Job ID = 6507875 SRX = SRX494960 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:16:03 prefetch.2.10.7: 1) Downloading 'SRR1198492'... 2020-06-26T13:16:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:16:53 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:16:54 prefetch.2.10.7: 'SRR1198492' is valid 2020-06-26T13:16:54 prefetch.2.10.7: 1) 'SRR1198492' was downloaded successfully Read 4465444 spots for SRR1198492/SRR1198492.sra Written 4465444 spots for SRR1198492/SRR1198492.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: 00:01:01 4465444 reads; of these: 4465444 (100.00%) were unpaired; of these: 829260 (18.57%) aligned 0 times 2898492 (64.91%) aligned exactly 1 time 737692 (16.52%) aligned >1 times 81.43% overall alignment rate Time searching: 00:01:01 Overall time: 00:01:01 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_rmdupse_core] 884765 / 3636184 = 0.2433 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 22:19:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.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 22:19:29: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:19:29: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:19:36: 1000000 INFO @ Fri, 26 Jun 2020 22:19:43: 2000000 INFO @ Fri, 26 Jun 2020 22:19:47: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:19:47: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:19:47: #1 total tags in treatment: 2751419 INFO @ Fri, 26 Jun 2020 22:19:47: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:19:47: #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 22:19:47: #1 tags after filtering in treatment: 2751419 INFO @ Fri, 26 Jun 2020 22:19:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:19:47: #1 finished! INFO @ Fri, 26 Jun 2020 22:19:47: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:19:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:19:48: #2 number of paired peaks: 1887 INFO @ Fri, 26 Jun 2020 22:19:48: start model_add_line... INFO @ Fri, 26 Jun 2020 22:19:48: start X-correlation... INFO @ Fri, 26 Jun 2020 22:19:48: end of X-cor INFO @ Fri, 26 Jun 2020 22:19:48: #2 finished! INFO @ Fri, 26 Jun 2020 22:19:48: #2 predicted fragment length is 182 bps INFO @ Fri, 26 Jun 2020 22:19:48: #2 alternative fragment length(s) may be 182 bps INFO @ Fri, 26 Jun 2020 22:19:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.05_model.r INFO @ Fri, 26 Jun 2020 22:19:48: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:19:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:19:54: #3 Call peaks for each chromosome... 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 22:19:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:19:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:19:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.05_summits.bed INFO @ Fri, 26 Jun 2020 22:19:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1784 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:19:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.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 22:19:59: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:19:59: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:20:05: 1000000 INFO @ Fri, 26 Jun 2020 22:20:10: 2000000 INFO @ Fri, 26 Jun 2020 22:20:14: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:20:14: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:20:14: #1 total tags in treatment: 2751419 INFO @ Fri, 26 Jun 2020 22:20:14: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:20:14: #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 22:20:14: #1 tags after filtering in treatment: 2751419 INFO @ Fri, 26 Jun 2020 22:20:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:20:14: #1 finished! INFO @ Fri, 26 Jun 2020 22:20:14: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:20:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:20:15: #2 number of paired peaks: 1887 INFO @ Fri, 26 Jun 2020 22:20:15: start model_add_line... INFO @ Fri, 26 Jun 2020 22:20:15: start X-correlation... INFO @ Fri, 26 Jun 2020 22:20:15: end of X-cor INFO @ Fri, 26 Jun 2020 22:20:15: #2 finished! INFO @ Fri, 26 Jun 2020 22:20:15: #2 predicted fragment length is 182 bps INFO @ Fri, 26 Jun 2020 22:20:15: #2 alternative fragment length(s) may be 182 bps INFO @ Fri, 26 Jun 2020 22:20:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.10_model.r INFO @ Fri, 26 Jun 2020 22:20:15: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:20:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:20:22: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:20:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:20:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:20:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.10_summits.bed INFO @ Fri, 26 Jun 2020 22:20:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (791 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 22:20:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.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 22:20:29: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:20:29: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:20:36: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:20:42: 2000000 INFO @ Fri, 26 Jun 2020 22:20:47: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:20:47: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:20:47: #1 total tags in treatment: 2751419 INFO @ Fri, 26 Jun 2020 22:20:47: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:20:47: #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 22:20:47: #1 tags after filtering in treatment: 2751419 INFO @ Fri, 26 Jun 2020 22:20:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:20:47: #1 finished! INFO @ Fri, 26 Jun 2020 22:20:47: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:20:47: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:20:47: #2 number of paired peaks: 1887 INFO @ Fri, 26 Jun 2020 22:20:47: start model_add_line... INFO @ Fri, 26 Jun 2020 22:20:47: start X-correlation... INFO @ Fri, 26 Jun 2020 22:20:47: end of X-cor INFO @ Fri, 26 Jun 2020 22:20:47: #2 finished! INFO @ Fri, 26 Jun 2020 22:20:47: #2 predicted fragment length is 182 bps INFO @ Fri, 26 Jun 2020 22:20:47: #2 alternative fragment length(s) may be 182 bps INFO @ Fri, 26 Jun 2020 22:20:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.20_model.r INFO @ Fri, 26 Jun 2020 22:20:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:20:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:20:55: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:20:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:20:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:20:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494960/SRX494960.20_summits.bed INFO @ Fri, 26 Jun 2020 22:20:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (284 records, 4 fields): 2 millis CompletedMACS2peakCalling