Job ID = 6529851 SRX = SRX5287825 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:08 26790115 reads; of these: 26790115 (100.00%) were unpaired; of these: 947559 (3.54%) aligned 0 times 19422429 (72.50%) aligned exactly 1 time 6420127 (23.96%) aligned >1 times 96.46% overall alignment rate Time searching: 00:11:09 Overall time: 00:11:09 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] 3479940 / 25842556 = 0.1347 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 03:13:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.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 03:13:46: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:13:46: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:13:53: 1000000 INFO @ Tue, 30 Jun 2020 03:14:00: 2000000 INFO @ Tue, 30 Jun 2020 03:14:07: 3000000 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 03:14:14: 4000000 INFO @ Tue, 30 Jun 2020 03:14:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.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 03:14:16: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:14:16: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:14:21: 5000000 INFO @ Tue, 30 Jun 2020 03:14:24: 1000000 INFO @ Tue, 30 Jun 2020 03:14:29: 6000000 INFO @ Tue, 30 Jun 2020 03:14:31: 2000000 INFO @ Tue, 30 Jun 2020 03:14:36: 7000000 INFO @ Tue, 30 Jun 2020 03:14:39: 3000000 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 03:14:44: 8000000 INFO @ Tue, 30 Jun 2020 03:14:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.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 03:14:46: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:14:46: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:14:46: 4000000 INFO @ Tue, 30 Jun 2020 03:14:52: 9000000 INFO @ Tue, 30 Jun 2020 03:14:53: 1000000 INFO @ Tue, 30 Jun 2020 03:14:54: 5000000 INFO @ Tue, 30 Jun 2020 03:14:59: 10000000 INFO @ Tue, 30 Jun 2020 03:14:59: 2000000 INFO @ Tue, 30 Jun 2020 03:15:01: 6000000 INFO @ Tue, 30 Jun 2020 03:15:06: 3000000 INFO @ Tue, 30 Jun 2020 03:15:07: 11000000 INFO @ Tue, 30 Jun 2020 03:15:09: 7000000 INFO @ Tue, 30 Jun 2020 03:15:12: 4000000 INFO @ Tue, 30 Jun 2020 03:15:15: 12000000 INFO @ Tue, 30 Jun 2020 03:15:17: 8000000 INFO @ Tue, 30 Jun 2020 03:15:19: 5000000 INFO @ Tue, 30 Jun 2020 03:15:23: 13000000 INFO @ Tue, 30 Jun 2020 03:15:24: 9000000 INFO @ Tue, 30 Jun 2020 03:15:25: 6000000 INFO @ Tue, 30 Jun 2020 03:15:30: 14000000 INFO @ Tue, 30 Jun 2020 03:15:32: 7000000 INFO @ Tue, 30 Jun 2020 03:15:32: 10000000 INFO @ Tue, 30 Jun 2020 03:15:38: 15000000 INFO @ Tue, 30 Jun 2020 03:15:38: 8000000 INFO @ Tue, 30 Jun 2020 03:15:40: 11000000 INFO @ Tue, 30 Jun 2020 03:15:45: 9000000 INFO @ Tue, 30 Jun 2020 03:15:45: 16000000 INFO @ Tue, 30 Jun 2020 03:15:47: 12000000 INFO @ Tue, 30 Jun 2020 03:15:51: 10000000 INFO @ Tue, 30 Jun 2020 03:15:53: 17000000 INFO @ Tue, 30 Jun 2020 03:15:55: 13000000 INFO @ Tue, 30 Jun 2020 03:15:58: 11000000 INFO @ Tue, 30 Jun 2020 03:16:01: 18000000 INFO @ Tue, 30 Jun 2020 03:16:02: 14000000 INFO @ Tue, 30 Jun 2020 03:16:05: 12000000 INFO @ Tue, 30 Jun 2020 03:16:09: 19000000 INFO @ Tue, 30 Jun 2020 03:16:10: 15000000 INFO @ Tue, 30 Jun 2020 03:16:12: 13000000 INFO @ Tue, 30 Jun 2020 03:16:16: 20000000 INFO @ Tue, 30 Jun 2020 03:16:17: 16000000 INFO @ Tue, 30 Jun 2020 03:16:18: 14000000 INFO @ Tue, 30 Jun 2020 03:16:24: 21000000 INFO @ Tue, 30 Jun 2020 03:16:25: 15000000 INFO @ Tue, 30 Jun 2020 03:16:25: 17000000 INFO @ Tue, 30 Jun 2020 03:16:31: 22000000 INFO @ Tue, 30 Jun 2020 03:16:32: 16000000 INFO @ Tue, 30 Jun 2020 03:16:33: 18000000 INFO @ Tue, 30 Jun 2020 03:16:35: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:16:35: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:16:35: #1 total tags in treatment: 22362616 INFO @ Tue, 30 Jun 2020 03:16:35: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:16:35: #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 03:16:35: #1 tags after filtering in treatment: 22362614 INFO @ Tue, 30 Jun 2020 03:16:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:16:35: #1 finished! INFO @ Tue, 30 Jun 2020 03:16:35: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:16:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:16:37: #2 number of paired peaks: 426 WARNING @ Tue, 30 Jun 2020 03:16:37: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Tue, 30 Jun 2020 03:16:37: start model_add_line... INFO @ Tue, 30 Jun 2020 03:16:37: start X-correlation... INFO @ Tue, 30 Jun 2020 03:16:37: end of X-cor INFO @ Tue, 30 Jun 2020 03:16:37: #2 finished! INFO @ Tue, 30 Jun 2020 03:16:37: #2 predicted fragment length is 61 bps INFO @ Tue, 30 Jun 2020 03:16:37: #2 alternative fragment length(s) may be 3,61 bps INFO @ Tue, 30 Jun 2020 03:16:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.05_model.r WARNING @ Tue, 30 Jun 2020 03:16:37: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:16:37: #2 You may need to consider one of the other alternative d(s): 3,61 WARNING @ Tue, 30 Jun 2020 03:16:37: #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 03:16:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:16:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:16:39: 17000000 INFO @ Tue, 30 Jun 2020 03:16:40: 19000000 INFO @ Tue, 30 Jun 2020 03:16:47: 20000000 INFO @ Tue, 30 Jun 2020 03:16:48: 18000000 INFO @ Tue, 30 Jun 2020 03:16:54: 21000000 INFO @ Tue, 30 Jun 2020 03:16:55: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:17:02: 22000000 INFO @ Tue, 30 Jun 2020 03:17:02: 20000000 INFO @ Tue, 30 Jun 2020 03:17:05: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:17:05: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:17:05: #1 total tags in treatment: 22362616 INFO @ Tue, 30 Jun 2020 03:17:05: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:17:05: #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 03:17:06: #1 tags after filtering in treatment: 22362614 INFO @ Tue, 30 Jun 2020 03:17:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:17:06: #1 finished! INFO @ Tue, 30 Jun 2020 03:17:06: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:17:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:17:08: #2 number of paired peaks: 426 WARNING @ Tue, 30 Jun 2020 03:17:08: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Tue, 30 Jun 2020 03:17:08: start model_add_line... INFO @ Tue, 30 Jun 2020 03:17:08: start X-correlation... INFO @ Tue, 30 Jun 2020 03:17:08: end of X-cor INFO @ Tue, 30 Jun 2020 03:17:08: #2 finished! INFO @ Tue, 30 Jun 2020 03:17:08: #2 predicted fragment length is 61 bps INFO @ Tue, 30 Jun 2020 03:17:08: #2 alternative fragment length(s) may be 3,61 bps INFO @ Tue, 30 Jun 2020 03:17:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.10_model.r WARNING @ Tue, 30 Jun 2020 03:17:08: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:17:08: #2 You may need to consider one of the other alternative d(s): 3,61 WARNING @ Tue, 30 Jun 2020 03:17:08: #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 03:17:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:17:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:17:09: 21000000 INFO @ Tue, 30 Jun 2020 03:17:15: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:17:16: 22000000 INFO @ Tue, 30 Jun 2020 03:17:19: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:17:19: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:17:19: #1 total tags in treatment: 22362616 INFO @ Tue, 30 Jun 2020 03:17:19: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:17:19: #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 03:17:20: #1 tags after filtering in treatment: 22362614 INFO @ Tue, 30 Jun 2020 03:17:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:17:20: #1 finished! INFO @ Tue, 30 Jun 2020 03:17:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:17:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:17:21: #2 number of paired peaks: 426 WARNING @ Tue, 30 Jun 2020 03:17:22: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Tue, 30 Jun 2020 03:17:22: start model_add_line... INFO @ Tue, 30 Jun 2020 03:17:22: start X-correlation... INFO @ Tue, 30 Jun 2020 03:17:22: end of X-cor INFO @ Tue, 30 Jun 2020 03:17:22: #2 finished! INFO @ Tue, 30 Jun 2020 03:17:22: #2 predicted fragment length is 61 bps INFO @ Tue, 30 Jun 2020 03:17:22: #2 alternative fragment length(s) may be 3,61 bps INFO @ Tue, 30 Jun 2020 03:17:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.20_model.r WARNING @ Tue, 30 Jun 2020 03:17:22: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:17:22: #2 You may need to consider one of the other alternative d(s): 3,61 WARNING @ Tue, 30 Jun 2020 03:17:22: #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 03:17:22: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:17:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:17:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:17:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:17:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.05_summits.bed INFO @ Tue, 30 Jun 2020 03:17:34: Done! pass1 - making usageList (681 chroms): 1 millis pass2 - checking and writing primary data (2393 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:17:45: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:17:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:18:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:18:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:18:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.10_summits.bed INFO @ Tue, 30 Jun 2020 03:18:05: Done! pass1 - making usageList (584 chroms): 1 millis pass2 - checking and writing primary data (1710 records, 4 fields): 33 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:18:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:18:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:18:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287825/SRX5287825.20_summits.bed INFO @ Tue, 30 Jun 2020 03:18:18: Done! pass1 - making usageList (454 chroms): 1 millis pass2 - checking and writing primary data (1259 records, 4 fields): 26 millis CompletedMACS2peakCalling