Job ID = 6368190 SRX = SRX494874 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:08:39 prefetch.2.10.7: 1) Downloading 'SRR1198406'... 2020-06-16T00:08:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:13:01 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:13:01 prefetch.2.10.7: 1) 'SRR1198406' was downloaded successfully Read 17698930 spots for SRR1198406/SRR1198406.sra Written 17698930 spots for SRR1198406/SRR1198406.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: 00:02:39 17698930 reads; of these: 17698930 (100.00%) were unpaired; of these: 8432867 (47.65%) aligned 0 times 7956282 (44.95%) aligned exactly 1 time 1309781 (7.40%) aligned >1 times 52.35% overall alignment rate Time searching: 00:02:39 Overall time: 00:02:39 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] 4767485 / 9266063 = 0.5145 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 09:19:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.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 09:19:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:26: 1000000 INFO @ Tue, 16 Jun 2020 09:19:33: 2000000 INFO @ Tue, 16 Jun 2020 09:19:39: 3000000 INFO @ Tue, 16 Jun 2020 09:19:46: 4000000 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 09:19:49: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:19:49: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:19:49: #1 total tags in treatment: 4498578 INFO @ Tue, 16 Jun 2020 09:19:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:19:49: #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 09:19:49: #1 tags after filtering in treatment: 4498578 INFO @ Tue, 16 Jun 2020 09:19:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:19:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:19:49: #2 number of paired peaks: 693 WARNING @ Tue, 16 Jun 2020 09:19:49: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Tue, 16 Jun 2020 09:19:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:19:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:19:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:19:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:19:49: #2 predicted fragment length is 128 bps INFO @ Tue, 16 Jun 2020 09:19:49: #2 alternative fragment length(s) may be 128 bps INFO @ Tue, 16 Jun 2020 09:19:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.05_model.r INFO @ Tue, 16 Jun 2020 09:19:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:19:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:19:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.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 09:19:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:57: 1000000 INFO @ Tue, 16 Jun 2020 09:19:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.05_summits.bed INFO @ Tue, 16 Jun 2020 09:20:04: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (872 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:20:05: 2000000 INFO @ Tue, 16 Jun 2020 09:20:12: 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 09:20:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.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 09:20:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:20: 4000000 INFO @ Tue, 16 Jun 2020 09:20:23: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:20:23: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:20:23: #1 total tags in treatment: 4498578 INFO @ Tue, 16 Jun 2020 09:20:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:23: #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 09:20:24: #1 tags after filtering in treatment: 4498578 INFO @ Tue, 16 Jun 2020 09:20:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:24: #2 number of paired peaks: 693 WARNING @ Tue, 16 Jun 2020 09:20:24: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:24: #2 predicted fragment length is 128 bps INFO @ Tue, 16 Jun 2020 09:20:24: #2 alternative fragment length(s) may be 128 bps INFO @ Tue, 16 Jun 2020 09:20:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.10_model.r INFO @ Tue, 16 Jun 2020 09:20:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:26: 1000000 INFO @ Tue, 16 Jun 2020 09:20:32: 2000000 INFO @ Tue, 16 Jun 2020 09:20:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:39: 3000000 INFO @ Tue, 16 Jun 2020 09:20:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.10_summits.bed INFO @ Tue, 16 Jun 2020 09:20:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (464 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:20:45: 4000000 INFO @ Tue, 16 Jun 2020 09:20:48: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:20:48: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:20:48: #1 total tags in treatment: 4498578 INFO @ Tue, 16 Jun 2020 09:20:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:48: #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 09:20:48: #1 tags after filtering in treatment: 4498578 INFO @ Tue, 16 Jun 2020 09:20:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:49: #2 number of paired peaks: 693 WARNING @ Tue, 16 Jun 2020 09:20:49: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:49: #2 predicted fragment length is 128 bps INFO @ Tue, 16 Jun 2020 09:20:49: #2 alternative fragment length(s) may be 128 bps INFO @ Tue, 16 Jun 2020 09:20:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.20_model.r INFO @ Tue, 16 Jun 2020 09:20:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:20:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494874/SRX494874.20_summits.bed INFO @ Tue, 16 Jun 2020 09:21:04: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (234 records, 4 fields): 2 millis CompletedMACS2peakCalling