Job ID = 6367279 SRX = SRX331041 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 'SRR947263'... 2020-06-15T23:13:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:13:44 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:13:44 prefetch.2.10.7: 'SRR947263' is valid 2020-06-15T23:13:44 prefetch.2.10.7: 1) 'SRR947263' was downloaded successfully Read 4439133 spots for SRR947263/SRR947263.sra Written 4439133 spots for SRR947263/SRR947263.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: 00:00:44 4439133 reads; of these: 4439133 (100.00%) were unpaired; of these: 64889 (1.46%) aligned 0 times 3644418 (82.10%) aligned exactly 1 time 729826 (16.44%) aligned >1 times 98.54% overall alignment rate Time searching: 00:00:44 Overall time: 00:00:44 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_rmdupse_core] 196128 / 4374244 = 0.0448 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 08:16:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.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 08:16:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:16:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:16:07: 1000000 INFO @ Tue, 16 Jun 2020 08:16:14: 2000000 INFO @ Tue, 16 Jun 2020 08:16:20: 3000000 INFO @ Tue, 16 Jun 2020 08:16:26: 4000000 INFO @ Tue, 16 Jun 2020 08:16:27: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:16:27: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:16:27: #1 total tags in treatment: 4178116 INFO @ Tue, 16 Jun 2020 08:16:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:27: #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 08:16:27: #1 tags after filtering in treatment: 4178116 INFO @ Tue, 16 Jun 2020 08:16:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:27: #2 number of paired peaks: 378 WARNING @ Tue, 16 Jun 2020 08:16:27: Fewer paired peaks (378) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 378 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:28: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:16:28: #2 alternative fragment length(s) may be 4,31,515,592 bps INFO @ Tue, 16 Jun 2020 08:16:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.05_model.r WARNING @ Tue, 16 Jun 2020 08:16:28: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:16:28: #2 You may need to consider one of the other alternative d(s): 4,31,515,592 WARNING @ Tue, 16 Jun 2020 08:16:28: #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 08:16:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:28: #3 Pre-compute pvalue-qvalue table... 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 08:16:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.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 08:16:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:16:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:16:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:37: 1000000 INFO @ Tue, 16 Jun 2020 08:16:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.05_summits.bed INFO @ Tue, 16 Jun 2020 08:16:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (368 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:16:42: 2000000 INFO @ Tue, 16 Jun 2020 08:16:47: 3000000 INFO @ Tue, 16 Jun 2020 08:16:52: 4000000 INFO @ Tue, 16 Jun 2020 08:16:53: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:16:53: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:16:53: #1 total tags in treatment: 4178116 INFO @ Tue, 16 Jun 2020 08:16:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:53: #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 08:16:53: #1 tags after filtering in treatment: 4178116 INFO @ Tue, 16 Jun 2020 08:16:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:53: #2 number of paired peaks: 378 WARNING @ Tue, 16 Jun 2020 08:16:53: Fewer paired peaks (378) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 378 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:53: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:16:53: #2 alternative fragment length(s) may be 4,31,515,592 bps INFO @ Tue, 16 Jun 2020 08:16:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.10_model.r WARNING @ Tue, 16 Jun 2020 08:16:53: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:16:53: #2 You may need to consider one of the other alternative d(s): 4,31,515,592 WARNING @ Tue, 16 Jun 2020 08:16:53: #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 08:16:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:53: #3 Pre-compute pvalue-qvalue table... 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 08:17:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:17:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.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 08:17:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:17:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.10_summits.bed INFO @ Tue, 16 Jun 2020 08:17:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (169 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:17:07: 1000000 INFO @ Tue, 16 Jun 2020 08:17:12: 2000000 INFO @ Tue, 16 Jun 2020 08:17:17: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:17:22: 4000000 INFO @ Tue, 16 Jun 2020 08:17:23: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:17:23: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:17:23: #1 total tags in treatment: 4178116 INFO @ Tue, 16 Jun 2020 08:17:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:23: #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 08:17:23: #1 tags after filtering in treatment: 4178116 INFO @ Tue, 16 Jun 2020 08:17:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:17:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:23: #2 number of paired peaks: 378 WARNING @ Tue, 16 Jun 2020 08:17:23: Fewer paired peaks (378) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 378 pairs to build model! INFO @ Tue, 16 Jun 2020 08:17:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:23: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:17:23: #2 alternative fragment length(s) may be 4,31,515,592 bps INFO @ Tue, 16 Jun 2020 08:17:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.20_model.r WARNING @ Tue, 16 Jun 2020 08:17:23: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:17:23: #2 You may need to consider one of the other alternative d(s): 4,31,515,592 WARNING @ Tue, 16 Jun 2020 08:17:23: #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 08:17:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:17:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:17:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331041/SRX331041.20_summits.bed INFO @ Tue, 16 Jun 2020 08:17:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (51 records, 4 fields): 1 millis CompletedMACS2peakCalling