Job ID = 6366197 SRX = SRX065722 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:45:22 prefetch.2.10.7: 1) Downloading 'SRR217428'... 2020-06-15T22:45:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:46:08 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:46:08 prefetch.2.10.7: 'SRR217428' is valid 2020-06-15T22:46:08 prefetch.2.10.7: 1) 'SRR217428' was downloaded successfully Read 8304966 spots for SRR217428/SRR217428.sra Written 8304966 spots for SRR217428/SRR217428.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: 00:00:53 8304966 reads; of these: 8304966 (100.00%) were unpaired; of these: 5479957 (65.98%) aligned 0 times 2331394 (28.07%) aligned exactly 1 time 493615 (5.94%) aligned >1 times 34.02% overall alignment rate Time searching: 00:00:53 Overall time: 00:00:53 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] 335844 / 2825009 = 0.1189 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 07:48:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.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 07:48:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:48:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:48:35: 1000000 INFO @ Tue, 16 Jun 2020 07:48:41: 2000000 INFO @ Tue, 16 Jun 2020 07:48:44: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:48:44: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:48:44: #1 total tags in treatment: 2489165 INFO @ Tue, 16 Jun 2020 07:48:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:48:44: #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 07:48:44: #1 tags after filtering in treatment: 2489165 INFO @ Tue, 16 Jun 2020 07:48:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:48:44: #1 finished! INFO @ Tue, 16 Jun 2020 07:48:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:48:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:48:44: #2 number of paired peaks: 515 WARNING @ Tue, 16 Jun 2020 07:48:44: Fewer paired peaks (515) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 515 pairs to build model! INFO @ Tue, 16 Jun 2020 07:48:44: start model_add_line... INFO @ Tue, 16 Jun 2020 07:48:44: start X-correlation... INFO @ Tue, 16 Jun 2020 07:48:44: end of X-cor INFO @ Tue, 16 Jun 2020 07:48:44: #2 finished! INFO @ Tue, 16 Jun 2020 07:48:44: #2 predicted fragment length is 110 bps INFO @ Tue, 16 Jun 2020 07:48:44: #2 alternative fragment length(s) may be 110 bps INFO @ Tue, 16 Jun 2020 07:48:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.05_model.r INFO @ Tue, 16 Jun 2020 07:48:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:48:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:48:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:48:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:48:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:48:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.05_summits.bed INFO @ Tue, 16 Jun 2020 07:48:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (535 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 07:49:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.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 07:49:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:49:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:49:05: 1000000 INFO @ Tue, 16 Jun 2020 07:49:11: 2000000 INFO @ Tue, 16 Jun 2020 07:49:13: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:49:13: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:49:13: #1 total tags in treatment: 2489165 INFO @ Tue, 16 Jun 2020 07:49:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:49:13: #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 07:49:13: #1 tags after filtering in treatment: 2489165 INFO @ Tue, 16 Jun 2020 07:49:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:49:13: #1 finished! INFO @ Tue, 16 Jun 2020 07:49:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:49:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:49:13: #2 number of paired peaks: 515 WARNING @ Tue, 16 Jun 2020 07:49:13: Fewer paired peaks (515) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 515 pairs to build model! INFO @ Tue, 16 Jun 2020 07:49:13: start model_add_line... INFO @ Tue, 16 Jun 2020 07:49:13: start X-correlation... INFO @ Tue, 16 Jun 2020 07:49:13: end of X-cor INFO @ Tue, 16 Jun 2020 07:49:13: #2 finished! INFO @ Tue, 16 Jun 2020 07:49:13: #2 predicted fragment length is 110 bps INFO @ Tue, 16 Jun 2020 07:49:13: #2 alternative fragment length(s) may be 110 bps INFO @ Tue, 16 Jun 2020 07:49:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.10_model.r INFO @ Tue, 16 Jun 2020 07:49:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:49:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:49:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:49:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:49:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:49:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.10_summits.bed INFO @ Tue, 16 Jun 2020 07:49:22: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (321 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 @ Tue, 16 Jun 2020 07:49:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.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 07:49:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:49:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:49:35: 1000000 INFO @ Tue, 16 Jun 2020 07:49:41: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:49:43: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:49:43: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:49:43: #1 total tags in treatment: 2489165 INFO @ Tue, 16 Jun 2020 07:49:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:49:43: #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 07:49:43: #1 tags after filtering in treatment: 2489165 INFO @ Tue, 16 Jun 2020 07:49:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:49:43: #1 finished! INFO @ Tue, 16 Jun 2020 07:49:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:49:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:49:44: #2 number of paired peaks: 515 WARNING @ Tue, 16 Jun 2020 07:49:44: Fewer paired peaks (515) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 515 pairs to build model! INFO @ Tue, 16 Jun 2020 07:49:44: start model_add_line... INFO @ Tue, 16 Jun 2020 07:49:44: start X-correlation... INFO @ Tue, 16 Jun 2020 07:49:44: end of X-cor INFO @ Tue, 16 Jun 2020 07:49:44: #2 finished! INFO @ Tue, 16 Jun 2020 07:49:44: #2 predicted fragment length is 110 bps INFO @ Tue, 16 Jun 2020 07:49:44: #2 alternative fragment length(s) may be 110 bps INFO @ Tue, 16 Jun 2020 07:49:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.20_model.r INFO @ Tue, 16 Jun 2020 07:49:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:49:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:49:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:49:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:49:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:49:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065722/SRX065722.20_summits.bed INFO @ Tue, 16 Jun 2020 07:49:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (153 records, 4 fields): 1 millis CompletedMACS2peakCalling