Job ID = 6366609 SRX = SRX208773 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:54:59 prefetch.2.10.7: 1) Downloading 'SRR628907'... 2020-06-15T22:54:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:57:08 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:57:08 prefetch.2.10.7: 1) 'SRR628907' was downloaded successfully Read 17247211 spots for SRR628907/SRR628907.sra Written 17247211 spots for SRR628907/SRR628907.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: 00:05:31 17247211 reads; of these: 17247211 (100.00%) were unpaired; of these: 2375389 (13.77%) aligned 0 times 11705762 (67.87%) aligned exactly 1 time 3166060 (18.36%) aligned >1 times 86.23% overall alignment rate Time searching: 00:05:31 Overall time: 00:05:31 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] 11556807 / 14871822 = 0.7771 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 08:07:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.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 08:07:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:14: 1000000 INFO @ Tue, 16 Jun 2020 08:07:22: 2000000 INFO @ Tue, 16 Jun 2020 08:07:31: 3000000 INFO @ Tue, 16 Jun 2020 08:07:33: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:07:33: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:07:33: #1 total tags in treatment: 3315015 INFO @ Tue, 16 Jun 2020 08:07:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:33: #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 08:07:33: #1 tags after filtering in treatment: 3315015 INFO @ Tue, 16 Jun 2020 08:07:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:33: #2 looking for paired plus/minus strand peaks... 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 08:07:34: #2 number of paired peaks: 1740 INFO @ Tue, 16 Jun 2020 08:07:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:34: #2 predicted fragment length is 275 bps INFO @ Tue, 16 Jun 2020 08:07:34: #2 alternative fragment length(s) may be 275 bps INFO @ Tue, 16 Jun 2020 08:07:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.05_model.r INFO @ Tue, 16 Jun 2020 08:07:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.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 08:07:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:45: 1000000 INFO @ Tue, 16 Jun 2020 08:07:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.05_summits.bed INFO @ Tue, 16 Jun 2020 08:07:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1638 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:07:53: 2000000 INFO @ Tue, 16 Jun 2020 08:08:02: 3000000 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 08:08:04: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:08:04: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:08:04: #1 total tags in treatment: 3315015 INFO @ Tue, 16 Jun 2020 08:08:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:04: #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 08:08:05: #1 tags after filtering in treatment: 3315015 INFO @ Tue, 16 Jun 2020 08:08:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:05: #2 number of paired peaks: 1740 INFO @ Tue, 16 Jun 2020 08:08:05: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:05: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:05: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:05: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:05: #2 predicted fragment length is 275 bps INFO @ Tue, 16 Jun 2020 08:08:05: #2 alternative fragment length(s) may be 275 bps INFO @ Tue, 16 Jun 2020 08:08:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.10_model.r INFO @ Tue, 16 Jun 2020 08:08:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.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 08:08:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:15: 1000000 INFO @ Tue, 16 Jun 2020 08:08:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.10_summits.bed INFO @ Tue, 16 Jun 2020 08:08:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1396 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:08:23: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:08:32: 3000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:08:35: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:08:35: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:08:35: #1 total tags in treatment: 3315015 INFO @ Tue, 16 Jun 2020 08:08:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:35: #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 08:08:35: #1 tags after filtering in treatment: 3315015 INFO @ Tue, 16 Jun 2020 08:08:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:35: #2 number of paired peaks: 1740 INFO @ Tue, 16 Jun 2020 08:08:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:35: #2 predicted fragment length is 275 bps INFO @ Tue, 16 Jun 2020 08:08:35: #2 alternative fragment length(s) may be 275 bps INFO @ Tue, 16 Jun 2020 08:08:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.20_model.r INFO @ Tue, 16 Jun 2020 08:08:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208773/SRX208773.20_summits.bed INFO @ Tue, 16 Jun 2020 08:08:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1113 records, 4 fields): 3 millis CompletedMACS2peakCalling