Job ID = 6365854 SRX = SRX003820 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:09:27 prefetch.2.10.7: 1) Downloading 'SRR015060'... 2020-06-15T22:09:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:20:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:20:14 prefetch.2.10.7: 1) 'SRR015060' was downloaded successfully Read 15150543 spots for SRR015060/SRR015060.sra Written 15150543 spots for SRR015060/SRR015060.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: 00:01:22 15150543 reads; of these: 15150543 (100.00%) were unpaired; of these: 10301155 (67.99%) aligned 0 times 4173616 (27.55%) aligned exactly 1 time 675772 (4.46%) aligned >1 times 32.01% overall alignment rate Time searching: 00:01:22 Overall time: 00:01:22 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] 650252 / 4849388 = 0.1341 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 07:23:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.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 07:23:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:23:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:23:53: 1000000 INFO @ Tue, 16 Jun 2020 07:23:59: 2000000 INFO @ Tue, 16 Jun 2020 07:24:06: 3000000 INFO @ Tue, 16 Jun 2020 07:24:12: 4000000 INFO @ Tue, 16 Jun 2020 07:24:13: #1 tag size is determined as 37 bps INFO @ Tue, 16 Jun 2020 07:24:13: #1 tag size = 37 INFO @ Tue, 16 Jun 2020 07:24:13: #1 total tags in treatment: 4199136 INFO @ Tue, 16 Jun 2020 07:24:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:24:13: #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 07:24:14: #1 tags after filtering in treatment: 4199136 INFO @ Tue, 16 Jun 2020 07:24:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:24:14: #1 finished! INFO @ Tue, 16 Jun 2020 07:24:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:24:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:24:14: #2 number of paired peaks: 2546 INFO @ Tue, 16 Jun 2020 07:24:14: start model_add_line... INFO @ Tue, 16 Jun 2020 07:24:14: start X-correlation... INFO @ Tue, 16 Jun 2020 07:24:14: end of X-cor INFO @ Tue, 16 Jun 2020 07:24:14: #2 finished! INFO @ Tue, 16 Jun 2020 07:24:14: #2 predicted fragment length is 80 bps INFO @ Tue, 16 Jun 2020 07:24:14: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 16 Jun 2020 07:24:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.05_model.r INFO @ Tue, 16 Jun 2020 07:24:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:24:14: #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 07:24:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.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 07:24:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:24:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:24:22: 1000000 INFO @ Tue, 16 Jun 2020 07:24:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:24:27: 2000000 INFO @ Tue, 16 Jun 2020 07:24:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:24:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:24:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.05_summits.bed INFO @ Tue, 16 Jun 2020 07:24:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (10069 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:24:33: 3000000 INFO @ Tue, 16 Jun 2020 07:24:38: 4000000 INFO @ Tue, 16 Jun 2020 07:24:39: #1 tag size is determined as 37 bps INFO @ Tue, 16 Jun 2020 07:24:39: #1 tag size = 37 INFO @ Tue, 16 Jun 2020 07:24:39: #1 total tags in treatment: 4199136 INFO @ Tue, 16 Jun 2020 07:24:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:24:39: #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 07:24:40: #1 tags after filtering in treatment: 4199136 INFO @ Tue, 16 Jun 2020 07:24:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:24:40: #1 finished! INFO @ Tue, 16 Jun 2020 07:24:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:24:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:24:40: #2 number of paired peaks: 2546 INFO @ Tue, 16 Jun 2020 07:24:40: start model_add_line... INFO @ Tue, 16 Jun 2020 07:24:40: start X-correlation... INFO @ Tue, 16 Jun 2020 07:24:40: end of X-cor INFO @ Tue, 16 Jun 2020 07:24:40: #2 finished! INFO @ Tue, 16 Jun 2020 07:24:40: #2 predicted fragment length is 80 bps INFO @ Tue, 16 Jun 2020 07:24:40: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 16 Jun 2020 07:24:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.10_model.r INFO @ Tue, 16 Jun 2020 07:24:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:24:40: #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 07:24:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.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 07:24:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:24:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:24:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:24:54: 1000000 INFO @ Tue, 16 Jun 2020 07:24:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:24:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:24:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.10_summits.bed INFO @ Tue, 16 Jun 2020 07:24:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4847 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:25:01: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:25:08: 3000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:25:15: 4000000 INFO @ Tue, 16 Jun 2020 07:25:17: #1 tag size is determined as 37 bps INFO @ Tue, 16 Jun 2020 07:25:17: #1 tag size = 37 INFO @ Tue, 16 Jun 2020 07:25:17: #1 total tags in treatment: 4199136 INFO @ Tue, 16 Jun 2020 07:25:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:25:17: #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 07:25:17: #1 tags after filtering in treatment: 4199136 INFO @ Tue, 16 Jun 2020 07:25:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:25:17: #1 finished! INFO @ Tue, 16 Jun 2020 07:25:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:25:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:25:17: #2 number of paired peaks: 2546 INFO @ Tue, 16 Jun 2020 07:25:17: start model_add_line... INFO @ Tue, 16 Jun 2020 07:25:17: start X-correlation... INFO @ Tue, 16 Jun 2020 07:25:17: end of X-cor INFO @ Tue, 16 Jun 2020 07:25:17: #2 finished! INFO @ Tue, 16 Jun 2020 07:25:17: #2 predicted fragment length is 80 bps INFO @ Tue, 16 Jun 2020 07:25:17: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 16 Jun 2020 07:25:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.20_model.r INFO @ Tue, 16 Jun 2020 07:25:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:25:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:25:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:25:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:25:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:25:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX003820/SRX003820.20_summits.bed INFO @ Tue, 16 Jun 2020 07:25:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2001 records, 4 fields): 3 millis CompletedMACS2peakCalling