Job ID = 6626464 SRX = SRX7262224 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: 00:01:20 6821424 reads; of these: 6821424 (100.00%) were unpaired; of these: 1078160 (15.81%) aligned 0 times 4456101 (65.33%) aligned exactly 1 time 1287163 (18.87%) aligned >1 times 84.19% overall alignment rate Time searching: 00:01:20 Overall time: 00:01:20 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] 411106 / 5743264 = 0.0716 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, 14 Jul 2020 07:06:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.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, 14 Jul 2020 07:06:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:06:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:06:44: 1000000 INFO @ Tue, 14 Jul 2020 07:06:49: 2000000 INFO @ Tue, 14 Jul 2020 07:06:54: 3000000 INFO @ Tue, 14 Jul 2020 07:07:00: 4000000 INFO @ Tue, 14 Jul 2020 07:07:05: 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, 14 Jul 2020 07:07:07: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:07:07: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:07:07: #1 total tags in treatment: 5332158 INFO @ Tue, 14 Jul 2020 07:07:07: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:07:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:07:07: #1 tags after filtering in treatment: 5332158 INFO @ Tue, 14 Jul 2020 07:07:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:07:07: #1 finished! INFO @ Tue, 14 Jul 2020 07:07:07: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:07:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:07:07: #2 number of paired peaks: 473 WARNING @ Tue, 14 Jul 2020 07:07:07: Fewer paired peaks (473) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 473 pairs to build model! INFO @ Tue, 14 Jul 2020 07:07:07: start model_add_line... INFO @ Tue, 14 Jul 2020 07:07:07: start X-correlation... INFO @ Tue, 14 Jul 2020 07:07:07: end of X-cor INFO @ Tue, 14 Jul 2020 07:07:07: #2 finished! INFO @ Tue, 14 Jul 2020 07:07:07: #2 predicted fragment length is 46 bps INFO @ Tue, 14 Jul 2020 07:07:07: #2 alternative fragment length(s) may be 4,46 bps INFO @ Tue, 14 Jul 2020 07:07:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.05_model.r WARNING @ Tue, 14 Jul 2020 07:07:07: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:07:07: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Tue, 14 Jul 2020 07:07:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:07:07: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:07:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:07:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.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, 14 Jul 2020 07:07:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:07:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:07:14: 1000000 INFO @ Tue, 14 Jul 2020 07:07:18: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:07:19: 2000000 INFO @ Tue, 14 Jul 2020 07:07:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:07:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:07:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.05_summits.bed INFO @ Tue, 14 Jul 2020 07:07:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (626 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:07:24: 3000000 INFO @ Tue, 14 Jul 2020 07:07:30: 4000000 INFO @ Tue, 14 Jul 2020 07:07:35: 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, 14 Jul 2020 07:07:37: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:07:37: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:07:37: #1 total tags in treatment: 5332158 INFO @ Tue, 14 Jul 2020 07:07:37: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:07:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:07:37: #1 tags after filtering in treatment: 5332158 INFO @ Tue, 14 Jul 2020 07:07:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:07:37: #1 finished! INFO @ Tue, 14 Jul 2020 07:07:37: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:07:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:07:37: #2 number of paired peaks: 473 WARNING @ Tue, 14 Jul 2020 07:07:37: Fewer paired peaks (473) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 473 pairs to build model! INFO @ Tue, 14 Jul 2020 07:07:37: start model_add_line... INFO @ Tue, 14 Jul 2020 07:07:37: start X-correlation... INFO @ Tue, 14 Jul 2020 07:07:37: end of X-cor INFO @ Tue, 14 Jul 2020 07:07:37: #2 finished! INFO @ Tue, 14 Jul 2020 07:07:37: #2 predicted fragment length is 46 bps INFO @ Tue, 14 Jul 2020 07:07:37: #2 alternative fragment length(s) may be 4,46 bps INFO @ Tue, 14 Jul 2020 07:07:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.10_model.r WARNING @ Tue, 14 Jul 2020 07:07:37: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:07:37: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Tue, 14 Jul 2020 07:07:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:07:37: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:07:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:07:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.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, 14 Jul 2020 07:07:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:07:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:07:44: 1000000 INFO @ Tue, 14 Jul 2020 07:07:48: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:07:49: 2000000 INFO @ Tue, 14 Jul 2020 07:07:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:07:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:07:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.10_summits.bed INFO @ Tue, 14 Jul 2020 07:07:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (380 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:07:54: 3000000 INFO @ Tue, 14 Jul 2020 07:08:00: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:08:05: 5000000 INFO @ Tue, 14 Jul 2020 07:08:07: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:08:07: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:08:07: #1 total tags in treatment: 5332158 INFO @ Tue, 14 Jul 2020 07:08:07: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:08:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:08:07: #1 tags after filtering in treatment: 5332158 INFO @ Tue, 14 Jul 2020 07:08:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:08:07: #1 finished! INFO @ Tue, 14 Jul 2020 07:08:07: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:08:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:08:07: #2 number of paired peaks: 473 WARNING @ Tue, 14 Jul 2020 07:08:07: Fewer paired peaks (473) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 473 pairs to build model! INFO @ Tue, 14 Jul 2020 07:08:07: start model_add_line... INFO @ Tue, 14 Jul 2020 07:08:07: start X-correlation... INFO @ Tue, 14 Jul 2020 07:08:07: end of X-cor INFO @ Tue, 14 Jul 2020 07:08:07: #2 finished! INFO @ Tue, 14 Jul 2020 07:08:07: #2 predicted fragment length is 46 bps INFO @ Tue, 14 Jul 2020 07:08:07: #2 alternative fragment length(s) may be 4,46 bps INFO @ Tue, 14 Jul 2020 07:08:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.20_model.r WARNING @ Tue, 14 Jul 2020 07:08:07: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:08:07: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Tue, 14 Jul 2020 07:08:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:08:07: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:08:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:08:19: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:08:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:08:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:08:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262224/SRX7262224.20_summits.bed INFO @ Tue, 14 Jul 2020 07:08:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (161 records, 4 fields): 20 millis CompletedMACS2peakCalling