Job ID = 6458570 SRX = SRX5343104 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:42:11 prefetch.2.10.7: 1) Downloading 'SRR8540881'... 2020-06-21T12:42:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:46:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:46:46 prefetch.2.10.7: 1) 'SRR8540881' was downloaded successfully 2020-06-21T12:46:46 prefetch.2.10.7: 'SRR8540881' has 0 unresolved dependencies Read 32207368 spots for SRR8540881/SRR8540881.sra Written 32207368 spots for SRR8540881/SRR8540881.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: 00:11:32 32207368 reads; of these: 32207368 (100.00%) were unpaired; of these: 1271735 (3.95%) aligned 0 times 21680801 (67.32%) aligned exactly 1 time 9254832 (28.74%) aligned >1 times 96.05% overall alignment rate Time searching: 00:11:32 Overall time: 00:11:32 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] 4797648 / 30935633 = 0.1551 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 22:09:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.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 22:09:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:09:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:09:55: 1000000 INFO @ Sun, 21 Jun 2020 22:10:01: 2000000 INFO @ Sun, 21 Jun 2020 22:10:07: 3000000 INFO @ Sun, 21 Jun 2020 22:10:14: 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 22:10:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.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 22:10:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:10:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:10:20: 5000000 INFO @ Sun, 21 Jun 2020 22:10:25: 1000000 INFO @ Sun, 21 Jun 2020 22:10:27: 6000000 INFO @ Sun, 21 Jun 2020 22:10:32: 2000000 INFO @ Sun, 21 Jun 2020 22:10:34: 7000000 INFO @ Sun, 21 Jun 2020 22:10:38: 3000000 INFO @ Sun, 21 Jun 2020 22:10:41: 8000000 INFO @ Sun, 21 Jun 2020 22:10:45: 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 22:10:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.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 22:10:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:10:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:10:48: 9000000 INFO @ Sun, 21 Jun 2020 22:10:53: 5000000 INFO @ Sun, 21 Jun 2020 22:10:55: 10000000 INFO @ Sun, 21 Jun 2020 22:10:56: 1000000 INFO @ Sun, 21 Jun 2020 22:11:00: 6000000 INFO @ Sun, 21 Jun 2020 22:11:03: 11000000 INFO @ Sun, 21 Jun 2020 22:11:04: 2000000 INFO @ Sun, 21 Jun 2020 22:11:08: 7000000 INFO @ Sun, 21 Jun 2020 22:11:10: 12000000 INFO @ Sun, 21 Jun 2020 22:11:12: 3000000 INFO @ Sun, 21 Jun 2020 22:11:16: 8000000 INFO @ Sun, 21 Jun 2020 22:11:18: 13000000 INFO @ Sun, 21 Jun 2020 22:11:20: 4000000 INFO @ Sun, 21 Jun 2020 22:11:23: 9000000 INFO @ Sun, 21 Jun 2020 22:11:26: 14000000 INFO @ Sun, 21 Jun 2020 22:11:28: 5000000 INFO @ Sun, 21 Jun 2020 22:11:31: 10000000 INFO @ Sun, 21 Jun 2020 22:11:33: 15000000 INFO @ Sun, 21 Jun 2020 22:11:36: 6000000 INFO @ Sun, 21 Jun 2020 22:11:39: 11000000 INFO @ Sun, 21 Jun 2020 22:11:41: 16000000 INFO @ Sun, 21 Jun 2020 22:11:44: 7000000 INFO @ Sun, 21 Jun 2020 22:11:46: 12000000 INFO @ Sun, 21 Jun 2020 22:11:49: 17000000 INFO @ Sun, 21 Jun 2020 22:11:53: 8000000 INFO @ Sun, 21 Jun 2020 22:11:54: 13000000 INFO @ Sun, 21 Jun 2020 22:11:57: 18000000 INFO @ Sun, 21 Jun 2020 22:12:01: 9000000 INFO @ Sun, 21 Jun 2020 22:12:02: 14000000 INFO @ Sun, 21 Jun 2020 22:12:05: 19000000 INFO @ Sun, 21 Jun 2020 22:12:09: 10000000 INFO @ Sun, 21 Jun 2020 22:12:10: 15000000 INFO @ Sun, 21 Jun 2020 22:12:13: 20000000 INFO @ Sun, 21 Jun 2020 22:12:17: 11000000 INFO @ Sun, 21 Jun 2020 22:12:18: 16000000 INFO @ Sun, 21 Jun 2020 22:12:21: 21000000 INFO @ Sun, 21 Jun 2020 22:12:25: 12000000 INFO @ Sun, 21 Jun 2020 22:12:25: 17000000 INFO @ Sun, 21 Jun 2020 22:12:29: 22000000 INFO @ Sun, 21 Jun 2020 22:12:33: 13000000 INFO @ Sun, 21 Jun 2020 22:12:33: 18000000 INFO @ Sun, 21 Jun 2020 22:12:37: 23000000 INFO @ Sun, 21 Jun 2020 22:12:41: 14000000 INFO @ Sun, 21 Jun 2020 22:12:41: 19000000 INFO @ Sun, 21 Jun 2020 22:12:44: 24000000 INFO @ Sun, 21 Jun 2020 22:12:49: 20000000 INFO @ Sun, 21 Jun 2020 22:12:49: 15000000 INFO @ Sun, 21 Jun 2020 22:12:52: 25000000 INFO @ Sun, 21 Jun 2020 22:12:56: 21000000 INFO @ Sun, 21 Jun 2020 22:12:57: 16000000 INFO @ Sun, 21 Jun 2020 22:13:00: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:13:02: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 22:13:02: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 22:13:02: #1 total tags in treatment: 26137985 INFO @ Sun, 21 Jun 2020 22:13:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:13:02: #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 22:13:03: #1 tags after filtering in treatment: 26137984 INFO @ Sun, 21 Jun 2020 22:13:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:13:03: #1 finished! INFO @ Sun, 21 Jun 2020 22:13:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:13:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:13:04: #2 number of paired peaks: 190 WARNING @ Sun, 21 Jun 2020 22:13:04: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Sun, 21 Jun 2020 22:13:04: start model_add_line... INFO @ Sun, 21 Jun 2020 22:13:04: start X-correlation... INFO @ Sun, 21 Jun 2020 22:13:04: end of X-cor INFO @ Sun, 21 Jun 2020 22:13:04: #2 finished! INFO @ Sun, 21 Jun 2020 22:13:04: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 22:13:04: #2 alternative fragment length(s) may be 2,54,560 bps INFO @ Sun, 21 Jun 2020 22:13:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.05_model.r WARNING @ Sun, 21 Jun 2020 22:13:04: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:13:04: #2 You may need to consider one of the other alternative d(s): 2,54,560 WARNING @ Sun, 21 Jun 2020 22:13:04: #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 22:13:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:13:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:13:05: 22000000 INFO @ Sun, 21 Jun 2020 22:13:05: 17000000 INFO @ Sun, 21 Jun 2020 22:13:12: 23000000 INFO @ Sun, 21 Jun 2020 22:13:13: 18000000 INFO @ Sun, 21 Jun 2020 22:13:19: 24000000 INFO @ Sun, 21 Jun 2020 22:13:20: 19000000 INFO @ Sun, 21 Jun 2020 22:13:27: 25000000 INFO @ Sun, 21 Jun 2020 22:13:29: 20000000 INFO @ Sun, 21 Jun 2020 22:13:35: 26000000 INFO @ Sun, 21 Jun 2020 22:13:36: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 22:13:36: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 22:13:36: #1 total tags in treatment: 26137985 INFO @ Sun, 21 Jun 2020 22:13:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:13:36: #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 22:13:37: 21000000 INFO @ Sun, 21 Jun 2020 22:13:37: #1 tags after filtering in treatment: 26137984 INFO @ Sun, 21 Jun 2020 22:13:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:13:37: #1 finished! INFO @ Sun, 21 Jun 2020 22:13:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:13:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:13:38: #2 number of paired peaks: 190 WARNING @ Sun, 21 Jun 2020 22:13:38: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Sun, 21 Jun 2020 22:13:38: start model_add_line... INFO @ Sun, 21 Jun 2020 22:13:38: start X-correlation... INFO @ Sun, 21 Jun 2020 22:13:38: end of X-cor INFO @ Sun, 21 Jun 2020 22:13:38: #2 finished! INFO @ Sun, 21 Jun 2020 22:13:38: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 22:13:38: #2 alternative fragment length(s) may be 2,54,560 bps INFO @ Sun, 21 Jun 2020 22:13:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.10_model.r WARNING @ Sun, 21 Jun 2020 22:13:38: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:13:38: #2 You may need to consider one of the other alternative d(s): 2,54,560 WARNING @ Sun, 21 Jun 2020 22:13:38: #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 22:13:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:13:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:13:44: 22000000 INFO @ Sun, 21 Jun 2020 22:13:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:13:51: 23000000 INFO @ Sun, 21 Jun 2020 22:13:59: 24000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:14:06: 25000000 INFO @ Sun, 21 Jun 2020 22:14:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:14:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:14:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.05_summits.bed INFO @ Sun, 21 Jun 2020 22:14:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:14:13: 26000000 INFO @ Sun, 21 Jun 2020 22:14:14: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 22:14:14: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 22:14:14: #1 total tags in treatment: 26137985 INFO @ Sun, 21 Jun 2020 22:14:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:14:14: #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 22:14:15: #1 tags after filtering in treatment: 26137984 INFO @ Sun, 21 Jun 2020 22:14:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:14:15: #1 finished! INFO @ Sun, 21 Jun 2020 22:14:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:14:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:14:17: #2 number of paired peaks: 190 WARNING @ Sun, 21 Jun 2020 22:14:17: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Sun, 21 Jun 2020 22:14:17: start model_add_line... INFO @ Sun, 21 Jun 2020 22:14:17: start X-correlation... INFO @ Sun, 21 Jun 2020 22:14:17: end of X-cor INFO @ Sun, 21 Jun 2020 22:14:17: #2 finished! INFO @ Sun, 21 Jun 2020 22:14:17: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 22:14:17: #2 alternative fragment length(s) may be 2,54,560 bps INFO @ Sun, 21 Jun 2020 22:14:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.20_model.r WARNING @ Sun, 21 Jun 2020 22:14:17: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:14:17: #2 You may need to consider one of the other alternative d(s): 2,54,560 WARNING @ Sun, 21 Jun 2020 22:14:17: #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 22:14:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:14:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:14:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:14:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:14:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:14:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.10_summits.bed INFO @ Sun, 21 Jun 2020 22:14:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:14:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:15:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:15:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:15:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343104/SRX5343104.20_summits.bed INFO @ Sun, 21 Jun 2020 22:15:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling