Job ID = 6529194 SRX = SRX040610 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: 00:03:15 15624373 reads; of these: 15624373 (100.00%) were unpaired; of these: 758279 (4.85%) aligned 0 times 11857416 (75.89%) aligned exactly 1 time 3008678 (19.26%) aligned >1 times 95.15% overall alignment rate Time searching: 00:03:15 Overall time: 00:03:15 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] 3048956 / 14866094 = 0.2051 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 02:21:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.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 02:21:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:21:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:22:04: 1000000 INFO @ Tue, 30 Jun 2020 02:22:09: 2000000 INFO @ Tue, 30 Jun 2020 02:22:15: 3000000 INFO @ Tue, 30 Jun 2020 02:22:20: 4000000 INFO @ Tue, 30 Jun 2020 02:22:26: 5000000 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 02:22:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.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 02:22:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:22:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:22:32: 6000000 INFO @ Tue, 30 Jun 2020 02:22:35: 1000000 INFO @ Tue, 30 Jun 2020 02:22:38: 7000000 INFO @ Tue, 30 Jun 2020 02:22:41: 2000000 INFO @ Tue, 30 Jun 2020 02:22:44: 8000000 INFO @ Tue, 30 Jun 2020 02:22:47: 3000000 INFO @ Tue, 30 Jun 2020 02:22:50: 9000000 INFO @ Tue, 30 Jun 2020 02:22:54: 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 02:22:57: 10000000 INFO @ Tue, 30 Jun 2020 02:22:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.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 02:22:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:22:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:23:00: 5000000 INFO @ Tue, 30 Jun 2020 02:23:03: 11000000 INFO @ Tue, 30 Jun 2020 02:23:05: 1000000 INFO @ Tue, 30 Jun 2020 02:23:06: 6000000 INFO @ Tue, 30 Jun 2020 02:23:09: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 02:23:09: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 02:23:09: #1 total tags in treatment: 11817138 INFO @ Tue, 30 Jun 2020 02:23:09: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:23:09: #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 02:23:09: #1 tags after filtering in treatment: 11817126 INFO @ Tue, 30 Jun 2020 02:23:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:23:09: #1 finished! INFO @ Tue, 30 Jun 2020 02:23:09: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:23:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:23:10: #2 number of paired peaks: 515 WARNING @ Tue, 30 Jun 2020 02:23:10: 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, 30 Jun 2020 02:23:10: start model_add_line... INFO @ Tue, 30 Jun 2020 02:23:10: start X-correlation... INFO @ Tue, 30 Jun 2020 02:23:10: end of X-cor INFO @ Tue, 30 Jun 2020 02:23:10: #2 finished! INFO @ Tue, 30 Jun 2020 02:23:10: #2 predicted fragment length is 113 bps INFO @ Tue, 30 Jun 2020 02:23:10: #2 alternative fragment length(s) may be 113 bps INFO @ Tue, 30 Jun 2020 02:23:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.05_model.r INFO @ Tue, 30 Jun 2020 02:23:10: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:23:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:23:11: 2000000 INFO @ Tue, 30 Jun 2020 02:23:13: 7000000 INFO @ Tue, 30 Jun 2020 02:23:18: 3000000 INFO @ Tue, 30 Jun 2020 02:23:19: 8000000 INFO @ Tue, 30 Jun 2020 02:23:24: 4000000 INFO @ Tue, 30 Jun 2020 02:23:25: 9000000 INFO @ Tue, 30 Jun 2020 02:23:30: 5000000 INFO @ Tue, 30 Jun 2020 02:23:32: 10000000 INFO @ Tue, 30 Jun 2020 02:23:33: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:23:37: 6000000 INFO @ Tue, 30 Jun 2020 02:23:38: 11000000 INFO @ Tue, 30 Jun 2020 02:23:43: 7000000 INFO @ Tue, 30 Jun 2020 02:23:43: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 02:23:43: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 02:23:43: #1 total tags in treatment: 11817138 INFO @ Tue, 30 Jun 2020 02:23:43: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:23:43: #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 02:23:44: #1 tags after filtering in treatment: 11817126 INFO @ Tue, 30 Jun 2020 02:23:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:23:44: #1 finished! INFO @ Tue, 30 Jun 2020 02:23:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:23:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:23:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:23:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:23:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.05_summits.bed INFO @ Tue, 30 Jun 2020 02:23:45: Done! INFO @ Tue, 30 Jun 2020 02:23:45: #2 number of paired peaks: 515 WARNING @ Tue, 30 Jun 2020 02:23:45: 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, 30 Jun 2020 02:23:45: start model_add_line... INFO @ Tue, 30 Jun 2020 02:23:45: start X-correlation... INFO @ Tue, 30 Jun 2020 02:23:45: end of X-cor INFO @ Tue, 30 Jun 2020 02:23:45: #2 finished! INFO @ Tue, 30 Jun 2020 02:23:45: #2 predicted fragment length is 113 bps INFO @ Tue, 30 Jun 2020 02:23:45: #2 alternative fragment length(s) may be 113 bps INFO @ Tue, 30 Jun 2020 02:23:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.10_model.r INFO @ Tue, 30 Jun 2020 02:23:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:23:45: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (591 chroms): 2 millis pass2 - checking and writing primary data (5187 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:23:49: 8000000 INFO @ Tue, 30 Jun 2020 02:23:55: 9000000 INFO @ Tue, 30 Jun 2020 02:24:01: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:24:06: 11000000 INFO @ Tue, 30 Jun 2020 02:24:09: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:24:11: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 02:24:11: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 02:24:11: #1 total tags in treatment: 11817138 INFO @ Tue, 30 Jun 2020 02:24:11: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:24:11: #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 02:24:12: #1 tags after filtering in treatment: 11817126 INFO @ Tue, 30 Jun 2020 02:24:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:24:12: #1 finished! INFO @ Tue, 30 Jun 2020 02:24:12: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:24:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:24:13: #2 number of paired peaks: 515 WARNING @ Tue, 30 Jun 2020 02:24:13: 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, 30 Jun 2020 02:24:13: start model_add_line... INFO @ Tue, 30 Jun 2020 02:24:13: start X-correlation... INFO @ Tue, 30 Jun 2020 02:24:13: end of X-cor INFO @ Tue, 30 Jun 2020 02:24:13: #2 finished! INFO @ Tue, 30 Jun 2020 02:24:13: #2 predicted fragment length is 113 bps INFO @ Tue, 30 Jun 2020 02:24:13: #2 alternative fragment length(s) may be 113 bps INFO @ Tue, 30 Jun 2020 02:24:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.20_model.r INFO @ Tue, 30 Jun 2020 02:24:13: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:24:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:24:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:24:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:24:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.10_summits.bed INFO @ Tue, 30 Jun 2020 02:24:20: Done! pass1 - making usageList (525 chroms): 1 millis pass2 - checking and writing primary data (2168 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:24:37: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:24:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:24:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:24:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX040610/SRX040610.20_summits.bed INFO @ Tue, 30 Jun 2020 02:24:49: Done! pass1 - making usageList (418 chroms): 1 millis pass2 - checking and writing primary data (904 records, 4 fields): 12 millis CompletedMACS2peakCalling