Job ID = 6529189 SRX = SRX033319 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: 00:02:53 12541820 reads; of these: 12541820 (100.00%) were unpaired; of these: 639399 (5.10%) aligned 0 times 9038636 (72.07%) aligned exactly 1 time 2863785 (22.83%) aligned >1 times 94.90% overall alignment rate Time searching: 00:02:53 Overall time: 00:02:53 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 1996116 / 11902421 = 0.1677 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 01:45:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.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 01:45:10: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:45:10: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:45:17: 1000000 INFO @ Tue, 30 Jun 2020 01:45:23: 2000000 INFO @ Tue, 30 Jun 2020 01:45:30: 3000000 INFO @ Tue, 30 Jun 2020 01:45:36: 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, 30 Jun 2020 01:45:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.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 01:45:40: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:45:40: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:45:42: 5000000 INFO @ Tue, 30 Jun 2020 01:45:46: 1000000 INFO @ Tue, 30 Jun 2020 01:45:49: 6000000 INFO @ Tue, 30 Jun 2020 01:45:52: 2000000 INFO @ Tue, 30 Jun 2020 01:45:55: 7000000 INFO @ Tue, 30 Jun 2020 01:45:58: 3000000 INFO @ Tue, 30 Jun 2020 01:46:02: 8000000 INFO @ Tue, 30 Jun 2020 01:46:04: 4000000 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, 30 Jun 2020 01:46:09: 9000000 INFO @ Tue, 30 Jun 2020 01:46:10: 5000000 INFO @ Tue, 30 Jun 2020 01:46:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.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 01:46:10: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:46:10: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:46:16: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:46:16: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:46:16: #1 total tags in treatment: 9906305 INFO @ Tue, 30 Jun 2020 01:46:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:46:16: #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 01:46:16: #1 tags after filtering in treatment: 9906292 INFO @ Tue, 30 Jun 2020 01:46:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:46:16: #1 finished! INFO @ Tue, 30 Jun 2020 01:46:16: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:46:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:46:16: 6000000 INFO @ Tue, 30 Jun 2020 01:46:17: 1000000 INFO @ Tue, 30 Jun 2020 01:46:17: #2 number of paired peaks: 230 WARNING @ Tue, 30 Jun 2020 01:46:17: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Tue, 30 Jun 2020 01:46:17: start model_add_line... INFO @ Tue, 30 Jun 2020 01:46:17: start X-correlation... INFO @ Tue, 30 Jun 2020 01:46:17: end of X-cor INFO @ Tue, 30 Jun 2020 01:46:17: #2 finished! INFO @ Tue, 30 Jun 2020 01:46:17: #2 predicted fragment length is 197 bps INFO @ Tue, 30 Jun 2020 01:46:17: #2 alternative fragment length(s) may be 155,197,230 bps INFO @ Tue, 30 Jun 2020 01:46:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.05_model.r INFO @ Tue, 30 Jun 2020 01:46:17: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:46:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:46:22: 7000000 INFO @ Tue, 30 Jun 2020 01:46:23: 2000000 INFO @ Tue, 30 Jun 2020 01:46:29: 8000000 INFO @ Tue, 30 Jun 2020 01:46:29: 3000000 INFO @ Tue, 30 Jun 2020 01:46:35: 4000000 INFO @ Tue, 30 Jun 2020 01:46:36: 9000000 INFO @ Tue, 30 Jun 2020 01:46:37: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:46:41: 5000000 INFO @ Tue, 30 Jun 2020 01:46:42: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:46:42: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:46:42: #1 total tags in treatment: 9906305 INFO @ Tue, 30 Jun 2020 01:46:42: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:46:42: #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 01:46:42: #1 tags after filtering in treatment: 9906292 INFO @ Tue, 30 Jun 2020 01:46:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:46:42: #1 finished! INFO @ Tue, 30 Jun 2020 01:46:42: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:46:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:46:43: #2 number of paired peaks: 230 WARNING @ Tue, 30 Jun 2020 01:46:43: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Tue, 30 Jun 2020 01:46:43: start model_add_line... INFO @ Tue, 30 Jun 2020 01:46:43: start X-correlation... INFO @ Tue, 30 Jun 2020 01:46:43: end of X-cor INFO @ Tue, 30 Jun 2020 01:46:43: #2 finished! INFO @ Tue, 30 Jun 2020 01:46:43: #2 predicted fragment length is 197 bps INFO @ Tue, 30 Jun 2020 01:46:43: #2 alternative fragment length(s) may be 155,197,230 bps INFO @ Tue, 30 Jun 2020 01:46:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.10_model.r INFO @ Tue, 30 Jun 2020 01:46:43: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:46:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:46:47: 6000000 INFO @ Tue, 30 Jun 2020 01:46:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:46:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:46:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.05_summits.bed INFO @ Tue, 30 Jun 2020 01:46:48: Done! pass1 - making usageList (572 chroms): 1 millis pass2 - checking and writing primary data (1147 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:46:53: 7000000 INFO @ Tue, 30 Jun 2020 01:46:59: 8000000 INFO @ Tue, 30 Jun 2020 01:47:03: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:47:05: 9000000 INFO @ Tue, 30 Jun 2020 01:47:11: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:47:11: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:47:11: #1 total tags in treatment: 9906305 INFO @ Tue, 30 Jun 2020 01:47:11: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:47:11: #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 01:47:11: #1 tags after filtering in treatment: 9906292 INFO @ Tue, 30 Jun 2020 01:47:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:47:11: #1 finished! INFO @ Tue, 30 Jun 2020 01:47:11: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:47:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:47:12: #2 number of paired peaks: 230 WARNING @ Tue, 30 Jun 2020 01:47:12: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Tue, 30 Jun 2020 01:47:12: start model_add_line... INFO @ Tue, 30 Jun 2020 01:47:12: start X-correlation... INFO @ Tue, 30 Jun 2020 01:47:12: end of X-cor INFO @ Tue, 30 Jun 2020 01:47:12: #2 finished! INFO @ Tue, 30 Jun 2020 01:47:12: #2 predicted fragment length is 197 bps INFO @ Tue, 30 Jun 2020 01:47:12: #2 alternative fragment length(s) may be 155,197,230 bps INFO @ Tue, 30 Jun 2020 01:47:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.20_model.r INFO @ Tue, 30 Jun 2020 01:47:12: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:47:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:47:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:47:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:47:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.10_summits.bed INFO @ Tue, 30 Jun 2020 01:47:14: Done! pass1 - making usageList (496 chroms): 1 millis pass2 - checking and writing primary data (865 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:47:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:47:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:47:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:47:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX033319/SRX033319.20_summits.bed INFO @ Tue, 30 Jun 2020 01:47:43: Done! pass1 - making usageList (364 chroms): 1 millis pass2 - checking and writing primary data (576 records, 4 fields): 20 millis CompletedMACS2peakCalling