Job ID = 6368779 SRX = SRX560683 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:30:12 prefetch.2.10.7: 1) Downloading 'SRR1314162'... 2020-06-16T00:30:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:31:32 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:31:32 prefetch.2.10.7: 'SRR1314162' is valid 2020-06-16T00:31:32 prefetch.2.10.7: 1) 'SRR1314162' was downloaded successfully 2020-06-16T00:31:32 prefetch.2.10.7: 'SRR1314162' has 0 unresolved dependencies Read 4904548 spots for SRR1314162/SRR1314162.sra Written 4904548 spots for SRR1314162/SRR1314162.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: 00:01:01 4904548 reads; of these: 4904548 (100.00%) were unpaired; of these: 2707624 (55.21%) aligned 0 times 1864812 (38.02%) aligned exactly 1 time 332112 (6.77%) aligned >1 times 44.79% overall alignment rate Time searching: 00:01:01 Overall time: 00:01:01 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] 2085196 / 2196924 = 0.9491 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 09:33:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.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 09:33:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:43: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:33:43: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:33:43: #1 total tags in treatment: 111728 INFO @ Tue, 16 Jun 2020 09:33:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:43: #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 09:33:43: #1 tags after filtering in treatment: 111728 INFO @ Tue, 16 Jun 2020 09:33:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:43: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:43: #2 number of paired peaks: 2682 INFO @ Tue, 16 Jun 2020 09:33:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:43: #2 predicted fragment length is 119 bps INFO @ Tue, 16 Jun 2020 09:33:43: #2 alternative fragment length(s) may be 119,238,294,486,571 bps INFO @ Tue, 16 Jun 2020 09:33:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.05_model.r WARNING @ Tue, 16 Jun 2020 09:33:43: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:33:43: #2 You may need to consider one of the other alternative d(s): 119,238,294,486,571 WARNING @ Tue, 16 Jun 2020 09:33:43: #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 09:33:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.05_summits.bed INFO @ Tue, 16 Jun 2020 09:33:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (104 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 09:34:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.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 09:34:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:14: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:34:14: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:34:14: #1 total tags in treatment: 111728 INFO @ Tue, 16 Jun 2020 09:34:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:14: #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 09:34:14: #1 tags after filtering in treatment: 111728 INFO @ Tue, 16 Jun 2020 09:34:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:14: #2 number of paired peaks: 2682 INFO @ Tue, 16 Jun 2020 09:34:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:14: #2 predicted fragment length is 119 bps INFO @ Tue, 16 Jun 2020 09:34:14: #2 alternative fragment length(s) may be 119,238,294,486,571 bps INFO @ Tue, 16 Jun 2020 09:34:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.10_model.r WARNING @ Tue, 16 Jun 2020 09:34:14: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:34:14: #2 You may need to consider one of the other alternative d(s): 119,238,294,486,571 WARNING @ Tue, 16 Jun 2020 09:34:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:34:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:34:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.10_summits.bed INFO @ Tue, 16 Jun 2020 09:34:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (44 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:34:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.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 09:34:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:44: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:34:44: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:34:44: #1 total tags in treatment: 111728 INFO @ Tue, 16 Jun 2020 09:34:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:44: #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 09:34:44: #1 tags after filtering in treatment: 111728 INFO @ Tue, 16 Jun 2020 09:34:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:44: #2 number of paired peaks: 2682 INFO @ Tue, 16 Jun 2020 09:34:44: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:44: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:44: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:44: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:44: #2 predicted fragment length is 119 bps INFO @ Tue, 16 Jun 2020 09:34:44: #2 alternative fragment length(s) may be 119,238,294,486,571 bps INFO @ Tue, 16 Jun 2020 09:34:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.20_model.r WARNING @ Tue, 16 Jun 2020 09:34:44: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:34:44: #2 You may need to consider one of the other alternative d(s): 119,238,294,486,571 WARNING @ Tue, 16 Jun 2020 09:34:44: #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 09:34:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:34:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX560683/SRX560683.20_summits.bed INFO @ Tue, 16 Jun 2020 09:34:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (15 records, 4 fields): 0 millis CompletedMACS2peakCalling