Job ID = 6458154 SRX = SRX495270 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:09:21 prefetch.2.10.7: 1) Downloading 'SRR1198775'... 2020-06-21T12:09:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:11:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:11:52 prefetch.2.10.7: 1) 'SRR1198775' was downloaded successfully Read 20447466 spots for SRR1198775/SRR1198775.sra Written 20447466 spots for SRR1198775/SRR1198775.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: 00:04:47 20447466 reads; of these: 20447466 (100.00%) were unpaired; of these: 2863377 (14.00%) aligned 0 times 12845690 (62.82%) aligned exactly 1 time 4738399 (23.17%) aligned >1 times 86.00% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 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 8 files... [bam_rmdupse_core] 4255571 / 17584089 = 0.2420 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 21:21:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.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 21:21:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:21:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:21:52: 1000000 INFO @ Sun, 21 Jun 2020 21:21:58: 2000000 INFO @ Sun, 21 Jun 2020 21:22:03: 3000000 INFO @ Sun, 21 Jun 2020 21:22:09: 4000000 INFO @ Sun, 21 Jun 2020 21:22:15: 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 21:22:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.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 21:22:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:22:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:22:20: 6000000 INFO @ Sun, 21 Jun 2020 21:22:23: 1000000 INFO @ Sun, 21 Jun 2020 21:22:27: 7000000 INFO @ Sun, 21 Jun 2020 21:22:29: 2000000 INFO @ Sun, 21 Jun 2020 21:22:33: 8000000 INFO @ Sun, 21 Jun 2020 21:22:35: 3000000 INFO @ Sun, 21 Jun 2020 21:22:39: 9000000 INFO @ Sun, 21 Jun 2020 21:22:42: 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 21:22:45: 10000000 INFO @ Sun, 21 Jun 2020 21:22:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.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 21:22:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:22:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:22:48: 5000000 INFO @ Sun, 21 Jun 2020 21:22:51: 11000000 INFO @ Sun, 21 Jun 2020 21:22:53: 1000000 INFO @ Sun, 21 Jun 2020 21:22:54: 6000000 INFO @ Sun, 21 Jun 2020 21:22:58: 12000000 INFO @ Sun, 21 Jun 2020 21:22:59: 2000000 INFO @ Sun, 21 Jun 2020 21:23:00: 7000000 INFO @ Sun, 21 Jun 2020 21:23:04: 13000000 INFO @ Sun, 21 Jun 2020 21:23:06: 3000000 INFO @ Sun, 21 Jun 2020 21:23:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:23:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:23:06: #1 total tags in treatment: 13328518 INFO @ Sun, 21 Jun 2020 21:23:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:23:06: #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 21:23:07: #1 tags after filtering in treatment: 13328418 INFO @ Sun, 21 Jun 2020 21:23:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:23:07: #1 finished! INFO @ Sun, 21 Jun 2020 21:23:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:23:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:23:07: 8000000 INFO @ Sun, 21 Jun 2020 21:23:08: #2 number of paired peaks: 522 WARNING @ Sun, 21 Jun 2020 21:23:08: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Sun, 21 Jun 2020 21:23:08: start model_add_line... INFO @ Sun, 21 Jun 2020 21:23:08: start X-correlation... INFO @ Sun, 21 Jun 2020 21:23:08: end of X-cor INFO @ Sun, 21 Jun 2020 21:23:08: #2 finished! INFO @ Sun, 21 Jun 2020 21:23:08: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 21:23:08: #2 alternative fragment length(s) may be 2,10,43,64,177,430,484,536,559,580,584 bps INFO @ Sun, 21 Jun 2020 21:23:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.05_model.r WARNING @ Sun, 21 Jun 2020 21:23:08: #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 21:23:08: #2 You may need to consider one of the other alternative d(s): 2,10,43,64,177,430,484,536,559,580,584 WARNING @ Sun, 21 Jun 2020 21:23:08: #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 21:23:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:23:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:23:12: 4000000 INFO @ Sun, 21 Jun 2020 21:23:13: 9000000 INFO @ Sun, 21 Jun 2020 21:23:18: 5000000 INFO @ Sun, 21 Jun 2020 21:23:19: 10000000 INFO @ Sun, 21 Jun 2020 21:23:24: 6000000 INFO @ Sun, 21 Jun 2020 21:23:25: 11000000 INFO @ Sun, 21 Jun 2020 21:23:31: 7000000 INFO @ Sun, 21 Jun 2020 21:23:32: 12000000 INFO @ Sun, 21 Jun 2020 21:23:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:23:37: 8000000 INFO @ Sun, 21 Jun 2020 21:23:38: 13000000 INFO @ Sun, 21 Jun 2020 21:23:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:23:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:23:40: #1 total tags in treatment: 13328518 INFO @ Sun, 21 Jun 2020 21:23:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:23:40: #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 21:23:41: #1 tags after filtering in treatment: 13328418 INFO @ Sun, 21 Jun 2020 21:23:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:23:41: #1 finished! INFO @ Sun, 21 Jun 2020 21:23:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:23:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:23:42: #2 number of paired peaks: 522 WARNING @ Sun, 21 Jun 2020 21:23:42: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Sun, 21 Jun 2020 21:23:42: start model_add_line... INFO @ Sun, 21 Jun 2020 21:23:42: start X-correlation... INFO @ Sun, 21 Jun 2020 21:23:42: end of X-cor INFO @ Sun, 21 Jun 2020 21:23:42: #2 finished! INFO @ Sun, 21 Jun 2020 21:23:42: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 21:23:42: #2 alternative fragment length(s) may be 2,10,43,64,177,430,484,536,559,580,584 bps INFO @ Sun, 21 Jun 2020 21:23:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.10_model.r WARNING @ Sun, 21 Jun 2020 21:23:42: #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 21:23:42: #2 You may need to consider one of the other alternative d(s): 2,10,43,64,177,430,484,536,559,580,584 WARNING @ Sun, 21 Jun 2020 21:23:42: #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 21:23:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:23:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:23:43: 9000000 INFO @ Sun, 21 Jun 2020 21:23:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:23:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:23:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.05_summits.bed INFO @ Sun, 21 Jun 2020 21:23:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:23:49: 10000000 INFO @ Sun, 21 Jun 2020 21:23:55: 11000000 INFO @ Sun, 21 Jun 2020 21:24:00: 12000000 INFO @ Sun, 21 Jun 2020 21:24:06: 13000000 INFO @ Sun, 21 Jun 2020 21:24:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:24:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:24:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:24:08: #1 total tags in treatment: 13328518 INFO @ Sun, 21 Jun 2020 21:24:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:24:08: #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 21:24:08: #1 tags after filtering in treatment: 13328418 INFO @ Sun, 21 Jun 2020 21:24:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:24:08: #1 finished! INFO @ Sun, 21 Jun 2020 21:24:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:24:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:24:09: #2 number of paired peaks: 522 WARNING @ Sun, 21 Jun 2020 21:24:09: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Sun, 21 Jun 2020 21:24:09: start model_add_line... INFO @ Sun, 21 Jun 2020 21:24:09: start X-correlation... INFO @ Sun, 21 Jun 2020 21:24:09: end of X-cor INFO @ Sun, 21 Jun 2020 21:24:09: #2 finished! INFO @ Sun, 21 Jun 2020 21:24:09: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 21:24:09: #2 alternative fragment length(s) may be 2,10,43,64,177,430,484,536,559,580,584 bps INFO @ Sun, 21 Jun 2020 21:24:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.20_model.r WARNING @ Sun, 21 Jun 2020 21:24:09: #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 21:24:09: #2 You may need to consider one of the other alternative d(s): 2,10,43,64,177,430,484,536,559,580,584 WARNING @ Sun, 21 Jun 2020 21:24:09: #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 21:24:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:24:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:24:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:24:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:24:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.10_summits.bed INFO @ Sun, 21 Jun 2020 21:24:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:24:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:24:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:24:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:24:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495270/SRX495270.20_summits.bed INFO @ Sun, 21 Jun 2020 21:24:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling