Job ID = 6456829 SRX = SRX3981717 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:21:54 prefetch.2.10.7: 1) Downloading 'SRR7050563'... 2020-06-21T11:21:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:23:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:23:06 prefetch.2.10.7: 'SRR7050563' is valid 2020-06-21T11:23:06 prefetch.2.10.7: 1) 'SRR7050563' was downloaded successfully 2020-06-21T11:23:06 prefetch.2.10.7: 'SRR7050563' has 0 unresolved dependencies Read 10867358 spots for SRR7050563/SRR7050563.sra Written 10867358 spots for SRR7050563/SRR7050563.sra 2020-06-21T11:23:55 prefetch.2.10.7: 1) Downloading 'SRR7050564'... 2020-06-21T11:23:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:24:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:24:54 prefetch.2.10.7: 'SRR7050564' is valid 2020-06-21T11:24:54 prefetch.2.10.7: 1) 'SRR7050564' was downloaded successfully 2020-06-21T11:24:54 prefetch.2.10.7: 'SRR7050564' has 0 unresolved dependencies Read 10988930 spots for SRR7050564/SRR7050564.sra Written 10988930 spots for SRR7050564/SRR7050564.sra 2020-06-21T11:25:44 prefetch.2.10.7: 1) Downloading 'SRR7050565'... 2020-06-21T11:25:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:27:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:27:08 prefetch.2.10.7: 'SRR7050565' is valid 2020-06-21T11:27:08 prefetch.2.10.7: 1) 'SRR7050565' was downloaded successfully 2020-06-21T11:27:08 prefetch.2.10.7: 'SRR7050565' has 0 unresolved dependencies Read 11044386 spots for SRR7050565/SRR7050565.sra Written 11044386 spots for SRR7050565/SRR7050565.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:14 32900674 reads; of these: 32900674 (100.00%) were unpaired; of these: 984693 (2.99%) aligned 0 times 23093374 (70.19%) aligned exactly 1 time 8822607 (26.82%) aligned >1 times 97.01% overall alignment rate Time searching: 00:10:15 Overall time: 00:10:15 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] 4169692 / 31915981 = 0.1306 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 20:45:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.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 20:45:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:45:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:45:39: 1000000 INFO @ Sun, 21 Jun 2020 20:45:47: 2000000 INFO @ Sun, 21 Jun 2020 20:45:54: 3000000 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 20:46:01: 4000000 INFO @ Sun, 21 Jun 2020 20:46:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.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 20:46:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:46:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:46:08: 5000000 INFO @ Sun, 21 Jun 2020 20:46:10: 1000000 INFO @ Sun, 21 Jun 2020 20:46:16: 6000000 INFO @ Sun, 21 Jun 2020 20:46:19: 2000000 INFO @ Sun, 21 Jun 2020 20:46:24: 7000000 INFO @ Sun, 21 Jun 2020 20:46:28: 3000000 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 20:46:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.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 20:46:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:46:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:46:33: 8000000 INFO @ Sun, 21 Jun 2020 20:46:36: 4000000 INFO @ Sun, 21 Jun 2020 20:46:41: 1000000 INFO @ Sun, 21 Jun 2020 20:46:41: 9000000 INFO @ Sun, 21 Jun 2020 20:46:44: 5000000 INFO @ Sun, 21 Jun 2020 20:46:49: 2000000 INFO @ Sun, 21 Jun 2020 20:46:49: 10000000 INFO @ Sun, 21 Jun 2020 20:46:52: 6000000 INFO @ Sun, 21 Jun 2020 20:46:57: 3000000 INFO @ Sun, 21 Jun 2020 20:46:57: 11000000 INFO @ Sun, 21 Jun 2020 20:47:00: 7000000 INFO @ Sun, 21 Jun 2020 20:47:05: 4000000 INFO @ Sun, 21 Jun 2020 20:47:06: 12000000 INFO @ Sun, 21 Jun 2020 20:47:07: 8000000 INFO @ Sun, 21 Jun 2020 20:47:13: 5000000 INFO @ Sun, 21 Jun 2020 20:47:14: 13000000 INFO @ Sun, 21 Jun 2020 20:47:15: 9000000 INFO @ Sun, 21 Jun 2020 20:47:21: 6000000 INFO @ Sun, 21 Jun 2020 20:47:22: 14000000 INFO @ Sun, 21 Jun 2020 20:47:23: 10000000 INFO @ Sun, 21 Jun 2020 20:47:30: 7000000 INFO @ Sun, 21 Jun 2020 20:47:30: 15000000 INFO @ Sun, 21 Jun 2020 20:47:31: 11000000 INFO @ Sun, 21 Jun 2020 20:47:38: 8000000 INFO @ Sun, 21 Jun 2020 20:47:38: 16000000 INFO @ Sun, 21 Jun 2020 20:47:38: 12000000 INFO @ Sun, 21 Jun 2020 20:47:46: 9000000 INFO @ Sun, 21 Jun 2020 20:47:46: 17000000 INFO @ Sun, 21 Jun 2020 20:47:46: 13000000 INFO @ Sun, 21 Jun 2020 20:47:54: 10000000 INFO @ Sun, 21 Jun 2020 20:47:54: 18000000 INFO @ Sun, 21 Jun 2020 20:47:54: 14000000 INFO @ Sun, 21 Jun 2020 20:48:02: 11000000 INFO @ Sun, 21 Jun 2020 20:48:02: 15000000 INFO @ Sun, 21 Jun 2020 20:48:02: 19000000 INFO @ Sun, 21 Jun 2020 20:48:10: 12000000 INFO @ Sun, 21 Jun 2020 20:48:10: 16000000 INFO @ Sun, 21 Jun 2020 20:48:10: 20000000 INFO @ Sun, 21 Jun 2020 20:48:18: 13000000 INFO @ Sun, 21 Jun 2020 20:48:18: 17000000 INFO @ Sun, 21 Jun 2020 20:48:18: 21000000 INFO @ Sun, 21 Jun 2020 20:48:26: 14000000 INFO @ Sun, 21 Jun 2020 20:48:26: 18000000 INFO @ Sun, 21 Jun 2020 20:48:26: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:48:34: 15000000 INFO @ Sun, 21 Jun 2020 20:48:34: 19000000 INFO @ Sun, 21 Jun 2020 20:48:34: 23000000 INFO @ Sun, 21 Jun 2020 20:48:42: 20000000 INFO @ Sun, 21 Jun 2020 20:48:42: 16000000 INFO @ Sun, 21 Jun 2020 20:48:42: 24000000 INFO @ Sun, 21 Jun 2020 20:48:49: 21000000 INFO @ Sun, 21 Jun 2020 20:48:50: 17000000 INFO @ Sun, 21 Jun 2020 20:48:50: 25000000 INFO @ Sun, 21 Jun 2020 20:48:57: 22000000 INFO @ Sun, 21 Jun 2020 20:48:57: 18000000 INFO @ Sun, 21 Jun 2020 20:48:58: 26000000 INFO @ Sun, 21 Jun 2020 20:49:05: 23000000 INFO @ Sun, 21 Jun 2020 20:49:05: 19000000 INFO @ Sun, 21 Jun 2020 20:49:06: 27000000 INFO @ Sun, 21 Jun 2020 20:49:12: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:49:12: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:49:12: #1 total tags in treatment: 27746289 INFO @ Sun, 21 Jun 2020 20:49:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:49:12: #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 20:49:12: #1 tags after filtering in treatment: 27746242 INFO @ Sun, 21 Jun 2020 20:49:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:49:12: #1 finished! INFO @ Sun, 21 Jun 2020 20:49:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:49:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:49:13: 20000000 INFO @ Sun, 21 Jun 2020 20:49:13: 24000000 INFO @ Sun, 21 Jun 2020 20:49:14: #2 number of paired peaks: 343 WARNING @ Sun, 21 Jun 2020 20:49:14: Fewer paired peaks (343) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 343 pairs to build model! INFO @ Sun, 21 Jun 2020 20:49:14: start model_add_line... INFO @ Sun, 21 Jun 2020 20:49:14: start X-correlation... INFO @ Sun, 21 Jun 2020 20:49:14: end of X-cor INFO @ Sun, 21 Jun 2020 20:49:14: #2 finished! INFO @ Sun, 21 Jun 2020 20:49:14: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:49:14: #2 alternative fragment length(s) may be 1,11,38,567,593 bps INFO @ Sun, 21 Jun 2020 20:49:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.05_model.r WARNING @ Sun, 21 Jun 2020 20:49:14: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:49:14: #2 You may need to consider one of the other alternative d(s): 1,11,38,567,593 WARNING @ Sun, 21 Jun 2020 20:49:14: #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 20:49:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:49:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:49:21: 21000000 INFO @ Sun, 21 Jun 2020 20:49:21: 25000000 INFO @ Sun, 21 Jun 2020 20:49:28: 22000000 INFO @ Sun, 21 Jun 2020 20:49:29: 26000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:49:36: 23000000 INFO @ Sun, 21 Jun 2020 20:49:37: 27000000 INFO @ Sun, 21 Jun 2020 20:49:43: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:49:43: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:49:43: #1 total tags in treatment: 27746289 INFO @ Sun, 21 Jun 2020 20:49:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:49:43: #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 20:49:44: #1 tags after filtering in treatment: 27746242 INFO @ Sun, 21 Jun 2020 20:49:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:49:44: #1 finished! INFO @ Sun, 21 Jun 2020 20:49:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:49:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:49:44: 24000000 INFO @ Sun, 21 Jun 2020 20:49:46: #2 number of paired peaks: 343 WARNING @ Sun, 21 Jun 2020 20:49:46: Fewer paired peaks (343) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 343 pairs to build model! INFO @ Sun, 21 Jun 2020 20:49:46: start model_add_line... INFO @ Sun, 21 Jun 2020 20:49:46: start X-correlation... INFO @ Sun, 21 Jun 2020 20:49:46: end of X-cor INFO @ Sun, 21 Jun 2020 20:49:46: #2 finished! INFO @ Sun, 21 Jun 2020 20:49:46: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:49:46: #2 alternative fragment length(s) may be 1,11,38,567,593 bps INFO @ Sun, 21 Jun 2020 20:49:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.10_model.r WARNING @ Sun, 21 Jun 2020 20:49:46: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:49:46: #2 You may need to consider one of the other alternative d(s): 1,11,38,567,593 WARNING @ Sun, 21 Jun 2020 20:49:46: #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 20:49:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:49:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:49:51: 25000000 INFO @ Sun, 21 Jun 2020 20:49:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:49:58: 26000000 INFO @ Sun, 21 Jun 2020 20:50:05: 27000000 INFO @ Sun, 21 Jun 2020 20:50:10: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:50:10: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:50:10: #1 total tags in treatment: 27746289 INFO @ Sun, 21 Jun 2020 20:50:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:50:10: #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 20:50:11: #1 tags after filtering in treatment: 27746242 INFO @ Sun, 21 Jun 2020 20:50:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:50:11: #1 finished! INFO @ Sun, 21 Jun 2020 20:50:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:50:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:50:12: #2 number of paired peaks: 343 WARNING @ Sun, 21 Jun 2020 20:50:12: Fewer paired peaks (343) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 343 pairs to build model! INFO @ Sun, 21 Jun 2020 20:50:12: start model_add_line... INFO @ Sun, 21 Jun 2020 20:50:13: start X-correlation... INFO @ Sun, 21 Jun 2020 20:50:13: end of X-cor INFO @ Sun, 21 Jun 2020 20:50:13: #2 finished! INFO @ Sun, 21 Jun 2020 20:50:13: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:50:13: #2 alternative fragment length(s) may be 1,11,38,567,593 bps INFO @ Sun, 21 Jun 2020 20:50:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.20_model.r WARNING @ Sun, 21 Jun 2020 20:50:13: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:50:13: #2 You may need to consider one of the other alternative d(s): 1,11,38,567,593 WARNING @ Sun, 21 Jun 2020 20:50:13: #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 20:50:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:50:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:50:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:50:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:50:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.05_summits.bed INFO @ Sun, 21 Jun 2020 20:50:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:50:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:50:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:50:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:50:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.10_summits.bed INFO @ Sun, 21 Jun 2020 20:50:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:50:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:51:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:51:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:51:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981717/SRX3981717.20_summits.bed INFO @ Sun, 21 Jun 2020 20:51:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling