Job ID = 6366913 SRX = SRX257658 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:05:53 prefetch.2.10.7: 1) Downloading 'SRR800669'... 2020-06-15T23:05:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:07:08 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:07:08 prefetch.2.10.7: 1) 'SRR800669' was downloaded successfully Read 11982884 spots for SRR800669/SRR800669.sra Written 11982884 spots for SRR800669/SRR800669.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: 00:03:42 11982884 reads; of these: 11982884 (100.00%) were unpaired; of these: 1115100 (9.31%) aligned 0 times 9281266 (77.45%) aligned exactly 1 time 1586518 (13.24%) aligned >1 times 90.69% overall alignment rate Time searching: 00:03:42 Overall time: 00:03:42 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] 1918026 / 10867784 = 0.1765 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 08:15:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.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 08:15:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:24: 1000000 INFO @ Tue, 16 Jun 2020 08:15:30: 2000000 INFO @ Tue, 16 Jun 2020 08:15:36: 3000000 INFO @ Tue, 16 Jun 2020 08:15:42: 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 08:15:47: 5000000 INFO @ Tue, 16 Jun 2020 08:15:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.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 08:15:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:54: 6000000 INFO @ Tue, 16 Jun 2020 08:15:54: 1000000 INFO @ Tue, 16 Jun 2020 08:16:00: 7000000 INFO @ Tue, 16 Jun 2020 08:16:01: 2000000 INFO @ Tue, 16 Jun 2020 08:16:06: 8000000 INFO @ Tue, 16 Jun 2020 08:16:07: 3000000 INFO @ Tue, 16 Jun 2020 08:16:12: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:16:12: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:16:12: #1 total tags in treatment: 8949758 INFO @ Tue, 16 Jun 2020 08:16:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:12: #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 08:16:12: #1 tags after filtering in treatment: 8949758 INFO @ Tue, 16 Jun 2020 08:16:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:13: #2 number of paired peaks: 796 WARNING @ Tue, 16 Jun 2020 08:16:13: Fewer paired peaks (796) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 796 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:13: #2 predicted fragment length is 154 bps INFO @ Tue, 16 Jun 2020 08:16:13: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 16 Jun 2020 08:16:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.05_model.r INFO @ Tue, 16 Jun 2020 08:16:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:16:13: 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 08:16:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.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 08:16:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:16:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:16:20: 5000000 INFO @ Tue, 16 Jun 2020 08:16:25: 1000000 INFO @ Tue, 16 Jun 2020 08:16:26: 6000000 INFO @ Tue, 16 Jun 2020 08:16:31: 2000000 INFO @ Tue, 16 Jun 2020 08:16:32: 7000000 INFO @ Tue, 16 Jun 2020 08:16:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:38: 3000000 INFO @ Tue, 16 Jun 2020 08:16:39: 8000000 INFO @ Tue, 16 Jun 2020 08:16:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.05_summits.bed INFO @ Tue, 16 Jun 2020 08:16:44: Done! INFO @ Tue, 16 Jun 2020 08:16:44: 4000000 INFO @ Tue, 16 Jun 2020 08:16:44: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:16:44: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:16:44: #1 total tags in treatment: 8949758 INFO @ Tue, 16 Jun 2020 08:16:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:44: #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 08:16:44: #1 tags after filtering in treatment: 8949758 INFO @ Tue, 16 Jun 2020 08:16:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:44: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1819 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:16:45: #2 number of paired peaks: 796 WARNING @ Tue, 16 Jun 2020 08:16:45: Fewer paired peaks (796) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 796 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:45: #2 predicted fragment length is 154 bps INFO @ Tue, 16 Jun 2020 08:16:45: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 16 Jun 2020 08:16:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.10_model.r INFO @ Tue, 16 Jun 2020 08:16:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:16:50: 5000000 INFO @ Tue, 16 Jun 2020 08:16:56: 6000000 INFO @ Tue, 16 Jun 2020 08:17:02: 7000000 INFO @ Tue, 16 Jun 2020 08:17:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:17:08: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:17:14: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:17:14: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:17:14: #1 total tags in treatment: 8949758 INFO @ Tue, 16 Jun 2020 08:17:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:14: #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 08:17:14: #1 tags after filtering in treatment: 8949758 INFO @ Tue, 16 Jun 2020 08:17:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:17:14: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:14: #2 number of paired peaks: 796 WARNING @ Tue, 16 Jun 2020 08:17:14: Fewer paired peaks (796) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 796 pairs to build model! INFO @ Tue, 16 Jun 2020 08:17:14: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:14: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:14: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:14: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:14: #2 predicted fragment length is 154 bps INFO @ Tue, 16 Jun 2020 08:17:14: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 16 Jun 2020 08:17:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.20_model.r INFO @ Tue, 16 Jun 2020 08:17:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:17:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.10_summits.bed INFO @ Tue, 16 Jun 2020 08:17:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1207 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:17:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:17:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257658/SRX257658.20_summits.bed INFO @ Tue, 16 Jun 2020 08:17:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (766 records, 4 fields): 2 millis CompletedMACS2peakCalling