Job ID = 14171861 SRX = SRX9986165 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: 00:04:57 21062679 reads; of these: 21062679 (100.00%) were unpaired; of these: 1998605 (9.49%) aligned 0 times 16255557 (77.18%) aligned exactly 1 time 2808517 (13.33%) aligned >1 times 90.51% overall alignment rate Time searching: 00:04:57 Overall time: 00:04:57 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_sort_core] merging from 8 files... [bam_rmdupse_core] 5735230 / 19064074 = 0.3008 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 13:20:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.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 @ Sat, 11 Dec 2021 13:20:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:20:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:20:43: 1000000 INFO @ Sat, 11 Dec 2021 13:20:50: 2000000 INFO @ Sat, 11 Dec 2021 13:20:58: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 13:21:05: 4000000 INFO @ Sat, 11 Dec 2021 13:21:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.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 @ Sat, 11 Dec 2021 13:21:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:21:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:21:12: 5000000 INFO @ Sat, 11 Dec 2021 13:21:14: 1000000 INFO @ Sat, 11 Dec 2021 13:21:20: 6000000 INFO @ Sat, 11 Dec 2021 13:21:22: 2000000 INFO @ Sat, 11 Dec 2021 13:21:28: 7000000 INFO @ Sat, 11 Dec 2021 13:21:30: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 13:21:36: 8000000 INFO @ Sat, 11 Dec 2021 13:21:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.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 @ Sat, 11 Dec 2021 13:21:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:21:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:21:38: 4000000 INFO @ Sat, 11 Dec 2021 13:21:44: 1000000 INFO @ Sat, 11 Dec 2021 13:21:44: 9000000 INFO @ Sat, 11 Dec 2021 13:21:46: 5000000 INFO @ Sat, 11 Dec 2021 13:21:51: 2000000 INFO @ Sat, 11 Dec 2021 13:21:52: 10000000 INFO @ Sat, 11 Dec 2021 13:21:54: 6000000 INFO @ Sat, 11 Dec 2021 13:21:58: 3000000 INFO @ Sat, 11 Dec 2021 13:22:00: 11000000 INFO @ Sat, 11 Dec 2021 13:22:02: 7000000 INFO @ Sat, 11 Dec 2021 13:22:05: 4000000 INFO @ Sat, 11 Dec 2021 13:22:08: 12000000 INFO @ Sat, 11 Dec 2021 13:22:10: 8000000 INFO @ Sat, 11 Dec 2021 13:22:12: 5000000 INFO @ Sat, 11 Dec 2021 13:22:16: 13000000 INFO @ Sat, 11 Dec 2021 13:22:18: 9000000 INFO @ Sat, 11 Dec 2021 13:22:19: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:22:19: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:22:19: #1 total tags in treatment: 13328844 INFO @ Sat, 11 Dec 2021 13:22:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:22:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:22:19: 6000000 INFO @ Sat, 11 Dec 2021 13:22:19: #1 tags after filtering in treatment: 13328744 INFO @ Sat, 11 Dec 2021 13:22:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:22:19: #1 finished! INFO @ Sat, 11 Dec 2021 13:22:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:22:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:22:20: #2 number of paired peaks: 159 WARNING @ Sat, 11 Dec 2021 13:22:20: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 11 Dec 2021 13:22:20: start model_add_line... INFO @ Sat, 11 Dec 2021 13:22:20: start X-correlation... INFO @ Sat, 11 Dec 2021 13:22:20: end of X-cor INFO @ Sat, 11 Dec 2021 13:22:20: #2 finished! INFO @ Sat, 11 Dec 2021 13:22:20: #2 predicted fragment length is 149 bps INFO @ Sat, 11 Dec 2021 13:22:20: #2 alternative fragment length(s) may be 89,120,149,174,206 bps INFO @ Sat, 11 Dec 2021 13:22:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.05_model.r INFO @ Sat, 11 Dec 2021 13:22:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:22:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:22:26: 7000000 INFO @ Sat, 11 Dec 2021 13:22:26: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:22:33: 8000000 INFO @ Sat, 11 Dec 2021 13:22:35: 11000000 INFO @ Sat, 11 Dec 2021 13:22:40: 9000000 INFO @ Sat, 11 Dec 2021 13:22:43: 12000000 INFO @ Sat, 11 Dec 2021 13:22:47: 10000000 INFO @ Sat, 11 Dec 2021 13:22:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:22:50: 13000000 INFO @ Sat, 11 Dec 2021 13:22:53: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:22:53: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:22:53: #1 total tags in treatment: 13328844 INFO @ Sat, 11 Dec 2021 13:22:53: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:22:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:22:54: #1 tags after filtering in treatment: 13328744 INFO @ Sat, 11 Dec 2021 13:22:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:22:54: #1 finished! INFO @ Sat, 11 Dec 2021 13:22:54: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:22:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:22:54: 11000000 INFO @ Sat, 11 Dec 2021 13:22:55: #2 number of paired peaks: 159 WARNING @ Sat, 11 Dec 2021 13:22:55: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 11 Dec 2021 13:22:55: start model_add_line... INFO @ Sat, 11 Dec 2021 13:22:55: start X-correlation... INFO @ Sat, 11 Dec 2021 13:22:55: end of X-cor INFO @ Sat, 11 Dec 2021 13:22:55: #2 finished! INFO @ Sat, 11 Dec 2021 13:22:55: #2 predicted fragment length is 149 bps INFO @ Sat, 11 Dec 2021 13:22:55: #2 alternative fragment length(s) may be 89,120,149,174,206 bps INFO @ Sat, 11 Dec 2021 13:22:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.10_model.r INFO @ Sat, 11 Dec 2021 13:22:55: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:22:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:23:00: 12000000 INFO @ Sat, 11 Dec 2021 13:23:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:23:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:23:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.05_summits.bed INFO @ Sat, 11 Dec 2021 13:23:01: Done! pass1 - making usageList (122 chroms): 1 millis pass2 - checking and writing primary data (4555 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:23:05: 13000000 INFO @ Sat, 11 Dec 2021 13:23:08: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:23:08: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:23:08: #1 total tags in treatment: 13328844 INFO @ Sat, 11 Dec 2021 13:23:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:23:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:23:08: #1 tags after filtering in treatment: 13328744 INFO @ Sat, 11 Dec 2021 13:23:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:23:08: #1 finished! INFO @ Sat, 11 Dec 2021 13:23:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:23:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:23:09: #2 number of paired peaks: 159 WARNING @ Sat, 11 Dec 2021 13:23:09: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 11 Dec 2021 13:23:09: start model_add_line... INFO @ Sat, 11 Dec 2021 13:23:09: start X-correlation... INFO @ Sat, 11 Dec 2021 13:23:09: end of X-cor INFO @ Sat, 11 Dec 2021 13:23:09: #2 finished! INFO @ Sat, 11 Dec 2021 13:23:09: #2 predicted fragment length is 149 bps INFO @ Sat, 11 Dec 2021 13:23:09: #2 alternative fragment length(s) may be 89,120,149,174,206 bps INFO @ Sat, 11 Dec 2021 13:23:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.20_model.r INFO @ Sat, 11 Dec 2021 13:23:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:23:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:23:22: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:23:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:23:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:23:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.10_summits.bed INFO @ Sat, 11 Dec 2021 13:23:36: Done! pass1 - making usageList (68 chroms): 1 millis pass2 - checking and writing primary data (1176 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:23:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:23:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:23:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:23:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986165/SRX9986165.20_summits.bed INFO @ Sat, 11 Dec 2021 13:23:50: Done! pass1 - making usageList (30 chroms): 0 millis pass2 - checking and writing primary data (119 records, 4 fields): 3 millis CompletedMACS2peakCalling