Job ID = 6366994 SRX = SRX257693 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:09:31 prefetch.2.10.7: 1) Downloading 'SRR800710'... 2020-06-15T23:09:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:10:21 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:10:21 prefetch.2.10.7: 'SRR800710' is valid 2020-06-15T23:10:21 prefetch.2.10.7: 1) 'SRR800710' was downloaded successfully Read 20952107 spots for SRR800710/SRR800710.sra Written 20952107 spots for SRR800710/SRR800710.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: 00:03:18 20952107 reads; of these: 20952107 (100.00%) were unpaired; of these: 613877 (2.93%) aligned 0 times 16790345 (80.14%) aligned exactly 1 time 3547885 (16.93%) aligned >1 times 97.07% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 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] 2047987 / 20338230 = 0.1007 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, 16 Jun 2020 08:18:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.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, 16 Jun 2020 08:18:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:32: 1000000 INFO @ Tue, 16 Jun 2020 08:18:37: 2000000 INFO @ Tue, 16 Jun 2020 08:18:42: 3000000 INFO @ Tue, 16 Jun 2020 08:18:47: 4000000 INFO @ Tue, 16 Jun 2020 08:18:51: 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 @ Tue, 16 Jun 2020 08:18:56: 6000000 INFO @ Tue, 16 Jun 2020 08:18:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.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, 16 Jun 2020 08:18:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:02: 7000000 INFO @ Tue, 16 Jun 2020 08:19:03: 1000000 INFO @ Tue, 16 Jun 2020 08:19:07: 8000000 INFO @ Tue, 16 Jun 2020 08:19:08: 2000000 INFO @ Tue, 16 Jun 2020 08:19:12: 9000000 INFO @ Tue, 16 Jun 2020 08:19:14: 3000000 INFO @ Tue, 16 Jun 2020 08:19:17: 10000000 INFO @ Tue, 16 Jun 2020 08:19:19: 4000000 INFO @ Tue, 16 Jun 2020 08:19:23: 11000000 INFO @ Tue, 16 Jun 2020 08:19:24: 5000000 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, 16 Jun 2020 08:19:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.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, 16 Jun 2020 08:19:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:28: 12000000 INFO @ Tue, 16 Jun 2020 08:19:30: 6000000 INFO @ Tue, 16 Jun 2020 08:19:33: 1000000 INFO @ Tue, 16 Jun 2020 08:19:33: 13000000 INFO @ Tue, 16 Jun 2020 08:19:35: 7000000 INFO @ Tue, 16 Jun 2020 08:19:38: 2000000 INFO @ Tue, 16 Jun 2020 08:19:39: 14000000 INFO @ Tue, 16 Jun 2020 08:19:40: 8000000 INFO @ Tue, 16 Jun 2020 08:19:43: 3000000 INFO @ Tue, 16 Jun 2020 08:19:44: 15000000 INFO @ Tue, 16 Jun 2020 08:19:45: 9000000 INFO @ Tue, 16 Jun 2020 08:19:48: 4000000 INFO @ Tue, 16 Jun 2020 08:19:49: 16000000 INFO @ Tue, 16 Jun 2020 08:19:51: 10000000 INFO @ Tue, 16 Jun 2020 08:19:54: 5000000 INFO @ Tue, 16 Jun 2020 08:19:54: 17000000 INFO @ Tue, 16 Jun 2020 08:19:56: 11000000 INFO @ Tue, 16 Jun 2020 08:19:59: 6000000 INFO @ Tue, 16 Jun 2020 08:19:59: 18000000 INFO @ Tue, 16 Jun 2020 08:20:01: 12000000 INFO @ Tue, 16 Jun 2020 08:20:01: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:20:01: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:20:01: #1 total tags in treatment: 18290243 INFO @ Tue, 16 Jun 2020 08:20:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:20:01: #1 tags after filtering in treatment: 18290243 INFO @ Tue, 16 Jun 2020 08:20:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:02: #2 number of paired peaks: 230 WARNING @ Tue, 16 Jun 2020 08:20:02: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:03: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:03: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:03: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:03: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:20:03: #2 alternative fragment length(s) may be 1,31,549 bps INFO @ Tue, 16 Jun 2020 08:20:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.05_model.r WARNING @ Tue, 16 Jun 2020 08:20:03: #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, 16 Jun 2020 08:20:03: #2 You may need to consider one of the other alternative d(s): 1,31,549 WARNING @ Tue, 16 Jun 2020 08:20:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:20:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:04: 7000000 INFO @ Tue, 16 Jun 2020 08:20:06: 13000000 INFO @ Tue, 16 Jun 2020 08:20:09: 8000000 INFO @ Tue, 16 Jun 2020 08:20:12: 14000000 INFO @ Tue, 16 Jun 2020 08:20:14: 9000000 INFO @ Tue, 16 Jun 2020 08:20:17: 15000000 INFO @ Tue, 16 Jun 2020 08:20:19: 10000000 INFO @ Tue, 16 Jun 2020 08:20:22: 16000000 INFO @ Tue, 16 Jun 2020 08:20:24: 11000000 INFO @ Tue, 16 Jun 2020 08:20:28: 17000000 INFO @ Tue, 16 Jun 2020 08:20:29: 12000000 INFO @ Tue, 16 Jun 2020 08:20:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:33: 18000000 INFO @ Tue, 16 Jun 2020 08:20:34: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:20:34: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:20:34: #1 total tags in treatment: 18290243 INFO @ Tue, 16 Jun 2020 08:20:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:20:34: 13000000 INFO @ Tue, 16 Jun 2020 08:20:35: #1 tags after filtering in treatment: 18290243 INFO @ Tue, 16 Jun 2020 08:20:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:36: #2 number of paired peaks: 230 WARNING @ Tue, 16 Jun 2020 08:20:36: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:36: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:36: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:36: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:36: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:20:36: #2 alternative fragment length(s) may be 1,31,549 bps INFO @ Tue, 16 Jun 2020 08:20:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.10_model.r WARNING @ Tue, 16 Jun 2020 08:20:36: #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, 16 Jun 2020 08:20:36: #2 You may need to consider one of the other alternative d(s): 1,31,549 WARNING @ Tue, 16 Jun 2020 08:20:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:20:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:40: 14000000 INFO @ Tue, 16 Jun 2020 08:20:44: 15000000 INFO @ Tue, 16 Jun 2020 08:20:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.05_summits.bed INFO @ Tue, 16 Jun 2020 08:20:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:49: 16000000 INFO @ Tue, 16 Jun 2020 08:20:54: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:20:59: 18000000 INFO @ Tue, 16 Jun 2020 08:21:01: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:21:01: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:21:01: #1 total tags in treatment: 18290243 INFO @ Tue, 16 Jun 2020 08:21:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:21:01: #1 tags after filtering in treatment: 18290243 INFO @ Tue, 16 Jun 2020 08:21:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:02: #2 number of paired peaks: 230 WARNING @ Tue, 16 Jun 2020 08:21:02: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:02: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:21:02: #2 alternative fragment length(s) may be 1,31,549 bps INFO @ Tue, 16 Jun 2020 08:21:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.20_model.r WARNING @ Tue, 16 Jun 2020 08:21:02: #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, 16 Jun 2020 08:21:02: #2 You may need to consider one of the other alternative d(s): 1,31,549 WARNING @ Tue, 16 Jun 2020 08:21:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:21:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.10_summits.bed INFO @ Tue, 16 Jun 2020 08:21:21: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:21:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:21:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257693/SRX257693.20_summits.bed INFO @ Tue, 16 Jun 2020 08:21:47: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling