Job ID = 6366326 SRX = SRX113600 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:44:52 prefetch.2.10.7: 1) Downloading 'SRR393700'... 2020-06-15T22:44:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:45:33 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:45:34 prefetch.2.10.7: 'SRR393700' is valid 2020-06-15T22:45:34 prefetch.2.10.7: 1) 'SRR393700' was downloaded successfully Read 7970866 spots for SRR393700/SRR393700.sra Written 7970866 spots for SRR393700/SRR393700.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: 00:01:48 7970866 reads; of these: 7970866 (100.00%) were unpaired; of these: 398562 (5.00%) aligned 0 times 5410801 (67.88%) aligned exactly 1 time 2161503 (27.12%) aligned >1 times 95.00% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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] 2994340 / 7572304 = 0.3954 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 07:49:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.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 07:49:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:49:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:49:52: 1000000 INFO @ Tue, 16 Jun 2020 07:49:57: 2000000 INFO @ Tue, 16 Jun 2020 07:50:01: 3000000 INFO @ Tue, 16 Jun 2020 07:50:06: 4000000 INFO @ Tue, 16 Jun 2020 07:50:09: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:50:09: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:50:09: #1 total tags in treatment: 4577964 INFO @ Tue, 16 Jun 2020 07:50:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:50:09: #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 07:50:09: #1 tags after filtering in treatment: 4577964 INFO @ Tue, 16 Jun 2020 07:50:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:50:09: #1 finished! INFO @ Tue, 16 Jun 2020 07:50:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:50:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:50:10: #2 number of paired peaks: 3579 INFO @ Tue, 16 Jun 2020 07:50:10: start model_add_line... INFO @ Tue, 16 Jun 2020 07:50:10: start X-correlation... INFO @ Tue, 16 Jun 2020 07:50:10: end of X-cor INFO @ Tue, 16 Jun 2020 07:50:10: #2 finished! INFO @ Tue, 16 Jun 2020 07:50:10: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 07:50:10: #2 alternative fragment length(s) may be 0,163,179,243 bps INFO @ Tue, 16 Jun 2020 07:50:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.05_model.r INFO @ Tue, 16 Jun 2020 07:50:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:50:10: #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 07:50:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.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 07:50:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:50:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:50:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:50:23: 1000000 INFO @ Tue, 16 Jun 2020 07:50:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:50:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:50:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.05_summits.bed INFO @ Tue, 16 Jun 2020 07:50:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (521 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:50:29: 2000000 INFO @ Tue, 16 Jun 2020 07:50:34: 3000000 INFO @ Tue, 16 Jun 2020 07:50:40: 4000000 INFO @ Tue, 16 Jun 2020 07:50:44: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:50:44: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:50:44: #1 total tags in treatment: 4577964 INFO @ Tue, 16 Jun 2020 07:50:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:50:44: #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 07:50:44: #1 tags after filtering in treatment: 4577964 INFO @ Tue, 16 Jun 2020 07:50:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:50:44: #1 finished! INFO @ Tue, 16 Jun 2020 07:50:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:50:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:50:44: #2 number of paired peaks: 3579 INFO @ Tue, 16 Jun 2020 07:50:44: start model_add_line... INFO @ Tue, 16 Jun 2020 07:50:44: start X-correlation... INFO @ Tue, 16 Jun 2020 07:50:44: end of X-cor INFO @ Tue, 16 Jun 2020 07:50:44: #2 finished! INFO @ Tue, 16 Jun 2020 07:50:44: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 07:50:44: #2 alternative fragment length(s) may be 0,163,179,243 bps INFO @ Tue, 16 Jun 2020 07:50:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.10_model.r INFO @ Tue, 16 Jun 2020 07:50:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:50:44: #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 07:50:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.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 07:50:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:50:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:50:52: 1000000 INFO @ Tue, 16 Jun 2020 07:50:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:50:58: 2000000 INFO @ Tue, 16 Jun 2020 07:51:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:51:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:51:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.10_summits.bed INFO @ Tue, 16 Jun 2020 07:51:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (217 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:51:04: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:51:09: 4000000 INFO @ Tue, 16 Jun 2020 07:51:13: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:51:13: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:51:13: #1 total tags in treatment: 4577964 INFO @ Tue, 16 Jun 2020 07:51:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:51:13: #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 07:51:13: #1 tags after filtering in treatment: 4577964 INFO @ Tue, 16 Jun 2020 07:51:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:51:13: #1 finished! INFO @ Tue, 16 Jun 2020 07:51:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:51:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:51:13: #2 number of paired peaks: 3579 INFO @ Tue, 16 Jun 2020 07:51:13: start model_add_line... INFO @ Tue, 16 Jun 2020 07:51:14: start X-correlation... INFO @ Tue, 16 Jun 2020 07:51:14: end of X-cor INFO @ Tue, 16 Jun 2020 07:51:14: #2 finished! INFO @ Tue, 16 Jun 2020 07:51:14: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 07:51:14: #2 alternative fragment length(s) may be 0,163,179,243 bps INFO @ Tue, 16 Jun 2020 07:51:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.20_model.r INFO @ Tue, 16 Jun 2020 07:51:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:51:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:51:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:51:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:51:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:51:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113600/SRX113600.20_summits.bed INFO @ Tue, 16 Jun 2020 07:51:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (71 records, 4 fields): 1 millis CompletedMACS2peakCalling