Job ID = 6456861 SRX = SRX3989973 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:23:24 prefetch.2.10.7: 1) Downloading 'SRR7059014'... 2020-06-21T11:23:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:29:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:29:08 prefetch.2.10.7: 1) 'SRR7059014' was downloaded successfully 2020-06-21T11:29:08 prefetch.2.10.7: 'SRR7059014' has 0 unresolved dependencies Read 32170953 spots for SRR7059014/SRR7059014.sra Written 32170953 spots for SRR7059014/SRR7059014.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: 00:12:56 32170953 reads; of these: 32170953 (100.00%) were unpaired; of these: 4146553 (12.89%) aligned 0 times 14974128 (46.55%) aligned exactly 1 time 13050272 (40.57%) aligned >1 times 87.11% overall alignment rate Time searching: 00:12:57 Overall time: 00:12:57 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 12 files... [bam_rmdupse_core] 11309994 / 28024400 = 0.4036 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 20:50:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.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 20:50:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:50:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:50:22: 1000000 INFO @ Sun, 21 Jun 2020 20:50:29: 2000000 INFO @ Sun, 21 Jun 2020 20:50:35: 3000000 INFO @ Sun, 21 Jun 2020 20:50:42: 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 20:50:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.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 20:50:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:50:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:50:49: 5000000 INFO @ Sun, 21 Jun 2020 20:50:52: 1000000 INFO @ Sun, 21 Jun 2020 20:50:56: 6000000 INFO @ Sun, 21 Jun 2020 20:50:59: 2000000 INFO @ Sun, 21 Jun 2020 20:51:03: 7000000 INFO @ Sun, 21 Jun 2020 20:51:07: 3000000 INFO @ Sun, 21 Jun 2020 20:51:10: 8000000 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 20:51:14: 4000000 INFO @ Sun, 21 Jun 2020 20:51:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.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 20:51:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:51:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:51:18: 9000000 INFO @ Sun, 21 Jun 2020 20:51:21: 5000000 INFO @ Sun, 21 Jun 2020 20:51:21: 1000000 INFO @ Sun, 21 Jun 2020 20:51:25: 10000000 INFO @ Sun, 21 Jun 2020 20:51:28: 6000000 INFO @ Sun, 21 Jun 2020 20:51:28: 2000000 INFO @ Sun, 21 Jun 2020 20:51:32: 11000000 INFO @ Sun, 21 Jun 2020 20:51:35: 3000000 INFO @ Sun, 21 Jun 2020 20:51:36: 7000000 INFO @ Sun, 21 Jun 2020 20:51:40: 12000000 INFO @ Sun, 21 Jun 2020 20:51:42: 4000000 INFO @ Sun, 21 Jun 2020 20:51:43: 8000000 INFO @ Sun, 21 Jun 2020 20:51:48: 13000000 INFO @ Sun, 21 Jun 2020 20:51:49: 5000000 INFO @ Sun, 21 Jun 2020 20:51:50: 9000000 INFO @ Sun, 21 Jun 2020 20:51:55: 6000000 INFO @ Sun, 21 Jun 2020 20:51:56: 14000000 INFO @ Sun, 21 Jun 2020 20:51:57: 10000000 INFO @ Sun, 21 Jun 2020 20:52:02: 7000000 INFO @ Sun, 21 Jun 2020 20:52:04: 15000000 INFO @ Sun, 21 Jun 2020 20:52:05: 11000000 INFO @ Sun, 21 Jun 2020 20:52:09: 8000000 INFO @ Sun, 21 Jun 2020 20:52:11: 16000000 INFO @ Sun, 21 Jun 2020 20:52:12: 12000000 INFO @ Sun, 21 Jun 2020 20:52:16: 9000000 INFO @ Sun, 21 Jun 2020 20:52:17: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:52:17: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:52:17: #1 total tags in treatment: 16714406 INFO @ Sun, 21 Jun 2020 20:52:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:52:17: #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 20:52:17: #1 tags after filtering in treatment: 16714403 INFO @ Sun, 21 Jun 2020 20:52:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:52:17: #1 finished! INFO @ Sun, 21 Jun 2020 20:52:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:52:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:52:19: #2 number of paired peaks: 463 WARNING @ Sun, 21 Jun 2020 20:52:19: Fewer paired peaks (463) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 463 pairs to build model! INFO @ Sun, 21 Jun 2020 20:52:19: start model_add_line... INFO @ Sun, 21 Jun 2020 20:52:19: start X-correlation... INFO @ Sun, 21 Jun 2020 20:52:19: end of X-cor INFO @ Sun, 21 Jun 2020 20:52:19: #2 finished! INFO @ Sun, 21 Jun 2020 20:52:19: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:52:19: #2 alternative fragment length(s) may be 2,30,518,548,578,595 bps INFO @ Sun, 21 Jun 2020 20:52:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.05_model.r WARNING @ Sun, 21 Jun 2020 20:52:19: #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 20:52:19: #2 You may need to consider one of the other alternative d(s): 2,30,518,548,578,595 WARNING @ Sun, 21 Jun 2020 20:52:19: #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 20:52:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:52:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:52:20: 13000000 INFO @ Sun, 21 Jun 2020 20:52:22: 10000000 INFO @ Sun, 21 Jun 2020 20:52:27: 14000000 INFO @ Sun, 21 Jun 2020 20:52:29: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:52:35: 15000000 INFO @ Sun, 21 Jun 2020 20:52:36: 12000000 INFO @ Sun, 21 Jun 2020 20:52:42: 16000000 INFO @ Sun, 21 Jun 2020 20:52:43: 13000000 INFO @ Sun, 21 Jun 2020 20:52:48: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:52:48: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:52:48: #1 total tags in treatment: 16714406 INFO @ Sun, 21 Jun 2020 20:52:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:52:48: #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 20:52:48: #1 tags after filtering in treatment: 16714403 INFO @ Sun, 21 Jun 2020 20:52:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:52:48: #1 finished! INFO @ Sun, 21 Jun 2020 20:52:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:52:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:52:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:52:49: #2 number of paired peaks: 463 WARNING @ Sun, 21 Jun 2020 20:52:49: Fewer paired peaks (463) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 463 pairs to build model! INFO @ Sun, 21 Jun 2020 20:52:49: start model_add_line... INFO @ Sun, 21 Jun 2020 20:52:49: 14000000 INFO @ Sun, 21 Jun 2020 20:52:49: start X-correlation... INFO @ Sun, 21 Jun 2020 20:52:49: end of X-cor INFO @ Sun, 21 Jun 2020 20:52:49: #2 finished! INFO @ Sun, 21 Jun 2020 20:52:49: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:52:49: #2 alternative fragment length(s) may be 2,30,518,548,578,595 bps INFO @ Sun, 21 Jun 2020 20:52:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.10_model.r WARNING @ Sun, 21 Jun 2020 20:52:49: #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 20:52:49: #2 You may need to consider one of the other alternative d(s): 2,30,518,548,578,595 WARNING @ Sun, 21 Jun 2020 20:52:49: #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 20:52:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:52:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:52:55: 15000000 INFO @ Sun, 21 Jun 2020 20:53:01: 16000000 INFO @ Sun, 21 Jun 2020 20:53:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:53:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:53:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.05_summits.bed INFO @ Sun, 21 Jun 2020 20:53:03: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:53:05: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:53:05: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:53:05: #1 total tags in treatment: 16714406 INFO @ Sun, 21 Jun 2020 20:53:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:53:05: #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 20:53:06: #1 tags after filtering in treatment: 16714403 INFO @ Sun, 21 Jun 2020 20:53:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:53:06: #1 finished! INFO @ Sun, 21 Jun 2020 20:53:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:53:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:53:07: #2 number of paired peaks: 463 WARNING @ Sun, 21 Jun 2020 20:53:07: Fewer paired peaks (463) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 463 pairs to build model! INFO @ Sun, 21 Jun 2020 20:53:07: start model_add_line... INFO @ Sun, 21 Jun 2020 20:53:07: start X-correlation... INFO @ Sun, 21 Jun 2020 20:53:07: end of X-cor INFO @ Sun, 21 Jun 2020 20:53:07: #2 finished! INFO @ Sun, 21 Jun 2020 20:53:07: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:53:07: #2 alternative fragment length(s) may be 2,30,518,548,578,595 bps INFO @ Sun, 21 Jun 2020 20:53:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.20_model.r WARNING @ Sun, 21 Jun 2020 20:53:07: #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 20:53:07: #2 You may need to consider one of the other alternative d(s): 2,30,518,548,578,595 WARNING @ Sun, 21 Jun 2020 20:53:07: #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 20:53:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:53:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:53:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:53:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:53:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:53:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.10_summits.bed INFO @ Sun, 21 Jun 2020 20:53:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:53:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:53:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:53:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:53:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3989973/SRX3989973.20_summits.bed INFO @ Sun, 21 Jun 2020 20:53:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling