20:29:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:29:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:29:22: 1000000 INFO @ Sun, 21 Jun 2020 20:29:27: 2000000 INFO @ Sun, 21 Jun 2020 20:29:32: 3000000 INFO @ Sun, 21 Jun 2020 20:29:37: 4000000 INFO @ Sun, 21 Jun 2020 20:29:42: 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 20:29:47: 6000000 INFO @ Sun, 21 Jun 2020 20:29:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.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 20:29:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:29:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:29:52: 7000000 INFO @ Sun, 21 Jun 2020 20:29:53: 1000000 INFO @ Sun, 21 Jun 2020 20:29:57: 8000000 INFO @ Sun, 21 Jun 2020 20:29:58: 2000000 INFO @ Sun, 21 Jun 2020 20:30:02: 9000000 INFO @ Sun, 21 Jun 2020 20:30:03: 3000000 INFO @ Sun, 21 Jun 2020 20:30:08: 10000000 INFO @ Sun, 21 Jun 2020 20:30:08: 4000000 INFO @ Sun, 21 Jun 2020 20:30:13: 11000000 INFO @ Sun, 21 Jun 2020 20:30:14: 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 @ Sun, 21 Jun 2020 20:30:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.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 20:30:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:30:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:30:18: 12000000 INFO @ Sun, 21 Jun 2020 20:30:19: 6000000 INFO @ Sun, 21 Jun 2020 20:30:23: 13000000 INFO @ Sun, 21 Jun 2020 20:30:24: 1000000 INFO @ Sun, 21 Jun 2020 20:30:24: 7000000 INFO @ Sun, 21 Jun 2020 20:30:29: 14000000 INFO @ Sun, 21 Jun 2020 20:30:30: 2000000 INFO @ Sun, 21 Jun 2020 20:30:30: 8000000 INFO @ Sun, 21 Jun 2020 20:30:34: 15000000 INFO @ Sun, 21 Jun 2020 20:30:35: 9000000 INFO @ Sun, 21 Jun 2020 20:30:36: 3000000 INFO @ Sun, 21 Jun 2020 20:30:40: 16000000 INFO @ Sun, 21 Jun 2020 20:30:41: 10000000 INFO @ Sun, 21 Jun 2020 20:30:42: 4000000 INFO @ Sun, 21 Jun 2020 20:30:45: 17000000 INFO @ Sun, 21 Jun 2020 20:30:46: 11000000 INFO @ Sun, 21 Jun 2020 20:30:48: 5000000 INFO @ Sun, 21 Jun 2020 20:30:51: 18000000 INFO @ Sun, 21 Jun 2020 20:30:52: 12000000 INFO @ Sun, 21 Jun 2020 20:30:54: 6000000 INFO @ Sun, 21 Jun 2020 20:30:56: 19000000 INFO @ Sun, 21 Jun 2020 20:30:57: 13000000 INFO @ Sun, 21 Jun 2020 20:31:00: 7000000 INFO @ Sun, 21 Jun 2020 20:31:02: 20000000 INFO @ Sun, 21 Jun 2020 20:31:03: 14000000 INFO @ Sun, 21 Jun 2020 20:31:07: 8000000 INFO @ Sun, 21 Jun 2020 20:31:07: 21000000 INFO @ Sun, 21 Jun 2020 20:31:08: 15000000 INFO @ Sun, 21 Jun 2020 20:31:13: 22000000 INFO @ Sun, 21 Jun 2020 20:31:13: 9000000 INFO @ Sun, 21 Jun 2020 20:31:14: 16000000 INFO @ Sun, 21 Jun 2020 20:31:18: 23000000 INFO @ Sun, 21 Jun 2020 20:31:19: 10000000 INFO @ Sun, 21 Jun 2020 20:31:19: 17000000 INFO @ Sun, 21 Jun 2020 20:31:24: 24000000 INFO @ Sun, 21 Jun 2020 20:31:25: 18000000 INFO @ Sun, 21 Jun 2020 20:31:25: 11000000 INFO @ Sun, 21 Jun 2020 20:31:29: 25000000 INFO @ Sun, 21 Jun 2020 20:31:30: 19000000 INFO @ Sun, 21 Jun 2020 20:31:31: 12000000 INFO @ Sun, 21 Jun 2020 20:31:35: 26000000 INFO @ Sun, 21 Jun 2020 20:31:36: 20000000 INFO @ Sun, 21 Jun 2020 20:31:37: 13000000 INFO @ Sun, 21 Jun 2020 20:31:41: 27000000 INFO @ Sun, 21 Jun 2020 20:31:41: 21000000 INFO @ Sun, 21 Jun 2020 20:31:43: 14000000 INFO @ Sun, 21 Jun 2020 20:31:46: 28000000 INFO @ Sun, 21 Jun 2020 20:31:47: 22000000 INFO @ Sun, 21 Jun 2020 20:31:49: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:31:49: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:31:49: #1 total tags in treatment: 28424304 INFO @ Sun, 21 Jun 2020 20:31:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:31:49: #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 20:31:49: 15000000 INFO @ Sun, 21 Jun 2020 20:31:50: #1 tags after filtering in treatment: 28424255 INFO @ Sun, 21 Jun 2020 20:31:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:31:50: #1 finished! INFO @ Sun, 21 Jun 2020 20:31:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:31:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:31:51: #2 number of paired peaks: 436 WARNING @ Sun, 21 Jun 2020 20:31:51: Fewer paired peaks (436) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 436 pairs to build model! INFO @ Sun, 21 Jun 2020 20:31:51: start model_add_line... INFO @ Sun, 21 Jun 2020 20:31:52: start X-correlation... INFO @ Sun, 21 Jun 2020 20:31:52: end of X-cor INFO @ Sun, 21 Jun 2020 20:31:52: #2 finished! INFO @ Sun, 21 Jun 2020 20:31:52: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 20:31:52: #2 alternative fragment length(s) may be 2,55 bps INFO @ Sun, 21 Jun 2020 20:31:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.05_model.r WARNING @ Sun, 21 Jun 2020 20:31:52: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:31:52: #2 You may need to consider one of the other alternative d(s): 2,55 WARNING @ Sun, 21 Jun 2020 20:31:52: #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 20:31:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:31:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:31:52: 23000000 INFO @ Sun, 21 Jun 2020 20:31:56: 16000000 INFO @ Sun, 21 Jun 2020 20:31:58: 24000000 INFO @ Sun, 21 Jun 2020 20:32:02: 17000000 INFO @ Sun, 21 Jun 2020 20:32:04: 25000000 INFO @ Sun, 21 Jun 2020 20:32:08: 18000000 INFO @ Sun, 21 Jun 2020 20:32:09: 26000000 INFO @ Sun, 21 Jun 2020 20:32:14: 19000000 INFO @ Sun, 21 Jun 2020 20:32:15: 27000000 INFO @ Sun, 21 Jun 2020 20:32:20: 20000000 INFO @ Sun, 21 Jun 2020 20:32:22: 28000000 INFO @ Sun, 21 Jun 2020 20:32:24: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:32:24: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:32:24: #1 total tags in treatment: 28424304 INFO @ Sun, 21 Jun 2020 20:32:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:32:24: #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 20:32:25: #1 tags after filtering in treatment: 28424255 INFO @ Sun, 21 Jun 2020 20:32:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:32:25: #1 finished! INFO @ Sun, 21 Jun 2020 20:32:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:32:25: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:32:26: 21000000 INFO @ Sun, 21 Jun 2020 20:32:27: #2 number of paired peaks: 436 WARNING @ Sun, 21 Jun 2020 20:32:27: Fewer paired peaks (436) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 436 pairs to build model! INFO @ Sun, 21 Jun 2020 20:32:27: start model_add_line... INFO @ Sun, 21 Jun 2020 20:32:27: start X-correlation... INFO @ Sun, 21 Jun 2020 20:32:27: end of X-cor INFO @ Sun, 21 Jun 2020 20:32:27: #2 finished! INFO @ Sun, 21 Jun 2020 20:32:27: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 20:32:27: #2 alternative fragment length(s) may be 2,55 bps INFO @ Sun, 21 Jun 2020 20:32:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.10_model.r WARNING @ Sun, 21 Jun 2020 20:32:27: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:32:27: #2 You may need to consider one of the other alternative d(s): 2,55 WARNING @ Sun, 21 Jun 2020 20:32:27: #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 20:32:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:32:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:32:32: 22000000 INFO @ Sun, 21 Jun 2020 20:32:38: 23000000 INFO @ Sun, 21 Jun 2020 20:32:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:32:44: 24000000 INFO @ Sun, 21 Jun 2020 20:32:50: 25000000 INFO @ Sun, 21 Jun 2020 20:32:56: 26000000 INFO @ Sun, 21 Jun 2020 20:33:02: 27000000 INFO @ Sun, 21 Jun 2020 20:33:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:33:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:33:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.05_summits.bed INFO @ Sun, 21 Jun 2020 20:33:05: Done! pass1 - making usageList (644 chroms): 2 millis pass2 - checking and writing primary data (4096 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:33:08: 28000000 INFO @ Sun, 21 Jun 2020 20:33:10: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:33:10: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:33:10: #1 total tags in treatment: 28424304 INFO @ Sun, 21 Jun 2020 20:33:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:33:10: #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 20:33:11: #1 tags after filtering in treatment: 28424255 INFO @ Sun, 21 Jun 2020 20:33:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:33:11: #1 finished! INFO @ Sun, 21 Jun 2020 20:33:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:33:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:33:13: #2 number of paired peaks: 436 WARNING @ Sun, 21 Jun 2020 20:33:13: Fewer paired peaks (436) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 436 pairs to build model! INFO @ Sun, 21 Jun 2020 20:33:13: start model_add_line... INFO @ Sun, 21 Jun 2020 20:33:13: start X-correlation... INFO @ Sun, 21 Jun 2020 20:33:13: end of X-cor INFO @ Sun, 21 Jun 2020 20:33:13: #2 finished! INFO @ Sun, 21 Jun 2020 20:33:13: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 20:33:13: #2 alternative fragment length(s) may be 2,55 bps INFO @ Sun, 21 Jun 2020 20:33:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.20_model.r WARNING @ Sun, 21 Jun 2020 20:33:13: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:33:13: #2 You may need to consider one of the other alternative d(s): 2,55 WARNING @ Sun, 21 Jun 2020 20:33:13: #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 20:33:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:33:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:33:18: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:33:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:33:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:33:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.10_summits.bed INFO @ Sun, 21 Jun 2020 20:33:42: Done! pass1 - making usageList (535 chroms): 1 millis pass2 - checking and writing primary data (2393 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:34:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:34:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:34:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:34:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981712/SRX3981712.20_summits.bed INFO @ Sun, 21 Jun 2020 20:34:26: Done! pass1 - making usageList (349 chroms): 1 millis pass2 - checking and writing primary data (920 records, 4 fields): 10 millis CompletedMACS2peakCalling