Job ID = 6529162 SRX = SRX017855 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:01:36 18952913 reads; of these: 18952913 (100.00%) were unpaired; of these: 15311765 (80.79%) aligned 0 times 2769572 (14.61%) aligned exactly 1 time 871576 (4.60%) aligned >1 times 19.21% overall alignment rate Time searching: 00:01:36 Overall time: 00:01:36 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 536745 / 3641148 = 0.1474 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, 30 Jun 2020 01:21:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 30 Jun 2020 01:21:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:21:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:21:37: 1000000 INFO @ Tue, 30 Jun 2020 01:21:42: 2000000 INFO @ Tue, 30 Jun 2020 01:21:48: 3000000 INFO @ Tue, 30 Jun 2020 01:21:49: #1 tag size is determined as 28 bps INFO @ Tue, 30 Jun 2020 01:21:49: #1 tag size = 28 INFO @ Tue, 30 Jun 2020 01:21:49: #1 total tags in treatment: 3104403 INFO @ Tue, 30 Jun 2020 01:21:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:21:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:21:49: #1 tags after filtering in treatment: 3104381 INFO @ Tue, 30 Jun 2020 01:21:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:21:49: #1 finished! INFO @ Tue, 30 Jun 2020 01:21:49: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:21:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:21:49: #2 number of paired peaks: 208 WARNING @ Tue, 30 Jun 2020 01:21:49: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Tue, 30 Jun 2020 01:21:49: start model_add_line... INFO @ Tue, 30 Jun 2020 01:21:49: start X-correlation... INFO @ Tue, 30 Jun 2020 01:21:49: end of X-cor INFO @ Tue, 30 Jun 2020 01:21:49: #2 finished! INFO @ Tue, 30 Jun 2020 01:21:49: #2 predicted fragment length is 67 bps INFO @ Tue, 30 Jun 2020 01:21:49: #2 alternative fragment length(s) may be 34,67 bps INFO @ Tue, 30 Jun 2020 01:21:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.05_model.r INFO @ Tue, 30 Jun 2020 01:21:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:21:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:21:56: #3 Call peaks for each chromosome... 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, 30 Jun 2020 01:22:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:22:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:22:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.05_summits.bed INFO @ Tue, 30 Jun 2020 01:22:00: Done! pass1 - making usageList (117 chroms): 1 millis pass2 - checking and writing primary data (244 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:22:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 30 Jun 2020 01:22:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:22:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:22:07: 1000000 INFO @ Tue, 30 Jun 2020 01:22:12: 2000000 INFO @ Tue, 30 Jun 2020 01:22:18: 3000000 INFO @ Tue, 30 Jun 2020 01:22:18: #1 tag size is determined as 28 bps INFO @ Tue, 30 Jun 2020 01:22:18: #1 tag size = 28 INFO @ Tue, 30 Jun 2020 01:22:18: #1 total tags in treatment: 3104403 INFO @ Tue, 30 Jun 2020 01:22:18: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:22:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:22:18: #1 tags after filtering in treatment: 3104381 INFO @ Tue, 30 Jun 2020 01:22:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:22:18: #1 finished! INFO @ Tue, 30 Jun 2020 01:22:18: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:22:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:22:19: #2 number of paired peaks: 208 WARNING @ Tue, 30 Jun 2020 01:22:19: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Tue, 30 Jun 2020 01:22:19: start model_add_line... INFO @ Tue, 30 Jun 2020 01:22:19: start X-correlation... INFO @ Tue, 30 Jun 2020 01:22:19: end of X-cor INFO @ Tue, 30 Jun 2020 01:22:19: #2 finished! INFO @ Tue, 30 Jun 2020 01:22:19: #2 predicted fragment length is 67 bps INFO @ Tue, 30 Jun 2020 01:22:19: #2 alternative fragment length(s) may be 34,67 bps INFO @ Tue, 30 Jun 2020 01:22:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.10_model.r INFO @ Tue, 30 Jun 2020 01:22:19: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:22:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:22:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:22:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:22:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:22:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.10_summits.bed INFO @ Tue, 30 Jun 2020 01:22:29: Done! BedGraph に変換中... pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (90 records, 4 fields): 3 millis 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 CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:22:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 30 Jun 2020 01:22:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:22:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:22:37: 1000000 INFO @ Tue, 30 Jun 2020 01:22:42: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:22:47: 3000000 INFO @ Tue, 30 Jun 2020 01:22:48: #1 tag size is determined as 28 bps INFO @ Tue, 30 Jun 2020 01:22:48: #1 tag size = 28 INFO @ Tue, 30 Jun 2020 01:22:48: #1 total tags in treatment: 3104403 INFO @ Tue, 30 Jun 2020 01:22:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:22:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:22:48: #1 tags after filtering in treatment: 3104381 INFO @ Tue, 30 Jun 2020 01:22:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:22:48: #1 finished! INFO @ Tue, 30 Jun 2020 01:22:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:22:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:22:48: #2 number of paired peaks: 208 WARNING @ Tue, 30 Jun 2020 01:22:48: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Tue, 30 Jun 2020 01:22:48: start model_add_line... INFO @ Tue, 30 Jun 2020 01:22:48: start X-correlation... INFO @ Tue, 30 Jun 2020 01:22:48: end of X-cor INFO @ Tue, 30 Jun 2020 01:22:48: #2 finished! INFO @ Tue, 30 Jun 2020 01:22:48: #2 predicted fragment length is 67 bps INFO @ Tue, 30 Jun 2020 01:22:48: #2 alternative fragment length(s) may be 34,67 bps INFO @ Tue, 30 Jun 2020 01:22:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.20_model.r INFO @ Tue, 30 Jun 2020 01:22:48: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:22:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:22:55: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:22:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:22:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:22:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX017855/SRX017855.20_summits.bed INFO @ Tue, 30 Jun 2020 01:22:59: Done! pass1 - making usageList (28 chroms): 0 millis pass2 - checking and writing primary data (40 records, 4 fields): 2 millis CompletedMACS2peakCalling