Job ID = 6454750 SRX = SRX2564135 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:19:54 prefetch.2.10.7: 1) Downloading 'SRR5259254'... 2020-06-21T09:19:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:33:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:33:48 prefetch.2.10.7: 1) 'SRR5259254' was downloaded successfully 2020-06-21T09:33:48 prefetch.2.10.7: 'SRR5259254' has 0 unresolved dependencies Read 54567797 spots for SRR5259254/SRR5259254.sra Written 54567797 spots for SRR5259254/SRR5259254.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: 00:18:08 54567797 reads; of these: 54567797 (100.00%) were unpaired; of these: 6773474 (12.41%) aligned 0 times 41904840 (76.79%) aligned exactly 1 time 5889483 (10.79%) aligned >1 times 87.59% overall alignment rate Time searching: 00:18:08 Overall time: 00:18:08 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] 12510259 / 47794323 = 0.2618 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 19:18:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.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 19:18:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:18:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:18:26: 1000000 INFO @ Sun, 21 Jun 2020 19:18:32: 2000000 INFO @ Sun, 21 Jun 2020 19:18:38: 3000000 INFO @ Sun, 21 Jun 2020 19:18:45: 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 19:18:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.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 19:18:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:18:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:18:52: 5000000 INFO @ Sun, 21 Jun 2020 19:18:56: 1000000 INFO @ Sun, 21 Jun 2020 19:18:58: 6000000 INFO @ Sun, 21 Jun 2020 19:19:04: 2000000 INFO @ Sun, 21 Jun 2020 19:19:05: 7000000 INFO @ Sun, 21 Jun 2020 19:19:12: 8000000 INFO @ Sun, 21 Jun 2020 19:19:12: 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 19:19:18: 9000000 INFO @ Sun, 21 Jun 2020 19:19:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.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 19:19:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:19:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:19:19: 4000000 INFO @ Sun, 21 Jun 2020 19:19:25: 10000000 INFO @ Sun, 21 Jun 2020 19:19:26: 1000000 INFO @ Sun, 21 Jun 2020 19:19:27: 5000000 INFO @ Sun, 21 Jun 2020 19:19:32: 11000000 INFO @ Sun, 21 Jun 2020 19:19:34: 2000000 INFO @ Sun, 21 Jun 2020 19:19:35: 6000000 INFO @ Sun, 21 Jun 2020 19:19:40: 12000000 INFO @ Sun, 21 Jun 2020 19:19:41: 3000000 INFO @ Sun, 21 Jun 2020 19:19:43: 7000000 INFO @ Sun, 21 Jun 2020 19:19:47: 13000000 INFO @ Sun, 21 Jun 2020 19:19:49: 4000000 INFO @ Sun, 21 Jun 2020 19:19:51: 8000000 INFO @ Sun, 21 Jun 2020 19:19:54: 14000000 INFO @ Sun, 21 Jun 2020 19:19:56: 5000000 INFO @ Sun, 21 Jun 2020 19:19:59: 9000000 INFO @ Sun, 21 Jun 2020 19:20:01: 15000000 INFO @ Sun, 21 Jun 2020 19:20:03: 6000000 INFO @ Sun, 21 Jun 2020 19:20:07: 10000000 INFO @ Sun, 21 Jun 2020 19:20:09: 16000000 INFO @ Sun, 21 Jun 2020 19:20:11: 7000000 INFO @ Sun, 21 Jun 2020 19:20:14: 11000000 INFO @ Sun, 21 Jun 2020 19:20:16: 17000000 INFO @ Sun, 21 Jun 2020 19:20:18: 8000000 INFO @ Sun, 21 Jun 2020 19:20:22: 12000000 INFO @ Sun, 21 Jun 2020 19:20:23: 18000000 INFO @ Sun, 21 Jun 2020 19:20:26: 9000000 INFO @ Sun, 21 Jun 2020 19:20:30: 13000000 INFO @ Sun, 21 Jun 2020 19:20:31: 19000000 INFO @ Sun, 21 Jun 2020 19:20:33: 10000000 INFO @ Sun, 21 Jun 2020 19:20:37: 14000000 INFO @ Sun, 21 Jun 2020 19:20:38: 20000000 INFO @ Sun, 21 Jun 2020 19:20:40: 11000000 INFO @ Sun, 21 Jun 2020 19:20:45: 21000000 INFO @ Sun, 21 Jun 2020 19:20:45: 15000000 INFO @ Sun, 21 Jun 2020 19:20:48: 12000000 INFO @ Sun, 21 Jun 2020 19:20:52: 22000000 INFO @ Sun, 21 Jun 2020 19:20:53: 16000000 INFO @ Sun, 21 Jun 2020 19:20:55: 13000000 INFO @ Sun, 21 Jun 2020 19:20:59: 23000000 INFO @ Sun, 21 Jun 2020 19:21:01: 17000000 INFO @ Sun, 21 Jun 2020 19:21:02: 14000000 INFO @ Sun, 21 Jun 2020 19:21:06: 24000000 INFO @ Sun, 21 Jun 2020 19:21:08: 18000000 INFO @ Sun, 21 Jun 2020 19:21:10: 15000000 INFO @ Sun, 21 Jun 2020 19:21:13: 25000000 INFO @ Sun, 21 Jun 2020 19:21:16: 19000000 INFO @ Sun, 21 Jun 2020 19:21:17: 16000000 INFO @ Sun, 21 Jun 2020 19:21:20: 26000000 INFO @ Sun, 21 Jun 2020 19:21:23: 20000000 INFO @ Sun, 21 Jun 2020 19:21:24: 17000000 INFO @ Sun, 21 Jun 2020 19:21:27: 27000000 INFO @ Sun, 21 Jun 2020 19:21:31: 21000000 INFO @ Sun, 21 Jun 2020 19:21:31: 18000000 INFO @ Sun, 21 Jun 2020 19:21:34: 28000000 INFO @ Sun, 21 Jun 2020 19:21:38: 22000000 INFO @ Sun, 21 Jun 2020 19:21:38: 19000000 INFO @ Sun, 21 Jun 2020 19:21:42: 29000000 INFO @ Sun, 21 Jun 2020 19:21:46: 20000000 INFO @ Sun, 21 Jun 2020 19:21:46: 23000000 INFO @ Sun, 21 Jun 2020 19:21:50: 30000000 INFO @ Sun, 21 Jun 2020 19:21:53: 21000000 INFO @ Sun, 21 Jun 2020 19:21:53: 24000000 INFO @ Sun, 21 Jun 2020 19:21:57: 31000000 INFO @ Sun, 21 Jun 2020 19:22:00: 22000000 INFO @ Sun, 21 Jun 2020 19:22:00: 25000000 INFO @ Sun, 21 Jun 2020 19:22:04: 32000000 INFO @ Sun, 21 Jun 2020 19:22:07: 23000000 INFO @ Sun, 21 Jun 2020 19:22:08: 26000000 INFO @ Sun, 21 Jun 2020 19:22:11: 33000000 INFO @ Sun, 21 Jun 2020 19:22:14: 24000000 INFO @ Sun, 21 Jun 2020 19:22:15: 27000000 INFO @ Sun, 21 Jun 2020 19:22:18: 34000000 INFO @ Sun, 21 Jun 2020 19:22:21: 25000000 INFO @ Sun, 21 Jun 2020 19:22:23: 28000000 INFO @ Sun, 21 Jun 2020 19:22:25: 35000000 INFO @ Sun, 21 Jun 2020 19:22:27: #1 tag size is determined as 71 bps INFO @ Sun, 21 Jun 2020 19:22:27: #1 tag size = 71 INFO @ Sun, 21 Jun 2020 19:22:27: #1 total tags in treatment: 35284064 INFO @ Sun, 21 Jun 2020 19:22:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:22:27: #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 19:22:28: 26000000 INFO @ Sun, 21 Jun 2020 19:22:29: #1 tags after filtering in treatment: 35284064 INFO @ Sun, 21 Jun 2020 19:22:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:22:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:22:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:22:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:22:31: #2 number of paired peaks: 172 WARNING @ Sun, 21 Jun 2020 19:22:31: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sun, 21 Jun 2020 19:22:31: start model_add_line... INFO @ Sun, 21 Jun 2020 19:22:31: start X-correlation... INFO @ Sun, 21 Jun 2020 19:22:31: end of X-cor INFO @ Sun, 21 Jun 2020 19:22:31: #2 finished! INFO @ Sun, 21 Jun 2020 19:22:31: #2 predicted fragment length is 127 bps INFO @ Sun, 21 Jun 2020 19:22:31: #2 alternative fragment length(s) may be 4,127 bps INFO @ Sun, 21 Jun 2020 19:22:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.05_model.r WARNING @ Sun, 21 Jun 2020 19:22:31: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:22:31: #2 You may need to consider one of the other alternative d(s): 4,127 WARNING @ Sun, 21 Jun 2020 19:22:31: #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 19:22:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:22:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:22:32: 29000000 INFO @ Sun, 21 Jun 2020 19:22:34: 27000000 INFO @ Sun, 21 Jun 2020 19:22:40: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:22:41: 28000000 INFO @ Sun, 21 Jun 2020 19:22:47: 31000000 INFO @ Sun, 21 Jun 2020 19:22:48: 29000000 INFO @ Sun, 21 Jun 2020 19:22:54: 30000000 INFO @ Sun, 21 Jun 2020 19:22:55: 32000000 INFO @ Sun, 21 Jun 2020 19:23:01: 31000000 INFO @ Sun, 21 Jun 2020 19:23:03: 33000000 INFO @ Sun, 21 Jun 2020 19:23:07: 32000000 INFO @ Sun, 21 Jun 2020 19:23:10: 34000000 INFO @ Sun, 21 Jun 2020 19:23:13: 33000000 INFO @ Sun, 21 Jun 2020 19:23:18: 35000000 INFO @ Sun, 21 Jun 2020 19:23:20: 34000000 INFO @ Sun, 21 Jun 2020 19:23:21: #1 tag size is determined as 71 bps INFO @ Sun, 21 Jun 2020 19:23:21: #1 tag size = 71 INFO @ Sun, 21 Jun 2020 19:23:21: #1 total tags in treatment: 35284064 INFO @ Sun, 21 Jun 2020 19:23:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:23:21: #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 19:23:22: #1 tags after filtering in treatment: 35284064 INFO @ Sun, 21 Jun 2020 19:23:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:23:22: #1 finished! INFO @ Sun, 21 Jun 2020 19:23:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:23:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:23:24: #2 number of paired peaks: 172 WARNING @ Sun, 21 Jun 2020 19:23:24: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sun, 21 Jun 2020 19:23:24: start model_add_line... INFO @ Sun, 21 Jun 2020 19:23:25: start X-correlation... INFO @ Sun, 21 Jun 2020 19:23:25: end of X-cor INFO @ Sun, 21 Jun 2020 19:23:25: #2 finished! INFO @ Sun, 21 Jun 2020 19:23:25: #2 predicted fragment length is 127 bps INFO @ Sun, 21 Jun 2020 19:23:25: #2 alternative fragment length(s) may be 4,127 bps INFO @ Sun, 21 Jun 2020 19:23:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.10_model.r WARNING @ Sun, 21 Jun 2020 19:23:25: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:23:25: #2 You may need to consider one of the other alternative d(s): 4,127 WARNING @ Sun, 21 Jun 2020 19:23:25: #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 19:23:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:23:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:23:26: 35000000 INFO @ Sun, 21 Jun 2020 19:23:29: #1 tag size is determined as 71 bps INFO @ Sun, 21 Jun 2020 19:23:29: #1 tag size = 71 INFO @ Sun, 21 Jun 2020 19:23:29: #1 total tags in treatment: 35284064 INFO @ Sun, 21 Jun 2020 19:23:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:23:29: #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 19:23:30: #1 tags after filtering in treatment: 35284064 INFO @ Sun, 21 Jun 2020 19:23:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:23:30: #1 finished! INFO @ Sun, 21 Jun 2020 19:23:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:23:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:23:32: #2 number of paired peaks: 172 WARNING @ Sun, 21 Jun 2020 19:23:32: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sun, 21 Jun 2020 19:23:32: start model_add_line... INFO @ Sun, 21 Jun 2020 19:23:33: start X-correlation... INFO @ Sun, 21 Jun 2020 19:23:33: end of X-cor INFO @ Sun, 21 Jun 2020 19:23:33: #2 finished! INFO @ Sun, 21 Jun 2020 19:23:33: #2 predicted fragment length is 127 bps INFO @ Sun, 21 Jun 2020 19:23:33: #2 alternative fragment length(s) may be 4,127 bps INFO @ Sun, 21 Jun 2020 19:23:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.20_model.r WARNING @ Sun, 21 Jun 2020 19:23:33: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:23:33: #2 You may need to consider one of the other alternative d(s): 4,127 WARNING @ Sun, 21 Jun 2020 19:23:33: #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 19:23:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:23:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:23:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:24:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:24:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:24:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.05_summits.bed INFO @ Sun, 21 Jun 2020 19:24:11: Done! pass1 - making usageList (467 chroms): 3 millis pass2 - checking and writing primary data (12150 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:24:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:24:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:25:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:25:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:25:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.10_summits.bed INFO @ Sun, 21 Jun 2020 19:25:04: Done! pass1 - making usageList (418 chroms): 2 millis pass2 - checking and writing primary data (8980 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:25:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:25:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:25:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564135/SRX2564135.20_summits.bed INFO @ Sun, 21 Jun 2020 19:25:12: Done! pass1 - making usageList (304 chroms): 2 millis pass2 - checking and writing primary data (5741 records, 4 fields): 23 millis CompletedMACS2peakCalling