Job ID = 6368317 SRX = SRX495000 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:11:20 prefetch.2.10.7: 1) Downloading 'SRR1198532'... 2020-06-16T00:11:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:12:34 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:12:35 prefetch.2.10.7: 'SRR1198532' is valid 2020-06-16T00:12:35 prefetch.2.10.7: 1) 'SRR1198532' was downloaded successfully Read 11715770 spots for SRR1198532/SRR1198532.sra Written 11715770 spots for SRR1198532/SRR1198532.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: 00:01:12 11715770 reads; of these: 11715770 (100.00%) were unpaired; of these: 6223365 (53.12%) aligned 0 times 4214710 (35.97%) aligned exactly 1 time 1277695 (10.91%) aligned >1 times 46.88% overall alignment rate Time searching: 00:01:12 Overall time: 00:01:12 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] 1746784 / 5492405 = 0.3180 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 09:15:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.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 09:15:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:15:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:52: 1000000 INFO @ Tue, 16 Jun 2020 09:15:58: 2000000 INFO @ Tue, 16 Jun 2020 09:16:03: 3000000 INFO @ Tue, 16 Jun 2020 09:16:07: #1 tag size is determined as 37 bps INFO @ Tue, 16 Jun 2020 09:16:07: #1 tag size = 37 INFO @ Tue, 16 Jun 2020 09:16:07: #1 total tags in treatment: 3745621 INFO @ Tue, 16 Jun 2020 09:16:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:07: #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 09:16:07: #1 tags after filtering in treatment: 3745621 INFO @ Tue, 16 Jun 2020 09:16:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:16:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:08: #2 number of paired peaks: 1432 INFO @ Tue, 16 Jun 2020 09:16:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:08: #2 predicted fragment length is 176 bps INFO @ Tue, 16 Jun 2020 09:16:08: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 16 Jun 2020 09:16:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.05_model.r INFO @ Tue, 16 Jun 2020 09:16:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:08: #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 09:16:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.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 09:16:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:16:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:16:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.05_summits.bed INFO @ Tue, 16 Jun 2020 09:16:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2424 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:16:24: 1000000 INFO @ Tue, 16 Jun 2020 09:16:30: 2000000 INFO @ Tue, 16 Jun 2020 09:16:36: 3000000 INFO @ Tue, 16 Jun 2020 09:16:40: #1 tag size is determined as 37 bps INFO @ Tue, 16 Jun 2020 09:16:40: #1 tag size = 37 INFO @ Tue, 16 Jun 2020 09:16:40: #1 total tags in treatment: 3745621 INFO @ Tue, 16 Jun 2020 09:16:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:40: #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 09:16:40: #1 tags after filtering in treatment: 3745621 INFO @ Tue, 16 Jun 2020 09:16:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:16:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:40: #2 number of paired peaks: 1432 INFO @ Tue, 16 Jun 2020 09:16:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:40: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:40: #2 predicted fragment length is 176 bps INFO @ Tue, 16 Jun 2020 09:16:40: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 16 Jun 2020 09:16:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.10_model.r INFO @ Tue, 16 Jun 2020 09:16:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:40: #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 09:16:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.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 09:16:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:16:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:16:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:52: 1000000 INFO @ Tue, 16 Jun 2020 09:16:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.10_summits.bed INFO @ Tue, 16 Jun 2020 09:16:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1646 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:16:58: 2000000 INFO @ Tue, 16 Jun 2020 09:17:04: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:17:08: #1 tag size is determined as 37 bps INFO @ Tue, 16 Jun 2020 09:17:08: #1 tag size = 37 INFO @ Tue, 16 Jun 2020 09:17:08: #1 total tags in treatment: 3745621 INFO @ Tue, 16 Jun 2020 09:17:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:08: #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 09:17:08: #1 tags after filtering in treatment: 3745621 INFO @ Tue, 16 Jun 2020 09:17:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:17:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:08: #2 number of paired peaks: 1432 INFO @ Tue, 16 Jun 2020 09:17:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:08: #2 predicted fragment length is 176 bps INFO @ Tue, 16 Jun 2020 09:17:08: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 16 Jun 2020 09:17:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.20_model.r INFO @ Tue, 16 Jun 2020 09:17:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:17:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495000/SRX495000.20_summits.bed INFO @ Tue, 16 Jun 2020 09:17:22: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1155 records, 4 fields): 3 millis CompletedMACS2peakCalling