Job ID = 6366019 SRX = SRX054211 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:03:27 prefetch.2.10.7: 1) Downloading 'SRR163977'... 2020-06-15T22:03:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:03:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:03:53 prefetch.2.10.7: 'SRR163977' is valid 2020-06-15T22:03:53 prefetch.2.10.7: 1) 'SRR163977' was downloaded successfully Read 3671631 spots for SRR163977/SRR163977.sra Written 3671631 spots for SRR163977/SRR163977.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: 00:00:01 Multiseed full-index search: 00:00:17 3671631 reads; of these: 3671631 (100.00%) were unpaired; of these: 2851617 (77.67%) aligned 0 times 727329 (19.81%) aligned exactly 1 time 92685 (2.52%) aligned >1 times 22.33% overall alignment rate Time searching: 00:00:18 Overall time: 00:00:18 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] 59231 / 820014 = 0.0722 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 07:05:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.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 07:05:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:05:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:05:15: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:05:15: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:05:15: #1 total tags in treatment: 760783 INFO @ Tue, 16 Jun 2020 07:05:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:05:15: #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 07:05:15: #1 tags after filtering in treatment: 760783 INFO @ Tue, 16 Jun 2020 07:05:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:05:15: #1 finished! INFO @ Tue, 16 Jun 2020 07:05:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:05:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:05:15: #2 number of paired peaks: 512 WARNING @ Tue, 16 Jun 2020 07:05:15: Fewer paired peaks (512) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 512 pairs to build model! INFO @ Tue, 16 Jun 2020 07:05:15: start model_add_line... INFO @ Tue, 16 Jun 2020 07:05:15: start X-correlation... INFO @ Tue, 16 Jun 2020 07:05:15: end of X-cor INFO @ Tue, 16 Jun 2020 07:05:15: #2 finished! INFO @ Tue, 16 Jun 2020 07:05:15: #2 predicted fragment length is 130 bps INFO @ Tue, 16 Jun 2020 07:05:15: #2 alternative fragment length(s) may be 130 bps INFO @ Tue, 16 Jun 2020 07:05:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.05_model.r INFO @ Tue, 16 Jun 2020 07:05:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:05:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:05:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:05:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:05:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:05:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.05_summits.bed INFO @ Tue, 16 Jun 2020 07:05:17: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (137 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 07:05:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.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 07:05:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:05:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:05:44: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:05:44: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:05:44: #1 total tags in treatment: 760783 INFO @ Tue, 16 Jun 2020 07:05:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:05:44: #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 07:05:44: #1 tags after filtering in treatment: 760783 INFO @ Tue, 16 Jun 2020 07:05:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:05:44: #1 finished! INFO @ Tue, 16 Jun 2020 07:05:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:05:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:05:45: #2 number of paired peaks: 512 WARNING @ Tue, 16 Jun 2020 07:05:45: Fewer paired peaks (512) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 512 pairs to build model! INFO @ Tue, 16 Jun 2020 07:05:45: start model_add_line... INFO @ Tue, 16 Jun 2020 07:05:45: start X-correlation... INFO @ Tue, 16 Jun 2020 07:05:45: end of X-cor INFO @ Tue, 16 Jun 2020 07:05:45: #2 finished! INFO @ Tue, 16 Jun 2020 07:05:45: #2 predicted fragment length is 130 bps INFO @ Tue, 16 Jun 2020 07:05:45: #2 alternative fragment length(s) may be 130 bps INFO @ Tue, 16 Jun 2020 07:05:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.10_model.r INFO @ Tue, 16 Jun 2020 07:05:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:05:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:05:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:05:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:05:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:05:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.10_summits.bed INFO @ Tue, 16 Jun 2020 07:05:47: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (31 records, 4 fields): 1 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 @ Tue, 16 Jun 2020 07:06:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.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 07:06:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:06:11: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:06:14: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:06:14: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:06:14: #1 total tags in treatment: 760783 INFO @ Tue, 16 Jun 2020 07:06:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:06:14: #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 07:06:14: #1 tags after filtering in treatment: 760783 INFO @ Tue, 16 Jun 2020 07:06:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:06:14: #1 finished! INFO @ Tue, 16 Jun 2020 07:06:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:06:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:06:14: #2 number of paired peaks: 512 WARNING @ Tue, 16 Jun 2020 07:06:14: Fewer paired peaks (512) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 512 pairs to build model! INFO @ Tue, 16 Jun 2020 07:06:14: start model_add_line... INFO @ Tue, 16 Jun 2020 07:06:14: start X-correlation... INFO @ Tue, 16 Jun 2020 07:06:14: end of X-cor INFO @ Tue, 16 Jun 2020 07:06:14: #2 finished! INFO @ Tue, 16 Jun 2020 07:06:14: #2 predicted fragment length is 130 bps INFO @ Tue, 16 Jun 2020 07:06:14: #2 alternative fragment length(s) may be 130 bps INFO @ Tue, 16 Jun 2020 07:06:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.20_model.r INFO @ Tue, 16 Jun 2020 07:06:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:06:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:06:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:06:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:06:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:06:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX054211/SRX054211.20_summits.bed INFO @ Tue, 16 Jun 2020 07:06:17: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling