Job ID = 6456629 SRX = SRX375354 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:06:39 prefetch.2.10.7: 1) Downloading 'SRR1027844'... 2020-06-21T11:06:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:13:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:13:13 prefetch.2.10.7: 1) 'SRR1027844' was downloaded successfully Read 48045955 spots for SRR1027844/SRR1027844.sra Written 48045955 spots for SRR1027844/SRR1027844.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: 00:14:58 48045955 reads; of these: 48045955 (100.00%) were unpaired; of these: 3177023 (6.61%) aligned 0 times 34222531 (71.23%) aligned exactly 1 time 10646401 (22.16%) aligned >1 times 93.39% overall alignment rate Time searching: 00:14:58 Overall time: 00:14:58 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 20 files... [bam_rmdupse_core] 13338224 / 44868932 = 0.2973 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 20:41:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.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 20:41:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:41:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:41:12: 1000000 INFO @ Sun, 21 Jun 2020 20:41:17: 2000000 INFO @ Sun, 21 Jun 2020 20:41:23: 3000000 INFO @ Sun, 21 Jun 2020 20:41:28: 4000000 INFO @ Sun, 21 Jun 2020 20:41:33: 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 20:41:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.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 20:41:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:41:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:41:39: 6000000 INFO @ Sun, 21 Jun 2020 20:41:42: 1000000 INFO @ Sun, 21 Jun 2020 20:41:45: 7000000 INFO @ Sun, 21 Jun 2020 20:41:48: 2000000 INFO @ Sun, 21 Jun 2020 20:41:50: 8000000 INFO @ Sun, 21 Jun 2020 20:41:54: 3000000 INFO @ Sun, 21 Jun 2020 20:41:56: 9000000 INFO @ Sun, 21 Jun 2020 20:41:59: 4000000 INFO @ Sun, 21 Jun 2020 20:42:02: 10000000 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 20:42:05: 5000000 INFO @ Sun, 21 Jun 2020 20:42:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.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 20:42:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:42:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:42:08: 11000000 INFO @ Sun, 21 Jun 2020 20:42:11: 6000000 INFO @ Sun, 21 Jun 2020 20:42:12: 1000000 INFO @ Sun, 21 Jun 2020 20:42:14: 12000000 INFO @ Sun, 21 Jun 2020 20:42:17: 7000000 INFO @ Sun, 21 Jun 2020 20:42:18: 2000000 INFO @ Sun, 21 Jun 2020 20:42:19: 13000000 INFO @ Sun, 21 Jun 2020 20:42:22: 8000000 INFO @ Sun, 21 Jun 2020 20:42:24: 3000000 INFO @ Sun, 21 Jun 2020 20:42:25: 14000000 INFO @ Sun, 21 Jun 2020 20:42:28: 9000000 INFO @ Sun, 21 Jun 2020 20:42:31: 4000000 INFO @ Sun, 21 Jun 2020 20:42:31: 15000000 INFO @ Sun, 21 Jun 2020 20:42:34: 10000000 INFO @ Sun, 21 Jun 2020 20:42:37: 16000000 INFO @ Sun, 21 Jun 2020 20:42:38: 5000000 INFO @ Sun, 21 Jun 2020 20:42:40: 11000000 INFO @ Sun, 21 Jun 2020 20:42:43: 17000000 INFO @ Sun, 21 Jun 2020 20:42:45: 6000000 INFO @ Sun, 21 Jun 2020 20:42:46: 12000000 INFO @ Sun, 21 Jun 2020 20:42:49: 18000000 INFO @ Sun, 21 Jun 2020 20:42:51: 7000000 INFO @ Sun, 21 Jun 2020 20:42:52: 13000000 INFO @ Sun, 21 Jun 2020 20:42:55: 19000000 INFO @ Sun, 21 Jun 2020 20:42:58: 8000000 INFO @ Sun, 21 Jun 2020 20:42:58: 14000000 INFO @ Sun, 21 Jun 2020 20:43:02: 20000000 INFO @ Sun, 21 Jun 2020 20:43:04: 15000000 INFO @ Sun, 21 Jun 2020 20:43:05: 9000000 INFO @ Sun, 21 Jun 2020 20:43:08: 21000000 INFO @ Sun, 21 Jun 2020 20:43:10: 16000000 INFO @ Sun, 21 Jun 2020 20:43:12: 10000000 INFO @ Sun, 21 Jun 2020 20:43:14: 22000000 INFO @ Sun, 21 Jun 2020 20:43:16: 17000000 INFO @ Sun, 21 Jun 2020 20:43:19: 11000000 INFO @ Sun, 21 Jun 2020 20:43:20: 23000000 INFO @ Sun, 21 Jun 2020 20:43:22: 18000000 INFO @ Sun, 21 Jun 2020 20:43:26: 12000000 INFO @ Sun, 21 Jun 2020 20:43:26: 24000000 INFO @ Sun, 21 Jun 2020 20:43:28: 19000000 INFO @ Sun, 21 Jun 2020 20:43:32: 25000000 INFO @ Sun, 21 Jun 2020 20:43:32: 13000000 INFO @ Sun, 21 Jun 2020 20:43:34: 20000000 INFO @ Sun, 21 Jun 2020 20:43:38: 26000000 INFO @ Sun, 21 Jun 2020 20:43:39: 14000000 INFO @ Sun, 21 Jun 2020 20:43:40: 21000000 INFO @ Sun, 21 Jun 2020 20:43:44: 27000000 INFO @ Sun, 21 Jun 2020 20:43:46: 15000000 INFO @ Sun, 21 Jun 2020 20:43:46: 22000000 INFO @ Sun, 21 Jun 2020 20:43:51: 28000000 INFO @ Sun, 21 Jun 2020 20:43:52: 23000000 INFO @ Sun, 21 Jun 2020 20:43:53: 16000000 INFO @ Sun, 21 Jun 2020 20:43:57: 29000000 INFO @ Sun, 21 Jun 2020 20:43:59: 24000000 INFO @ Sun, 21 Jun 2020 20:44:00: 17000000 INFO @ Sun, 21 Jun 2020 20:44:03: 30000000 INFO @ Sun, 21 Jun 2020 20:44:05: 25000000 INFO @ Sun, 21 Jun 2020 20:44:07: 18000000 INFO @ Sun, 21 Jun 2020 20:44:09: 31000000 INFO @ Sun, 21 Jun 2020 20:44:11: 26000000 INFO @ Sun, 21 Jun 2020 20:44:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:44:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:44:13: #1 total tags in treatment: 31530708 INFO @ Sun, 21 Jun 2020 20:44:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:44:13: #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 20:44:13: #1 tags after filtering in treatment: 31530699 INFO @ Sun, 21 Jun 2020 20:44:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:44:13: #1 finished! INFO @ Sun, 21 Jun 2020 20:44:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:44:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:44:13: 19000000 INFO @ Sun, 21 Jun 2020 20:44:15: #2 number of paired peaks: 372 WARNING @ Sun, 21 Jun 2020 20:44:15: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Sun, 21 Jun 2020 20:44:15: start model_add_line... INFO @ Sun, 21 Jun 2020 20:44:15: start X-correlation... INFO @ Sun, 21 Jun 2020 20:44:15: end of X-cor INFO @ Sun, 21 Jun 2020 20:44:15: #2 finished! INFO @ Sun, 21 Jun 2020 20:44:15: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:44:15: #2 alternative fragment length(s) may be 2,11 bps INFO @ Sun, 21 Jun 2020 20:44:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.05_model.r WARNING @ Sun, 21 Jun 2020 20:44:15: #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 20:44:15: #2 You may need to consider one of the other alternative d(s): 2,11 WARNING @ Sun, 21 Jun 2020 20:44:15: #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 20:44:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:44:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:44:17: 27000000 INFO @ Sun, 21 Jun 2020 20:44:20: 20000000 INFO @ Sun, 21 Jun 2020 20:44:23: 28000000 INFO @ Sun, 21 Jun 2020 20:44:27: 21000000 INFO @ Sun, 21 Jun 2020 20:44:29: 29000000 INFO @ Sun, 21 Jun 2020 20:44:34: 22000000 INFO @ Sun, 21 Jun 2020 20:44:35: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:44:41: 23000000 INFO @ Sun, 21 Jun 2020 20:44:41: 31000000 INFO @ Sun, 21 Jun 2020 20:44:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:44:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:44:45: #1 total tags in treatment: 31530708 INFO @ Sun, 21 Jun 2020 20:44:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:44:45: #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 20:44:46: #1 tags after filtering in treatment: 31530699 INFO @ Sun, 21 Jun 2020 20:44:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:44:46: #1 finished! INFO @ Sun, 21 Jun 2020 20:44:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:44:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:44:48: #2 number of paired peaks: 372 WARNING @ Sun, 21 Jun 2020 20:44:48: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Sun, 21 Jun 2020 20:44:48: start model_add_line... INFO @ Sun, 21 Jun 2020 20:44:48: start X-correlation... INFO @ Sun, 21 Jun 2020 20:44:48: end of X-cor INFO @ Sun, 21 Jun 2020 20:44:48: #2 finished! INFO @ Sun, 21 Jun 2020 20:44:48: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:44:48: #2 alternative fragment length(s) may be 2,11 bps INFO @ Sun, 21 Jun 2020 20:44:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.10_model.r WARNING @ Sun, 21 Jun 2020 20:44:48: #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 20:44:48: #2 You may need to consider one of the other alternative d(s): 2,11 WARNING @ Sun, 21 Jun 2020 20:44:48: #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 20:44:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:44:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:44:48: 24000000 INFO @ Sun, 21 Jun 2020 20:44:55: 25000000 INFO @ Sun, 21 Jun 2020 20:45:01: 26000000 INFO @ Sun, 21 Jun 2020 20:45:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:45:08: 27000000 INFO @ Sun, 21 Jun 2020 20:45:15: 28000000 INFO @ Sun, 21 Jun 2020 20:45:21: 29000000 INFO @ Sun, 21 Jun 2020 20:45:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:45:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:45:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.05_summits.bed INFO @ Sun, 21 Jun 2020 20:45:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:45:28: 30000000 INFO @ Sun, 21 Jun 2020 20:45:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:45:34: 31000000 INFO @ Sun, 21 Jun 2020 20:45:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:45:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:45:38: #1 total tags in treatment: 31530708 INFO @ Sun, 21 Jun 2020 20:45:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:45:38: #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 20:45:39: #1 tags after filtering in treatment: 31530699 INFO @ Sun, 21 Jun 2020 20:45:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:45:39: #1 finished! INFO @ Sun, 21 Jun 2020 20:45:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:45:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:45:41: #2 number of paired peaks: 372 WARNING @ Sun, 21 Jun 2020 20:45:41: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Sun, 21 Jun 2020 20:45:41: start model_add_line... INFO @ Sun, 21 Jun 2020 20:45:41: start X-correlation... INFO @ Sun, 21 Jun 2020 20:45:41: end of X-cor INFO @ Sun, 21 Jun 2020 20:45:41: #2 finished! INFO @ Sun, 21 Jun 2020 20:45:41: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:45:41: #2 alternative fragment length(s) may be 2,11 bps INFO @ Sun, 21 Jun 2020 20:45:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.20_model.r WARNING @ Sun, 21 Jun 2020 20:45:41: #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 20:45:41: #2 You may need to consider one of the other alternative d(s): 2,11 WARNING @ Sun, 21 Jun 2020 20:45:41: #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 20:45:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:45:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:45:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:45:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:45:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.10_summits.bed INFO @ Sun, 21 Jun 2020 20:45:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:46:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:46:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:46:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:46:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX375354/SRX375354.20_summits.bed INFO @ Sun, 21 Jun 2020 20:46:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling