Job ID = 6529178 SRX = SRX032110 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:55 16900509 reads; of these: 16900509 (100.00%) were unpaired; of these: 617143 (3.65%) aligned 0 times 12732030 (75.34%) aligned exactly 1 time 3551336 (21.01%) aligned >1 times 96.35% overall alignment rate Time searching: 00:03:56 Overall time: 00:03:56 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] 3401567 / 16283366 = 0.2089 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 01:28:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.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 01:28:33: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:28:33: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:28:38: 1000000 INFO @ Tue, 30 Jun 2020 01:28:44: 2000000 INFO @ Tue, 30 Jun 2020 01:28:50: 3000000 INFO @ Tue, 30 Jun 2020 01:28:55: 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 01:29:01: 5000000 INFO @ Tue, 30 Jun 2020 01:29:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.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 01:29:03: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:29:03: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:29:07: 6000000 INFO @ Tue, 30 Jun 2020 01:29:09: 1000000 INFO @ Tue, 30 Jun 2020 01:29:13: 7000000 INFO @ Tue, 30 Jun 2020 01:29:14: 2000000 INFO @ Tue, 30 Jun 2020 01:29:18: 8000000 INFO @ Tue, 30 Jun 2020 01:29:20: 3000000 INFO @ Tue, 30 Jun 2020 01:29:24: 9000000 INFO @ Tue, 30 Jun 2020 01:29:27: 4000000 INFO @ Tue, 30 Jun 2020 01:29:30: 10000000 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 01:29:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.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 01:29:33: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:29:33: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:29:33: 5000000 INFO @ Tue, 30 Jun 2020 01:29:37: 11000000 INFO @ Tue, 30 Jun 2020 01:29:39: 1000000 INFO @ Tue, 30 Jun 2020 01:29:39: 6000000 INFO @ Tue, 30 Jun 2020 01:29:43: 12000000 INFO @ Tue, 30 Jun 2020 01:29:45: 2000000 INFO @ Tue, 30 Jun 2020 01:29:45: 7000000 INFO @ Tue, 30 Jun 2020 01:29:49: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:29:49: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:29:49: #1 total tags in treatment: 12881799 INFO @ Tue, 30 Jun 2020 01:29:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:29:49: #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 01:29:49: #1 tags after filtering in treatment: 12881788 INFO @ Tue, 30 Jun 2020 01:29:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:29:49: #1 finished! INFO @ Tue, 30 Jun 2020 01:29:49: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:29:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:29:50: #2 number of paired peaks: 253 WARNING @ Tue, 30 Jun 2020 01:29:50: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Tue, 30 Jun 2020 01:29:50: start model_add_line... INFO @ Tue, 30 Jun 2020 01:29:50: start X-correlation... INFO @ Tue, 30 Jun 2020 01:29:50: end of X-cor INFO @ Tue, 30 Jun 2020 01:29:50: #2 finished! INFO @ Tue, 30 Jun 2020 01:29:50: #2 predicted fragment length is 95 bps INFO @ Tue, 30 Jun 2020 01:29:50: #2 alternative fragment length(s) may be 4,40,95,142 bps INFO @ Tue, 30 Jun 2020 01:29:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.05_model.r INFO @ Tue, 30 Jun 2020 01:29:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:29:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:29:51: 3000000 INFO @ Tue, 30 Jun 2020 01:29:52: 8000000 INFO @ Tue, 30 Jun 2020 01:29:58: 4000000 INFO @ Tue, 30 Jun 2020 01:29:58: 9000000 INFO @ Tue, 30 Jun 2020 01:30:04: 5000000 INFO @ Tue, 30 Jun 2020 01:30:04: 10000000 INFO @ Tue, 30 Jun 2020 01:30:10: 6000000 INFO @ Tue, 30 Jun 2020 01:30:11: 11000000 INFO @ Tue, 30 Jun 2020 01:30:16: 7000000 INFO @ Tue, 30 Jun 2020 01:30:18: 12000000 INFO @ Tue, 30 Jun 2020 01:30:19: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:30:22: 8000000 INFO @ Tue, 30 Jun 2020 01:30:23: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:30:23: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:30:23: #1 total tags in treatment: 12881799 INFO @ Tue, 30 Jun 2020 01:30:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:30:23: #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 01:30:24: #1 tags after filtering in treatment: 12881788 INFO @ Tue, 30 Jun 2020 01:30:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:30:24: #1 finished! INFO @ Tue, 30 Jun 2020 01:30:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:30:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:30:25: #2 number of paired peaks: 253 WARNING @ Tue, 30 Jun 2020 01:30:25: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Tue, 30 Jun 2020 01:30:25: start model_add_line... INFO @ Tue, 30 Jun 2020 01:30:25: start X-correlation... INFO @ Tue, 30 Jun 2020 01:30:25: end of X-cor INFO @ Tue, 30 Jun 2020 01:30:25: #2 finished! INFO @ Tue, 30 Jun 2020 01:30:25: #2 predicted fragment length is 95 bps INFO @ Tue, 30 Jun 2020 01:30:25: #2 alternative fragment length(s) may be 4,40,95,142 bps INFO @ Tue, 30 Jun 2020 01:30:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.10_model.r INFO @ Tue, 30 Jun 2020 01:30:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:30:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:30:29: 9000000 INFO @ Tue, 30 Jun 2020 01:30:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:30:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:30:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.05_summits.bed INFO @ Tue, 30 Jun 2020 01:30:33: Done! pass1 - making usageList (558 chroms): 1 millis pass2 - checking and writing primary data (1522 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:30:34: 10000000 INFO @ Tue, 30 Jun 2020 01:30:41: 11000000 INFO @ Tue, 30 Jun 2020 01:30:47: 12000000 INFO @ Tue, 30 Jun 2020 01:30:52: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:30:52: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:30:52: #1 total tags in treatment: 12881799 INFO @ Tue, 30 Jun 2020 01:30:52: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:30:52: #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 01:30:53: #1 tags after filtering in treatment: 12881788 INFO @ Tue, 30 Jun 2020 01:30:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:30:53: #1 finished! INFO @ Tue, 30 Jun 2020 01:30:53: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:30:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:30:53: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:30:54: #2 number of paired peaks: 253 WARNING @ Tue, 30 Jun 2020 01:30:54: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Tue, 30 Jun 2020 01:30:54: start model_add_line... INFO @ Tue, 30 Jun 2020 01:30:54: start X-correlation... INFO @ Tue, 30 Jun 2020 01:30:54: end of X-cor INFO @ Tue, 30 Jun 2020 01:30:54: #2 finished! INFO @ Tue, 30 Jun 2020 01:30:54: #2 predicted fragment length is 95 bps INFO @ Tue, 30 Jun 2020 01:30:54: #2 alternative fragment length(s) may be 4,40,95,142 bps INFO @ Tue, 30 Jun 2020 01:30:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.20_model.r INFO @ Tue, 30 Jun 2020 01:30:54: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:30:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:31:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:31:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:31:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.10_summits.bed INFO @ Tue, 30 Jun 2020 01:31:08: Done! pass1 - making usageList (458 chroms): 1 millis pass2 - checking and writing primary data (1282 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:31:22: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:31:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:31:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:31:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX032110/SRX032110.20_summits.bed INFO @ Tue, 30 Jun 2020 01:31:37: Done! pass1 - making usageList (295 chroms): 1 millis pass2 - checking and writing primary data (601 records, 4 fields): 10 millis CompletedMACS2peakCalling