Job ID = 6529454 SRX = SRX287591 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: 00:07:43 23008083 reads; of these: 23008083 (100.00%) were unpaired; of these: 1567476 (6.81%) aligned 0 times 14607472 (63.49%) aligned exactly 1 time 6833135 (29.70%) aligned >1 times 93.19% overall alignment rate Time searching: 00:07:43 Overall time: 00:07:43 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 12 files... [bam_rmdupse_core] 4170637 / 21440607 = 0.1945 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 02:18:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.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 02:18:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:18:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:18:42: 1000000 INFO @ Tue, 30 Jun 2020 02:18:49: 2000000 INFO @ Tue, 30 Jun 2020 02:18:55: 3000000 INFO @ Tue, 30 Jun 2020 02:19:01: 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 02:19:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.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 02:19:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:19:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:19:08: 5000000 INFO @ Tue, 30 Jun 2020 02:19:12: 1000000 INFO @ Tue, 30 Jun 2020 02:19:15: 6000000 INFO @ Tue, 30 Jun 2020 02:19:19: 2000000 INFO @ Tue, 30 Jun 2020 02:19:22: 7000000 INFO @ Tue, 30 Jun 2020 02:19:26: 3000000 INFO @ Tue, 30 Jun 2020 02:19:29: 8000000 INFO @ Tue, 30 Jun 2020 02:19:33: 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 02:19:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.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 02:19:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:19:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:19:36: 9000000 INFO @ Tue, 30 Jun 2020 02:19:40: 5000000 INFO @ Tue, 30 Jun 2020 02:19:43: 10000000 INFO @ Tue, 30 Jun 2020 02:19:43: 1000000 INFO @ Tue, 30 Jun 2020 02:19:48: 6000000 INFO @ Tue, 30 Jun 2020 02:19:50: 11000000 INFO @ Tue, 30 Jun 2020 02:19:50: 2000000 INFO @ Tue, 30 Jun 2020 02:19:55: 7000000 INFO @ Tue, 30 Jun 2020 02:19:57: 12000000 INFO @ Tue, 30 Jun 2020 02:19:57: 3000000 INFO @ Tue, 30 Jun 2020 02:20:03: 8000000 INFO @ Tue, 30 Jun 2020 02:20:04: 13000000 INFO @ Tue, 30 Jun 2020 02:20:05: 4000000 INFO @ Tue, 30 Jun 2020 02:20:10: 9000000 INFO @ Tue, 30 Jun 2020 02:20:11: 14000000 INFO @ Tue, 30 Jun 2020 02:20:13: 5000000 INFO @ Tue, 30 Jun 2020 02:20:18: 10000000 INFO @ Tue, 30 Jun 2020 02:20:19: 15000000 INFO @ Tue, 30 Jun 2020 02:20:20: 6000000 INFO @ Tue, 30 Jun 2020 02:20:26: 11000000 INFO @ Tue, 30 Jun 2020 02:20:26: 16000000 INFO @ Tue, 30 Jun 2020 02:20:28: 7000000 INFO @ Tue, 30 Jun 2020 02:20:33: 17000000 INFO @ Tue, 30 Jun 2020 02:20:34: 12000000 INFO @ Tue, 30 Jun 2020 02:20:35: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:20:35: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:20:35: #1 total tags in treatment: 17269970 INFO @ Tue, 30 Jun 2020 02:20:35: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:20:35: #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 02:20:36: 8000000 INFO @ Tue, 30 Jun 2020 02:20:36: #1 tags after filtering in treatment: 17269970 INFO @ Tue, 30 Jun 2020 02:20:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:20:36: #1 finished! INFO @ Tue, 30 Jun 2020 02:20:36: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:20:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:20:37: #2 number of paired peaks: 660 WARNING @ Tue, 30 Jun 2020 02:20:37: Fewer paired peaks (660) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 660 pairs to build model! INFO @ Tue, 30 Jun 2020 02:20:37: start model_add_line... INFO @ Tue, 30 Jun 2020 02:20:37: start X-correlation... INFO @ Tue, 30 Jun 2020 02:20:37: end of X-cor INFO @ Tue, 30 Jun 2020 02:20:37: #2 finished! INFO @ Tue, 30 Jun 2020 02:20:37: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:20:37: #2 alternative fragment length(s) may be 2,18 bps INFO @ Tue, 30 Jun 2020 02:20:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.05_model.r WARNING @ Tue, 30 Jun 2020 02:20:37: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:20:37: #2 You may need to consider one of the other alternative d(s): 2,18 WARNING @ Tue, 30 Jun 2020 02:20:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:20:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:20:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:20:41: 13000000 INFO @ Tue, 30 Jun 2020 02:20:43: 9000000 INFO @ Tue, 30 Jun 2020 02:20:49: 14000000 INFO @ Tue, 30 Jun 2020 02:20:50: 10000000 INFO @ Tue, 30 Jun 2020 02:20:56: 15000000 INFO @ Tue, 30 Jun 2020 02:20:57: 11000000 INFO @ Tue, 30 Jun 2020 02:21:03: 16000000 INFO @ Tue, 30 Jun 2020 02:21:04: 12000000 INFO @ Tue, 30 Jun 2020 02:21:11: 17000000 INFO @ Tue, 30 Jun 2020 02:21:12: 13000000 INFO @ Tue, 30 Jun 2020 02:21:12: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:21:13: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:21:13: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:21:13: #1 total tags in treatment: 17269970 INFO @ Tue, 30 Jun 2020 02:21:13: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:21:13: #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 02:21:13: #1 tags after filtering in treatment: 17269970 INFO @ Tue, 30 Jun 2020 02:21:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:21:13: #1 finished! INFO @ Tue, 30 Jun 2020 02:21:13: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:21:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:21:15: #2 number of paired peaks: 660 WARNING @ Tue, 30 Jun 2020 02:21:15: Fewer paired peaks (660) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 660 pairs to build model! INFO @ Tue, 30 Jun 2020 02:21:15: start model_add_line... INFO @ Tue, 30 Jun 2020 02:21:15: start X-correlation... INFO @ Tue, 30 Jun 2020 02:21:15: end of X-cor INFO @ Tue, 30 Jun 2020 02:21:15: #2 finished! INFO @ Tue, 30 Jun 2020 02:21:15: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:21:15: #2 alternative fragment length(s) may be 2,18 bps INFO @ Tue, 30 Jun 2020 02:21:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.10_model.r WARNING @ Tue, 30 Jun 2020 02:21:15: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:21:15: #2 You may need to consider one of the other alternative d(s): 2,18 WARNING @ Tue, 30 Jun 2020 02:21:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:21:15: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:21:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:21:19: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:21:25: 15000000 INFO @ Tue, 30 Jun 2020 02:21:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:21:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:21:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.05_summits.bed INFO @ Tue, 30 Jun 2020 02:21:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:21:32: 16000000 INFO @ Tue, 30 Jun 2020 02:21:39: 17000000 INFO @ Tue, 30 Jun 2020 02:21:41: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:21:41: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:21:41: #1 total tags in treatment: 17269970 INFO @ Tue, 30 Jun 2020 02:21:41: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:21:41: #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 02:21:41: #1 tags after filtering in treatment: 17269970 INFO @ Tue, 30 Jun 2020 02:21:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:21:41: #1 finished! INFO @ Tue, 30 Jun 2020 02:21:41: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:21:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:21:43: #2 number of paired peaks: 660 WARNING @ Tue, 30 Jun 2020 02:21:43: Fewer paired peaks (660) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 660 pairs to build model! INFO @ Tue, 30 Jun 2020 02:21:43: start model_add_line... INFO @ Tue, 30 Jun 2020 02:21:43: start X-correlation... INFO @ Tue, 30 Jun 2020 02:21:43: end of X-cor INFO @ Tue, 30 Jun 2020 02:21:43: #2 finished! INFO @ Tue, 30 Jun 2020 02:21:43: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:21:43: #2 alternative fragment length(s) may be 2,18 bps INFO @ Tue, 30 Jun 2020 02:21:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.20_model.r WARNING @ Tue, 30 Jun 2020 02:21:43: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:21:43: #2 You may need to consider one of the other alternative d(s): 2,18 WARNING @ Tue, 30 Jun 2020 02:21:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:21:43: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:21:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:21:49: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:22:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:22:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:22:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.10_summits.bed INFO @ Tue, 30 Jun 2020 02:22:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:22:17: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:22:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:22:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:22:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287591/SRX287591.20_summits.bed INFO @ Tue, 30 Jun 2020 02:22:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling