Job ID = 6507936 SRX = SRX495098 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:27:02 prefetch.2.10.7: 1) Downloading 'SRR1198630'... 2020-06-26T13:27:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:28:11 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:28:12 prefetch.2.10.7: 'SRR1198630' is valid 2020-06-26T13:28:12 prefetch.2.10.7: 1) 'SRR1198630' was downloaded successfully Read 13681119 spots for SRR1198630/SRR1198630.sra Written 13681119 spots for SRR1198630/SRR1198630.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:02 13681119 reads; of these: 13681119 (100.00%) were unpaired; of these: 4006041 (29.28%) aligned 0 times 7380179 (53.94%) aligned exactly 1 time 2294899 (16.77%) aligned >1 times 70.72% overall alignment rate Time searching: 00:02:03 Overall time: 00:02:03 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] 2007222 / 9675078 = 0.2075 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 @ Fri, 26 Jun 2020 22:33:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.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 @ Fri, 26 Jun 2020 22:33:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:33:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:33:30: 1000000 INFO @ Fri, 26 Jun 2020 22:33:36: 2000000 INFO @ Fri, 26 Jun 2020 22:33:41: 3000000 INFO @ Fri, 26 Jun 2020 22:33:47: 4000000 INFO @ Fri, 26 Jun 2020 22:33:53: 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 @ Fri, 26 Jun 2020 22:33:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.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 @ Fri, 26 Jun 2020 22:33:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:33:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:33:59: 6000000 INFO @ Fri, 26 Jun 2020 22:34:02: 1000000 INFO @ Fri, 26 Jun 2020 22:34:05: 7000000 INFO @ Fri, 26 Jun 2020 22:34:08: 2000000 INFO @ Fri, 26 Jun 2020 22:34:10: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:34:10: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:34:10: #1 total tags in treatment: 7667856 INFO @ Fri, 26 Jun 2020 22:34:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:34:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:34:10: #1 tags after filtering in treatment: 7667856 INFO @ Fri, 26 Jun 2020 22:34:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:34:10: #1 finished! INFO @ Fri, 26 Jun 2020 22:34:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:34:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:34:10: #2 number of paired peaks: 776 WARNING @ Fri, 26 Jun 2020 22:34:10: Fewer paired peaks (776) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 776 pairs to build model! INFO @ Fri, 26 Jun 2020 22:34:10: start model_add_line... INFO @ Fri, 26 Jun 2020 22:34:10: start X-correlation... INFO @ Fri, 26 Jun 2020 22:34:10: end of X-cor INFO @ Fri, 26 Jun 2020 22:34:10: #2 finished! INFO @ Fri, 26 Jun 2020 22:34:10: #2 predicted fragment length is 113 bps INFO @ Fri, 26 Jun 2020 22:34:10: #2 alternative fragment length(s) may be 113 bps INFO @ Fri, 26 Jun 2020 22:34:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.05_model.r INFO @ Fri, 26 Jun 2020 22:34:10: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:34:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:34:15: 3000000 INFO @ Fri, 26 Jun 2020 22:34:20: 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 @ Fri, 26 Jun 2020 22:34:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.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 @ Fri, 26 Jun 2020 22:34:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:34:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:34:27: 5000000 INFO @ Fri, 26 Jun 2020 22:34:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:34:31: 1000000 INFO @ Fri, 26 Jun 2020 22:34:33: 6000000 INFO @ Fri, 26 Jun 2020 22:34:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:34:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:34:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.05_summits.bed INFO @ Fri, 26 Jun 2020 22:34:37: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (14951 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:34:38: 2000000 INFO @ Fri, 26 Jun 2020 22:34:39: 7000000 INFO @ Fri, 26 Jun 2020 22:34:44: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:34:44: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:34:44: #1 total tags in treatment: 7667856 INFO @ Fri, 26 Jun 2020 22:34:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:34:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:34:44: #1 tags after filtering in treatment: 7667856 INFO @ Fri, 26 Jun 2020 22:34:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:34:44: #1 finished! INFO @ Fri, 26 Jun 2020 22:34:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:34:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:34:44: 3000000 INFO @ Fri, 26 Jun 2020 22:34:44: #2 number of paired peaks: 776 WARNING @ Fri, 26 Jun 2020 22:34:44: Fewer paired peaks (776) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 776 pairs to build model! INFO @ Fri, 26 Jun 2020 22:34:44: start model_add_line... INFO @ Fri, 26 Jun 2020 22:34:44: start X-correlation... INFO @ Fri, 26 Jun 2020 22:34:44: end of X-cor INFO @ Fri, 26 Jun 2020 22:34:44: #2 finished! INFO @ Fri, 26 Jun 2020 22:34:44: #2 predicted fragment length is 113 bps INFO @ Fri, 26 Jun 2020 22:34:44: #2 alternative fragment length(s) may be 113 bps INFO @ Fri, 26 Jun 2020 22:34:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.10_model.r INFO @ Fri, 26 Jun 2020 22:34:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:34:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:34:50: 4000000 INFO @ Fri, 26 Jun 2020 22:34:56: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:35:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:35:02: 6000000 INFO @ Fri, 26 Jun 2020 22:35:08: 7000000 INFO @ Fri, 26 Jun 2020 22:35:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:35:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:35:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.10_summits.bed INFO @ Fri, 26 Jun 2020 22:35:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5790 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:35:12: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:35:12: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:35:12: #1 total tags in treatment: 7667856 INFO @ Fri, 26 Jun 2020 22:35:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:35:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:35:12: #1 tags after filtering in treatment: 7667856 INFO @ Fri, 26 Jun 2020 22:35:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:35:12: #1 finished! INFO @ Fri, 26 Jun 2020 22:35:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:35:12: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:35:13: #2 number of paired peaks: 776 WARNING @ Fri, 26 Jun 2020 22:35:13: Fewer paired peaks (776) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 776 pairs to build model! INFO @ Fri, 26 Jun 2020 22:35:13: start model_add_line... INFO @ Fri, 26 Jun 2020 22:35:13: start X-correlation... INFO @ Fri, 26 Jun 2020 22:35:13: end of X-cor INFO @ Fri, 26 Jun 2020 22:35:13: #2 finished! INFO @ Fri, 26 Jun 2020 22:35:13: #2 predicted fragment length is 113 bps INFO @ Fri, 26 Jun 2020 22:35:13: #2 alternative fragment length(s) may be 113 bps INFO @ Fri, 26 Jun 2020 22:35:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.20_model.r INFO @ Fri, 26 Jun 2020 22:35:13: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:35:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:35:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:35:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:35:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:35:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495098/SRX495098.20_summits.bed INFO @ Fri, 26 Jun 2020 22:35:37: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1686 records, 4 fields): 3 millis CompletedMACS2peakCalling