Job ID = 6366697 SRX = SRX2228853 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:57:38 prefetch.2.10.7: 1) Downloading 'SRR4380309'... 2020-06-15T22:57:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:58:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:58:15 prefetch.2.10.7: 'SRR4380309' is valid 2020-06-15T22:58:15 prefetch.2.10.7: 1) 'SRR4380309' was downloaded successfully Read 5242953 spots for SRR4380309/SRR4380309.sra Written 5242953 spots for SRR4380309/SRR4380309.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: 00:01:10 5242953 reads; of these: 5242953 (100.00%) were unpaired; of these: 512955 (9.78%) aligned 0 times 3956221 (75.46%) aligned exactly 1 time 773777 (14.76%) aligned >1 times 90.22% overall alignment rate Time searching: 00:01:10 Overall time: 00:01:10 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] 935615 / 4729998 = 0.1978 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 08:01:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.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 08:01:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:29: 1000000 INFO @ Tue, 16 Jun 2020 08:01:35: 2000000 INFO @ Tue, 16 Jun 2020 08:01:40: 3000000 INFO @ Tue, 16 Jun 2020 08:01:45: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:01:45: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:01:45: #1 total tags in treatment: 3794383 INFO @ Tue, 16 Jun 2020 08:01:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:01:45: #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 08:01:45: #1 tags after filtering in treatment: 3794383 INFO @ Tue, 16 Jun 2020 08:01:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:01:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:01:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:01:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:01:45: #2 number of paired peaks: 558 WARNING @ Tue, 16 Jun 2020 08:01:45: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Tue, 16 Jun 2020 08:01:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:01:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:01:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:01:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:01:45: #2 predicted fragment length is 180 bps INFO @ Tue, 16 Jun 2020 08:01:45: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 16 Jun 2020 08:01:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.05_model.r INFO @ Tue, 16 Jun 2020 08:01:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:01:45: #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 08:01:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.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 08:01:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:01:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.05_summits.bed INFO @ Tue, 16 Jun 2020 08:01:59: Done! INFO @ Tue, 16 Jun 2020 08:01:59: 1000000 pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (708 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:02:05: 2000000 INFO @ Tue, 16 Jun 2020 08:02:10: 3000000 INFO @ Tue, 16 Jun 2020 08:02:15: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:02:15: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:02:15: #1 total tags in treatment: 3794383 INFO @ Tue, 16 Jun 2020 08:02:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:15: #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 08:02:15: #1 tags after filtering in treatment: 3794383 INFO @ Tue, 16 Jun 2020 08:02:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:15: #2 number of paired peaks: 558 WARNING @ Tue, 16 Jun 2020 08:02:15: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Tue, 16 Jun 2020 08:02:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:15: #2 predicted fragment length is 180 bps INFO @ Tue, 16 Jun 2020 08:02:15: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 16 Jun 2020 08:02:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.10_model.r INFO @ Tue, 16 Jun 2020 08:02:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:15: #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 08:02:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.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 08:02:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.10_summits.bed INFO @ Tue, 16 Jun 2020 08:02:29: Done! INFO @ Tue, 16 Jun 2020 08:02:29: 1000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (449 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:02:35: 2000000 INFO @ Tue, 16 Jun 2020 08:02:40: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:02:45: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:02:45: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:02:45: #1 total tags in treatment: 3794383 INFO @ Tue, 16 Jun 2020 08:02:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:45: #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 08:02:45: #1 tags after filtering in treatment: 3794383 INFO @ Tue, 16 Jun 2020 08:02:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:45: #2 number of paired peaks: 558 WARNING @ Tue, 16 Jun 2020 08:02:45: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Tue, 16 Jun 2020 08:02:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:45: #2 predicted fragment length is 180 bps INFO @ Tue, 16 Jun 2020 08:02:45: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 16 Jun 2020 08:02:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.20_model.r INFO @ Tue, 16 Jun 2020 08:02:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:02:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228853/SRX2228853.20_summits.bed INFO @ Tue, 16 Jun 2020 08:02:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (264 records, 4 fields): 1 millis CompletedMACS2peakCalling