Job ID = 6366912 SRX = SRX257657 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:02:38 prefetch.2.10.7: 1) Downloading 'SRR800668'... 2020-06-15T23:02:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:04:02 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:04:02 prefetch.2.10.7: 1) 'SRR800668' was downloaded successfully Read 30487356 spots for SRR800668/SRR800668.sra Written 30487356 spots for SRR800668/SRR800668.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: 00:05:01 30487356 reads; of these: 30487356 (100.00%) were unpaired; of these: 2944513 (9.66%) aligned 0 times 22653372 (74.30%) aligned exactly 1 time 4889471 (16.04%) aligned >1 times 90.34% overall alignment rate Time searching: 00:05:01 Overall time: 00:05:01 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_sort_core] merging from 8 files... [bam_rmdupse_core] 22065189 / 27542843 = 0.8011 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 08:14:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.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 08:14:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:39: 1000000 INFO @ Tue, 16 Jun 2020 08:14:45: 2000000 INFO @ Tue, 16 Jun 2020 08:14:50: 3000000 INFO @ Tue, 16 Jun 2020 08:14:55: 4000000 INFO @ Tue, 16 Jun 2020 08:15:00: 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 @ Tue, 16 Jun 2020 08:15:03: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:15:03: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:15:03: #1 total tags in treatment: 5477654 INFO @ Tue, 16 Jun 2020 08:15:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:03: #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 08:15:03: #1 tags after filtering in treatment: 5477654 INFO @ Tue, 16 Jun 2020 08:15:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:03: #2 number of paired peaks: 1348 INFO @ Tue, 16 Jun 2020 08:15:03: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:03: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:03: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:03: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:03: #2 predicted fragment length is 110 bps INFO @ Tue, 16 Jun 2020 08:15:03: #2 alternative fragment length(s) may be 4,110 bps INFO @ Tue, 16 Jun 2020 08:15:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.05_model.r INFO @ Tue, 16 Jun 2020 08:15:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.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 08:15:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:09: 1000000 INFO @ Tue, 16 Jun 2020 08:15:15: 2000000 INFO @ Tue, 16 Jun 2020 08:15:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:20: 3000000 INFO @ Tue, 16 Jun 2020 08:15:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.05_summits.bed INFO @ Tue, 16 Jun 2020 08:15:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2073 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:15:25: 4000000 INFO @ Tue, 16 Jun 2020 08:15:31: 5000000 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 08:15:33: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:15:33: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:15:33: #1 total tags in treatment: 5477654 INFO @ Tue, 16 Jun 2020 08:15:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:33: #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 08:15:33: #1 tags after filtering in treatment: 5477654 INFO @ Tue, 16 Jun 2020 08:15:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:34: #2 number of paired peaks: 1348 INFO @ Tue, 16 Jun 2020 08:15:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:34: #2 predicted fragment length is 110 bps INFO @ Tue, 16 Jun 2020 08:15:34: #2 alternative fragment length(s) may be 4,110 bps INFO @ Tue, 16 Jun 2020 08:15:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.10_model.r INFO @ Tue, 16 Jun 2020 08:15:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.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 08:15:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:39: 1000000 INFO @ Tue, 16 Jun 2020 08:15:45: 2000000 INFO @ Tue, 16 Jun 2020 08:15:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:50: 3000000 INFO @ Tue, 16 Jun 2020 08:15:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.10_summits.bed INFO @ Tue, 16 Jun 2020 08:15:55: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1114 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:15:55: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:16:01: 5000000 INFO @ Tue, 16 Jun 2020 08:16:03: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:16:03: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:16:03: #1 total tags in treatment: 5477654 INFO @ Tue, 16 Jun 2020 08:16:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:03: #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 08:16:03: #1 tags after filtering in treatment: 5477654 INFO @ Tue, 16 Jun 2020 08:16:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:04: #2 number of paired peaks: 1348 INFO @ Tue, 16 Jun 2020 08:16:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:04: #2 predicted fragment length is 110 bps INFO @ Tue, 16 Jun 2020 08:16:04: #2 alternative fragment length(s) may be 4,110 bps INFO @ Tue, 16 Jun 2020 08:16:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.20_model.r INFO @ Tue, 16 Jun 2020 08:16:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:16:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257657/SRX257657.20_summits.bed INFO @ Tue, 16 Jun 2020 08:16:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (600 records, 4 fields): 1 millis CompletedMACS2peakCalling