Job ID = 6529105 SRX = SRX466543 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:04:15 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 255391 (1.19%) aligned 0 times 17821481 (82.85%) aligned exactly 1 time 3432737 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:04:15 Overall time: 00:04:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3667886 / 21254218 = 0.1726 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 @ Tue, 30 Jun 2020 01:18:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 30 Jun 2020 01:18:33: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:18:33: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:18:38: 1000000 INFO @ Tue, 30 Jun 2020 01:18:44: 2000000 INFO @ Tue, 30 Jun 2020 01:18:50: 3000000 INFO @ Tue, 30 Jun 2020 01:18:56: 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 @ Tue, 30 Jun 2020 01:19:01: 5000000 INFO @ Tue, 30 Jun 2020 01:19:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 30 Jun 2020 01:19:03: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:19:03: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:19:07: 6000000 INFO @ Tue, 30 Jun 2020 01:19:09: 1000000 INFO @ Tue, 30 Jun 2020 01:19:13: 7000000 INFO @ Tue, 30 Jun 2020 01:19:14: 2000000 INFO @ Tue, 30 Jun 2020 01:19:19: 8000000 INFO @ Tue, 30 Jun 2020 01:19:20: 3000000 INFO @ Tue, 30 Jun 2020 01:19:24: 9000000 INFO @ Tue, 30 Jun 2020 01:19:26: 4000000 INFO @ Tue, 30 Jun 2020 01:19:30: 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 @ Tue, 30 Jun 2020 01:19:31: 5000000 INFO @ Tue, 30 Jun 2020 01:19:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 30 Jun 2020 01:19:33: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:19:33: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:19:35: 11000000 INFO @ Tue, 30 Jun 2020 01:19:37: 6000000 INFO @ Tue, 30 Jun 2020 01:19:39: 1000000 INFO @ Tue, 30 Jun 2020 01:19:41: 12000000 INFO @ Tue, 30 Jun 2020 01:19:43: 7000000 INFO @ Tue, 30 Jun 2020 01:19:46: 2000000 INFO @ Tue, 30 Jun 2020 01:19:47: 13000000 INFO @ Tue, 30 Jun 2020 01:19:49: 8000000 INFO @ Tue, 30 Jun 2020 01:19:52: 3000000 INFO @ Tue, 30 Jun 2020 01:19:53: 14000000 INFO @ Tue, 30 Jun 2020 01:19:55: 9000000 INFO @ Tue, 30 Jun 2020 01:19:58: 15000000 INFO @ Tue, 30 Jun 2020 01:19:58: 4000000 INFO @ Tue, 30 Jun 2020 01:20:00: 10000000 INFO @ Tue, 30 Jun 2020 01:20:04: 16000000 INFO @ Tue, 30 Jun 2020 01:20:05: 5000000 INFO @ Tue, 30 Jun 2020 01:20:06: 11000000 INFO @ Tue, 30 Jun 2020 01:20:09: 17000000 INFO @ Tue, 30 Jun 2020 01:20:11: 6000000 INFO @ Tue, 30 Jun 2020 01:20:12: 12000000 INFO @ Tue, 30 Jun 2020 01:20:13: #1 tag size is determined as 42 bps INFO @ Tue, 30 Jun 2020 01:20:13: #1 tag size = 42 INFO @ Tue, 30 Jun 2020 01:20:13: #1 total tags in treatment: 17586332 INFO @ Tue, 30 Jun 2020 01:20:13: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:20:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:20:13: #1 tags after filtering in treatment: 17586332 INFO @ Tue, 30 Jun 2020 01:20:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:20:13: #1 finished! INFO @ Tue, 30 Jun 2020 01:20:13: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:20:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:20:14: #2 number of paired peaks: 206 WARNING @ Tue, 30 Jun 2020 01:20:14: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Tue, 30 Jun 2020 01:20:14: start model_add_line... INFO @ Tue, 30 Jun 2020 01:20:14: start X-correlation... INFO @ Tue, 30 Jun 2020 01:20:14: end of X-cor INFO @ Tue, 30 Jun 2020 01:20:14: #2 finished! INFO @ Tue, 30 Jun 2020 01:20:14: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:20:14: #2 alternative fragment length(s) may be 1,39,563,583 bps INFO @ Tue, 30 Jun 2020 01:20:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.05_model.r WARNING @ Tue, 30 Jun 2020 01:20:14: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:20:14: #2 You may need to consider one of the other alternative d(s): 1,39,563,583 WARNING @ Tue, 30 Jun 2020 01:20:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:20:14: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:20:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:20:17: 7000000 INFO @ Tue, 30 Jun 2020 01:20:17: 13000000 INFO @ Tue, 30 Jun 2020 01:20:23: 14000000 INFO @ Tue, 30 Jun 2020 01:20:24: 8000000 INFO @ Tue, 30 Jun 2020 01:20:29: 15000000 INFO @ Tue, 30 Jun 2020 01:20:30: 9000000 INFO @ Tue, 30 Jun 2020 01:20:35: 16000000 INFO @ Tue, 30 Jun 2020 01:20:37: 10000000 INFO @ Tue, 30 Jun 2020 01:20:40: 17000000 INFO @ Tue, 30 Jun 2020 01:20:43: 11000000 INFO @ Tue, 30 Jun 2020 01:20:43: #1 tag size is determined as 42 bps INFO @ Tue, 30 Jun 2020 01:20:43: #1 tag size = 42 INFO @ Tue, 30 Jun 2020 01:20:43: #1 total tags in treatment: 17586332 INFO @ Tue, 30 Jun 2020 01:20:43: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:20:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:20:44: #1 tags after filtering in treatment: 17586332 INFO @ Tue, 30 Jun 2020 01:20:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:20:44: #1 finished! INFO @ Tue, 30 Jun 2020 01:20:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:20:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:20:45: #2 number of paired peaks: 206 WARNING @ Tue, 30 Jun 2020 01:20:45: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Tue, 30 Jun 2020 01:20:45: start model_add_line... INFO @ Tue, 30 Jun 2020 01:20:45: start X-correlation... INFO @ Tue, 30 Jun 2020 01:20:45: end of X-cor INFO @ Tue, 30 Jun 2020 01:20:45: #2 finished! INFO @ Tue, 30 Jun 2020 01:20:45: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:20:45: #2 alternative fragment length(s) may be 1,39,563,583 bps INFO @ Tue, 30 Jun 2020 01:20:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.10_model.r WARNING @ Tue, 30 Jun 2020 01:20:45: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:20:45: #2 You may need to consider one of the other alternative d(s): 1,39,563,583 WARNING @ Tue, 30 Jun 2020 01:20:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:20:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:20:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:20:48: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:20:49: 12000000 INFO @ Tue, 30 Jun 2020 01:20:56: 13000000 INFO @ Tue, 30 Jun 2020 01:21:02: 14000000 INFO @ Tue, 30 Jun 2020 01:21:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:21:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:21:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.05_summits.bed INFO @ Tue, 30 Jun 2020 01:21:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:21:08: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:21:15: 16000000 INFO @ Tue, 30 Jun 2020 01:21:18: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:21:21: 17000000 INFO @ Tue, 30 Jun 2020 01:21:25: #1 tag size is determined as 42 bps INFO @ Tue, 30 Jun 2020 01:21:25: #1 tag size = 42 INFO @ Tue, 30 Jun 2020 01:21:25: #1 total tags in treatment: 17586332 INFO @ Tue, 30 Jun 2020 01:21:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:21:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:21:25: #1 tags after filtering in treatment: 17586332 INFO @ Tue, 30 Jun 2020 01:21:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:21:25: #1 finished! INFO @ Tue, 30 Jun 2020 01:21:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:21:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:21:26: #2 number of paired peaks: 206 WARNING @ Tue, 30 Jun 2020 01:21:26: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Tue, 30 Jun 2020 01:21:26: start model_add_line... INFO @ Tue, 30 Jun 2020 01:21:26: start X-correlation... INFO @ Tue, 30 Jun 2020 01:21:26: end of X-cor INFO @ Tue, 30 Jun 2020 01:21:26: #2 finished! INFO @ Tue, 30 Jun 2020 01:21:26: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:21:26: #2 alternative fragment length(s) may be 1,39,563,583 bps INFO @ Tue, 30 Jun 2020 01:21:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.20_model.r WARNING @ Tue, 30 Jun 2020 01:21:27: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:21:27: #2 You may need to consider one of the other alternative d(s): 1,39,563,583 WARNING @ Tue, 30 Jun 2020 01:21:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:21:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:21:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:21:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:21:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:21:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.10_summits.bed INFO @ Tue, 30 Jun 2020 01:21:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:21:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:22:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:22:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:22:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466543/SRX466543.20_summits.bed INFO @ Tue, 30 Jun 2020 01:22:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling