Job ID = 6529413 SRX = SRX2564149 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: 00:11:28 43930448 reads; of these: 43930448 (100.00%) were unpaired; of these: 19548631 (44.50%) aligned 0 times 18597844 (42.33%) aligned exactly 1 time 5783973 (13.17%) aligned >1 times 55.50% overall alignment rate Time searching: 00:11:28 Overall time: 00:11:28 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] 6112149 / 24381817 = 0.2507 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 02:14:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.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 02:14:36: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:14:36: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:14:45: 1000000 INFO @ Tue, 30 Jun 2020 02:14:53: 2000000 INFO @ Tue, 30 Jun 2020 02:15:02: 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 02:15:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.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 02:15:06: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:15:06: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:15:11: 4000000 INFO @ Tue, 30 Jun 2020 02:15:15: 1000000 INFO @ Tue, 30 Jun 2020 02:15:20: 5000000 INFO @ Tue, 30 Jun 2020 02:15:23: 2000000 INFO @ Tue, 30 Jun 2020 02:15:30: 6000000 INFO @ Tue, 30 Jun 2020 02:15:32: 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 02:15:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.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 02:15:36: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:15:36: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:15:40: 7000000 INFO @ Tue, 30 Jun 2020 02:15:41: 4000000 INFO @ Tue, 30 Jun 2020 02:15:47: 1000000 INFO @ Tue, 30 Jun 2020 02:15:50: 5000000 INFO @ Tue, 30 Jun 2020 02:15:50: 8000000 INFO @ Tue, 30 Jun 2020 02:15:57: 2000000 INFO @ Tue, 30 Jun 2020 02:15:58: 6000000 INFO @ Tue, 30 Jun 2020 02:16:01: 9000000 INFO @ Tue, 30 Jun 2020 02:16:07: 7000000 INFO @ Tue, 30 Jun 2020 02:16:07: 3000000 INFO @ Tue, 30 Jun 2020 02:16:11: 10000000 INFO @ Tue, 30 Jun 2020 02:16:16: 8000000 INFO @ Tue, 30 Jun 2020 02:16:17: 4000000 INFO @ Tue, 30 Jun 2020 02:16:21: 11000000 INFO @ Tue, 30 Jun 2020 02:16:25: 9000000 INFO @ Tue, 30 Jun 2020 02:16:28: 5000000 INFO @ Tue, 30 Jun 2020 02:16:31: 12000000 INFO @ Tue, 30 Jun 2020 02:16:34: 10000000 INFO @ Tue, 30 Jun 2020 02:16:38: 6000000 INFO @ Tue, 30 Jun 2020 02:16:41: 13000000 INFO @ Tue, 30 Jun 2020 02:16:43: 11000000 INFO @ Tue, 30 Jun 2020 02:16:48: 7000000 INFO @ Tue, 30 Jun 2020 02:16:51: 14000000 INFO @ Tue, 30 Jun 2020 02:16:52: 12000000 INFO @ Tue, 30 Jun 2020 02:16:58: 8000000 INFO @ Tue, 30 Jun 2020 02:17:00: 13000000 INFO @ Tue, 30 Jun 2020 02:17:02: 15000000 INFO @ Tue, 30 Jun 2020 02:17:08: 9000000 INFO @ Tue, 30 Jun 2020 02:17:09: 14000000 INFO @ Tue, 30 Jun 2020 02:17:12: 16000000 INFO @ Tue, 30 Jun 2020 02:17:18: 10000000 INFO @ Tue, 30 Jun 2020 02:17:19: 15000000 INFO @ Tue, 30 Jun 2020 02:17:22: 17000000 INFO @ Tue, 30 Jun 2020 02:17:27: 16000000 INFO @ Tue, 30 Jun 2020 02:17:28: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:17:32: 18000000 INFO @ Tue, 30 Jun 2020 02:17:35: #1 tag size is determined as 72 bps INFO @ Tue, 30 Jun 2020 02:17:35: #1 tag size = 72 INFO @ Tue, 30 Jun 2020 02:17:35: #1 total tags in treatment: 18269668 INFO @ Tue, 30 Jun 2020 02:17:35: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:17:35: #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 02:17:35: #1 tags after filtering in treatment: 18269668 INFO @ Tue, 30 Jun 2020 02:17:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:17:35: #1 finished! INFO @ Tue, 30 Jun 2020 02:17:35: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:17:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:17:36: 17000000 INFO @ Tue, 30 Jun 2020 02:17:37: #2 number of paired peaks: 587 WARNING @ Tue, 30 Jun 2020 02:17:37: Fewer paired peaks (587) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 587 pairs to build model! INFO @ Tue, 30 Jun 2020 02:17:37: start model_add_line... INFO @ Tue, 30 Jun 2020 02:17:37: start X-correlation... INFO @ Tue, 30 Jun 2020 02:17:37: end of X-cor INFO @ Tue, 30 Jun 2020 02:17:37: #2 finished! INFO @ Tue, 30 Jun 2020 02:17:37: #2 predicted fragment length is 55 bps INFO @ Tue, 30 Jun 2020 02:17:37: #2 alternative fragment length(s) may be 3,55 bps INFO @ Tue, 30 Jun 2020 02:17:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.05_model.r WARNING @ Tue, 30 Jun 2020 02:17:37: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:17:37: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Tue, 30 Jun 2020 02:17:37: #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 02:17:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:17:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:17:38: 12000000 INFO @ Tue, 30 Jun 2020 02:17:45: 18000000 INFO @ Tue, 30 Jun 2020 02:17:47: 13000000 INFO @ Tue, 30 Jun 2020 02:17:48: #1 tag size is determined as 72 bps INFO @ Tue, 30 Jun 2020 02:17:48: #1 tag size = 72 INFO @ Tue, 30 Jun 2020 02:17:48: #1 total tags in treatment: 18269668 INFO @ Tue, 30 Jun 2020 02:17:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:17:48: #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 02:17:48: #1 tags after filtering in treatment: 18269668 INFO @ Tue, 30 Jun 2020 02:17:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:17:48: #1 finished! INFO @ Tue, 30 Jun 2020 02:17:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:17:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:17:49: #2 number of paired peaks: 587 WARNING @ Tue, 30 Jun 2020 02:17:49: Fewer paired peaks (587) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 587 pairs to build model! INFO @ Tue, 30 Jun 2020 02:17:49: start model_add_line... INFO @ Tue, 30 Jun 2020 02:17:50: start X-correlation... INFO @ Tue, 30 Jun 2020 02:17:50: end of X-cor INFO @ Tue, 30 Jun 2020 02:17:50: #2 finished! INFO @ Tue, 30 Jun 2020 02:17:50: #2 predicted fragment length is 55 bps INFO @ Tue, 30 Jun 2020 02:17:50: #2 alternative fragment length(s) may be 3,55 bps INFO @ Tue, 30 Jun 2020 02:17:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.10_model.r WARNING @ Tue, 30 Jun 2020 02:17:50: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:17:50: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Tue, 30 Jun 2020 02:17:50: #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 02:17:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:17:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:17:56: 14000000 INFO @ Tue, 30 Jun 2020 02:18:05: 15000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:18:12: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:18:14: 16000000 INFO @ Tue, 30 Jun 2020 02:18:23: 17000000 INFO @ Tue, 30 Jun 2020 02:18:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:18:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:18:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:18:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.05_summits.bed INFO @ Tue, 30 Jun 2020 02:18:30: Done! pass1 - making usageList (647 chroms): 1 millis pass2 - checking and writing primary data (3278 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:18:32: 18000000 INFO @ Tue, 30 Jun 2020 02:18:34: #1 tag size is determined as 72 bps INFO @ Tue, 30 Jun 2020 02:18:34: #1 tag size = 72 INFO @ Tue, 30 Jun 2020 02:18:34: #1 total tags in treatment: 18269668 INFO @ Tue, 30 Jun 2020 02:18:34: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:18:34: #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 02:18:35: #1 tags after filtering in treatment: 18269668 INFO @ Tue, 30 Jun 2020 02:18:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:18:35: #1 finished! INFO @ Tue, 30 Jun 2020 02:18:35: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:18:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:18:36: #2 number of paired peaks: 587 WARNING @ Tue, 30 Jun 2020 02:18:36: Fewer paired peaks (587) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 587 pairs to build model! INFO @ Tue, 30 Jun 2020 02:18:36: start model_add_line... INFO @ Tue, 30 Jun 2020 02:18:36: start X-correlation... INFO @ Tue, 30 Jun 2020 02:18:36: end of X-cor INFO @ Tue, 30 Jun 2020 02:18:36: #2 finished! INFO @ Tue, 30 Jun 2020 02:18:36: #2 predicted fragment length is 55 bps INFO @ Tue, 30 Jun 2020 02:18:36: #2 alternative fragment length(s) may be 3,55 bps INFO @ Tue, 30 Jun 2020 02:18:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.20_model.r WARNING @ Tue, 30 Jun 2020 02:18:36: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:18:36: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Tue, 30 Jun 2020 02:18:36: #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 02:18:36: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:18:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:18:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:18:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:18:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.10_summits.bed INFO @ Tue, 30 Jun 2020 02:18:42: Done! pass1 - making usageList (548 chroms): 2 millis pass2 - checking and writing primary data (2096 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:19:13: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:19:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:19:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:19:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564149/SRX2564149.20_summits.bed INFO @ Tue, 30 Jun 2020 02:19:32: Done! pass1 - making usageList (447 chroms): 1 millis pass2 - checking and writing primary data (1311 records, 4 fields): 14 millis CompletedMACS2peakCalling