Job ID = 6366938 SRX = SRX257663 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:13:16 prefetch.2.10.7: 1) Downloading 'SRR800674'... 2020-06-15T23:13:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:15:18 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:15:18 prefetch.2.10.7: 1) 'SRR800674' was downloaded successfully Read 20920487 spots for SRR800674/SRR800674.sra Written 20920487 spots for SRR800674/SRR800674.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: 00:04:57 20920487 reads; of these: 20920487 (100.00%) were unpaired; of these: 738847 (3.53%) aligned 0 times 16613945 (79.41%) aligned exactly 1 time 3567695 (17.05%) aligned >1 times 96.47% overall alignment rate Time searching: 00:04:57 Overall time: 00:04:57 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 9078571 / 20181640 = 0.4498 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 08:26:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.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 08:26:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:26: 1000000 INFO @ Tue, 16 Jun 2020 08:26:31: 2000000 INFO @ Tue, 16 Jun 2020 08:26:37: 3000000 INFO @ Tue, 16 Jun 2020 08:26:43: 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, 16 Jun 2020 08:26:48: 5000000 INFO @ Tue, 16 Jun 2020 08:26:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.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 08:26:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:55: 6000000 INFO @ Tue, 16 Jun 2020 08:26:56: 1000000 INFO @ Tue, 16 Jun 2020 08:27:01: 7000000 INFO @ Tue, 16 Jun 2020 08:27:03: 2000000 INFO @ Tue, 16 Jun 2020 08:27:08: 8000000 INFO @ Tue, 16 Jun 2020 08:27:09: 3000000 INFO @ Tue, 16 Jun 2020 08:27:14: 9000000 INFO @ Tue, 16 Jun 2020 08:27:16: 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 @ Tue, 16 Jun 2020 08:27:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.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 08:27:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:21: 10000000 INFO @ Tue, 16 Jun 2020 08:27:23: 5000000 INFO @ Tue, 16 Jun 2020 08:27:27: 1000000 INFO @ Tue, 16 Jun 2020 08:27:28: 11000000 INFO @ Tue, 16 Jun 2020 08:27:29: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:27:29: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:27:29: #1 total tags in treatment: 11103069 INFO @ Tue, 16 Jun 2020 08:27:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:29: #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 08:27:29: #1 tags after filtering in treatment: 11103069 INFO @ Tue, 16 Jun 2020 08:27:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:30: 6000000 INFO @ Tue, 16 Jun 2020 08:27:30: #2 number of paired peaks: 504 WARNING @ Tue, 16 Jun 2020 08:27:30: Fewer paired peaks (504) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 504 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:30: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:30: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:30: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:30: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:30: #2 predicted fragment length is 58 bps INFO @ Tue, 16 Jun 2020 08:27:30: #2 alternative fragment length(s) may be 4,58 bps INFO @ Tue, 16 Jun 2020 08:27:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.05_model.r WARNING @ Tue, 16 Jun 2020 08:27:30: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:27:30: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Tue, 16 Jun 2020 08:27:30: #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 08:27:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:35: 2000000 INFO @ Tue, 16 Jun 2020 08:27:37: 7000000 INFO @ Tue, 16 Jun 2020 08:27:42: 3000000 INFO @ Tue, 16 Jun 2020 08:27:44: 8000000 INFO @ Tue, 16 Jun 2020 08:27:50: 4000000 INFO @ Tue, 16 Jun 2020 08:27:51: 9000000 INFO @ Tue, 16 Jun 2020 08:27:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:57: 5000000 INFO @ Tue, 16 Jun 2020 08:27:58: 10000000 INFO @ Tue, 16 Jun 2020 08:28:05: 6000000 INFO @ Tue, 16 Jun 2020 08:28:05: 11000000 INFO @ Tue, 16 Jun 2020 08:28:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.05_summits.bed INFO @ Tue, 16 Jun 2020 08:28:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1256 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:28:06: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:28:06: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:28:06: #1 total tags in treatment: 11103069 INFO @ Tue, 16 Jun 2020 08:28:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:06: #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 08:28:06: #1 tags after filtering in treatment: 11103069 INFO @ Tue, 16 Jun 2020 08:28:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:06: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:07: #2 number of paired peaks: 504 WARNING @ Tue, 16 Jun 2020 08:28:07: Fewer paired peaks (504) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 504 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:07: #2 predicted fragment length is 58 bps INFO @ Tue, 16 Jun 2020 08:28:07: #2 alternative fragment length(s) may be 4,58 bps INFO @ Tue, 16 Jun 2020 08:28:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.10_model.r WARNING @ Tue, 16 Jun 2020 08:28:07: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:28:07: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Tue, 16 Jun 2020 08:28:07: #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 08:28:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:12: 7000000 INFO @ Tue, 16 Jun 2020 08:28:19: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:28:26: 9000000 INFO @ Tue, 16 Jun 2020 08:28:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:32: 10000000 INFO @ Tue, 16 Jun 2020 08:28:39: 11000000 INFO @ Tue, 16 Jun 2020 08:28:40: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:28:40: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:28:40: #1 total tags in treatment: 11103069 INFO @ Tue, 16 Jun 2020 08:28:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:40: #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 08:28:40: #1 tags after filtering in treatment: 11103069 INFO @ Tue, 16 Jun 2020 08:28:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:40: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.10_summits.bed INFO @ Tue, 16 Jun 2020 08:28:41: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (788 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:28:41: #2 number of paired peaks: 504 WARNING @ Tue, 16 Jun 2020 08:28:41: Fewer paired peaks (504) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 504 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:41: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:41: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:41: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:41: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:41: #2 predicted fragment length is 58 bps INFO @ Tue, 16 Jun 2020 08:28:41: #2 alternative fragment length(s) may be 4,58 bps INFO @ Tue, 16 Jun 2020 08:28:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.20_model.r WARNING @ Tue, 16 Jun 2020 08:28:41: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:28:41: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Tue, 16 Jun 2020 08:28:41: #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 08:28:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:29:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257663/SRX257663.20_summits.bed INFO @ Tue, 16 Jun 2020 08:29:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (334 records, 4 fields): 1 millis CompletedMACS2peakCalling