Job ID = 6529515 SRX = SRX287882 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: 00:08:24 26274958 reads; of these: 26274958 (100.00%) were unpaired; of these: 1650818 (6.28%) aligned 0 times 16699045 (63.55%) aligned exactly 1 time 7925095 (30.16%) aligned >1 times 93.72% overall alignment rate Time searching: 00:08:24 Overall time: 00:08:24 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] 5590830 / 24624140 = 0.2270 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 02:21:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.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 02:21:59: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:21:59: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:22:06: 1000000 INFO @ Tue, 30 Jun 2020 02:22:12: 2000000 INFO @ Tue, 30 Jun 2020 02:22:18: 3000000 INFO @ Tue, 30 Jun 2020 02:22:24: 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 02:22:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.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 02:22:29: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:22:29: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:22:31: 5000000 INFO @ Tue, 30 Jun 2020 02:22:36: 1000000 INFO @ Tue, 30 Jun 2020 02:22:37: 6000000 INFO @ Tue, 30 Jun 2020 02:22:42: 2000000 INFO @ Tue, 30 Jun 2020 02:22:44: 7000000 INFO @ Tue, 30 Jun 2020 02:22:49: 3000000 INFO @ Tue, 30 Jun 2020 02:22:51: 8000000 INFO @ Tue, 30 Jun 2020 02:22:55: 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 02:22:57: 9000000 INFO @ Tue, 30 Jun 2020 02:22:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.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 02:22:59: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:22:59: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:23:02: 5000000 INFO @ Tue, 30 Jun 2020 02:23:04: 10000000 INFO @ Tue, 30 Jun 2020 02:23:07: 1000000 INFO @ Tue, 30 Jun 2020 02:23:08: 6000000 INFO @ Tue, 30 Jun 2020 02:23:11: 11000000 INFO @ Tue, 30 Jun 2020 02:23:13: 2000000 INFO @ Tue, 30 Jun 2020 02:23:15: 7000000 INFO @ Tue, 30 Jun 2020 02:23:18: 12000000 INFO @ Tue, 30 Jun 2020 02:23:20: 3000000 INFO @ Tue, 30 Jun 2020 02:23:21: 8000000 INFO @ Tue, 30 Jun 2020 02:23:25: 13000000 INFO @ Tue, 30 Jun 2020 02:23:27: 4000000 INFO @ Tue, 30 Jun 2020 02:23:28: 9000000 INFO @ Tue, 30 Jun 2020 02:23:31: 14000000 INFO @ Tue, 30 Jun 2020 02:23:34: 5000000 INFO @ Tue, 30 Jun 2020 02:23:35: 10000000 INFO @ Tue, 30 Jun 2020 02:23:38: 15000000 INFO @ Tue, 30 Jun 2020 02:23:41: 6000000 INFO @ Tue, 30 Jun 2020 02:23:41: 11000000 INFO @ Tue, 30 Jun 2020 02:23:45: 16000000 INFO @ Tue, 30 Jun 2020 02:23:48: 7000000 INFO @ Tue, 30 Jun 2020 02:23:48: 12000000 INFO @ Tue, 30 Jun 2020 02:23:52: 17000000 INFO @ Tue, 30 Jun 2020 02:23:55: 13000000 INFO @ Tue, 30 Jun 2020 02:23:55: 8000000 INFO @ Tue, 30 Jun 2020 02:23:58: 18000000 INFO @ Tue, 30 Jun 2020 02:24:01: 14000000 INFO @ Tue, 30 Jun 2020 02:24:02: 9000000 INFO @ Tue, 30 Jun 2020 02:24:05: 19000000 INFO @ Tue, 30 Jun 2020 02:24:06: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:24:06: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:24:06: #1 total tags in treatment: 19033310 INFO @ Tue, 30 Jun 2020 02:24:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:24:06: #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 02:24:06: #1 tags after filtering in treatment: 19033310 INFO @ Tue, 30 Jun 2020 02:24:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:24:06: #1 finished! INFO @ Tue, 30 Jun 2020 02:24:06: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:24:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:24:08: #2 number of paired peaks: 645 WARNING @ Tue, 30 Jun 2020 02:24:08: Fewer paired peaks (645) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 645 pairs to build model! INFO @ Tue, 30 Jun 2020 02:24:08: start model_add_line... INFO @ Tue, 30 Jun 2020 02:24:08: 15000000 INFO @ Tue, 30 Jun 2020 02:24:08: start X-correlation... INFO @ Tue, 30 Jun 2020 02:24:08: end of X-cor INFO @ Tue, 30 Jun 2020 02:24:08: #2 finished! INFO @ Tue, 30 Jun 2020 02:24:08: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:24:08: #2 alternative fragment length(s) may be 2,32,545,573 bps INFO @ Tue, 30 Jun 2020 02:24:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.05_model.r WARNING @ Tue, 30 Jun 2020 02:24:08: #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 02:24:08: #2 You may need to consider one of the other alternative d(s): 2,32,545,573 WARNING @ Tue, 30 Jun 2020 02:24:08: #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 02:24:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:24:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:24:09: 10000000 INFO @ Tue, 30 Jun 2020 02:24:15: 16000000 INFO @ Tue, 30 Jun 2020 02:24:15: 11000000 INFO @ Tue, 30 Jun 2020 02:24:21: 17000000 INFO @ Tue, 30 Jun 2020 02:24:22: 12000000 INFO @ Tue, 30 Jun 2020 02:24:27: 18000000 INFO @ Tue, 30 Jun 2020 02:24:29: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:24:34: 19000000 INFO @ Tue, 30 Jun 2020 02:24:34: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:24:34: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:24:34: #1 total tags in treatment: 19033310 INFO @ Tue, 30 Jun 2020 02:24:34: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:24:34: #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 02:24:35: #1 tags after filtering in treatment: 19033310 INFO @ Tue, 30 Jun 2020 02:24:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:24:35: #1 finished! INFO @ Tue, 30 Jun 2020 02:24:35: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:24:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:24:36: 14000000 INFO @ Tue, 30 Jun 2020 02:24:36: #2 number of paired peaks: 645 WARNING @ Tue, 30 Jun 2020 02:24:36: Fewer paired peaks (645) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 645 pairs to build model! INFO @ Tue, 30 Jun 2020 02:24:36: start model_add_line... INFO @ Tue, 30 Jun 2020 02:24:36: start X-correlation... INFO @ Tue, 30 Jun 2020 02:24:37: end of X-cor INFO @ Tue, 30 Jun 2020 02:24:37: #2 finished! INFO @ Tue, 30 Jun 2020 02:24:37: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:24:37: #2 alternative fragment length(s) may be 2,32,545,573 bps INFO @ Tue, 30 Jun 2020 02:24:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.10_model.r WARNING @ Tue, 30 Jun 2020 02:24:37: #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 02:24:37: #2 You may need to consider one of the other alternative d(s): 2,32,545,573 WARNING @ Tue, 30 Jun 2020 02:24:37: #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 02:24:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:24:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:24:43: 15000000 INFO @ Tue, 30 Jun 2020 02:24:44: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:24:50: 16000000 INFO @ Tue, 30 Jun 2020 02:24:56: 17000000 INFO @ Tue, 30 Jun 2020 02:25:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:25:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:25:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.05_summits.bed INFO @ Tue, 30 Jun 2020 02:25:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:25:02: 18000000 INFO @ Tue, 30 Jun 2020 02:25:09: 19000000 INFO @ Tue, 30 Jun 2020 02:25:10: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:25:10: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:25:10: #1 total tags in treatment: 19033310 INFO @ Tue, 30 Jun 2020 02:25:10: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:25:10: #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 02:25:10: #1 tags after filtering in treatment: 19033310 INFO @ Tue, 30 Jun 2020 02:25:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:25:10: #1 finished! INFO @ Tue, 30 Jun 2020 02:25:10: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:25:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:25:12: #2 number of paired peaks: 645 WARNING @ Tue, 30 Jun 2020 02:25:12: Fewer paired peaks (645) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 645 pairs to build model! INFO @ Tue, 30 Jun 2020 02:25:12: start model_add_line... INFO @ Tue, 30 Jun 2020 02:25:12: start X-correlation... INFO @ Tue, 30 Jun 2020 02:25:12: end of X-cor INFO @ Tue, 30 Jun 2020 02:25:12: #2 finished! INFO @ Tue, 30 Jun 2020 02:25:12: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:25:12: #2 alternative fragment length(s) may be 2,32,545,573 bps INFO @ Tue, 30 Jun 2020 02:25:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.20_model.r WARNING @ Tue, 30 Jun 2020 02:25:12: #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 02:25:12: #2 You may need to consider one of the other alternative d(s): 2,32,545,573 WARNING @ Tue, 30 Jun 2020 02:25:12: #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 02:25:12: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:25:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:25:13: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:25:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:25:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:25:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.10_summits.bed INFO @ Tue, 30 Jun 2020 02:25:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:25:48: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:26:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:26:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:26:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287882/SRX287882.20_summits.bed INFO @ Tue, 30 Jun 2020 02:26:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling