Job ID = 6529938 SRX = SRX5416216 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: 00:11:00 40792123 reads; of these: 40792123 (100.00%) were unpaired; of these: 3135806 (7.69%) aligned 0 times 23701876 (58.10%) aligned exactly 1 time 13954441 (34.21%) aligned >1 times 92.31% overall alignment rate Time searching: 00:11:00 Overall time: 00:11:00 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 16 files... [bam_rmdupse_core] 12662549 / 37656317 = 0.3363 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 03:19:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.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 03:19:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:19:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:19:26: 1000000 INFO @ Tue, 30 Jun 2020 03:19:31: 2000000 INFO @ Tue, 30 Jun 2020 03:19:37: 3000000 INFO @ Tue, 30 Jun 2020 03:19:43: 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 03:19:48: 5000000 INFO @ Tue, 30 Jun 2020 03:19:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.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 03:19:50: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:19:50: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:19:55: 6000000 INFO @ Tue, 30 Jun 2020 03:19:57: 1000000 INFO @ Tue, 30 Jun 2020 03:20:01: 7000000 INFO @ Tue, 30 Jun 2020 03:20:03: 2000000 INFO @ Tue, 30 Jun 2020 03:20:08: 8000000 INFO @ Tue, 30 Jun 2020 03:20:10: 3000000 INFO @ Tue, 30 Jun 2020 03:20:14: 9000000 INFO @ Tue, 30 Jun 2020 03:20:16: 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 03:20:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.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 03:20:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:20:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:20:21: 10000000 INFO @ Tue, 30 Jun 2020 03:20:23: 5000000 INFO @ Tue, 30 Jun 2020 03:20:27: 1000000 INFO @ Tue, 30 Jun 2020 03:20:28: 11000000 INFO @ Tue, 30 Jun 2020 03:20:30: 6000000 INFO @ Tue, 30 Jun 2020 03:20:34: 2000000 INFO @ Tue, 30 Jun 2020 03:20:35: 12000000 INFO @ Tue, 30 Jun 2020 03:20:37: 7000000 INFO @ Tue, 30 Jun 2020 03:20:41: 3000000 INFO @ Tue, 30 Jun 2020 03:20:42: 13000000 INFO @ Tue, 30 Jun 2020 03:20:45: 8000000 INFO @ Tue, 30 Jun 2020 03:20:48: 4000000 INFO @ Tue, 30 Jun 2020 03:20:49: 14000000 INFO @ Tue, 30 Jun 2020 03:20:52: 9000000 INFO @ Tue, 30 Jun 2020 03:20:55: 5000000 INFO @ Tue, 30 Jun 2020 03:20:56: 15000000 INFO @ Tue, 30 Jun 2020 03:20:58: 10000000 INFO @ Tue, 30 Jun 2020 03:21:02: 6000000 INFO @ Tue, 30 Jun 2020 03:21:03: 16000000 INFO @ Tue, 30 Jun 2020 03:21:05: 11000000 INFO @ Tue, 30 Jun 2020 03:21:08: 7000000 INFO @ Tue, 30 Jun 2020 03:21:10: 17000000 INFO @ Tue, 30 Jun 2020 03:21:12: 12000000 INFO @ Tue, 30 Jun 2020 03:21:15: 8000000 INFO @ Tue, 30 Jun 2020 03:21:16: 18000000 INFO @ Tue, 30 Jun 2020 03:21:19: 13000000 INFO @ Tue, 30 Jun 2020 03:21:22: 9000000 INFO @ Tue, 30 Jun 2020 03:21:23: 19000000 INFO @ Tue, 30 Jun 2020 03:21:26: 14000000 INFO @ Tue, 30 Jun 2020 03:21:29: 10000000 INFO @ Tue, 30 Jun 2020 03:21:30: 20000000 INFO @ Tue, 30 Jun 2020 03:21:33: 15000000 INFO @ Tue, 30 Jun 2020 03:21:35: 11000000 INFO @ Tue, 30 Jun 2020 03:21:37: 21000000 INFO @ Tue, 30 Jun 2020 03:21:39: 16000000 INFO @ Tue, 30 Jun 2020 03:21:42: 12000000 INFO @ Tue, 30 Jun 2020 03:21:44: 22000000 INFO @ Tue, 30 Jun 2020 03:21:46: 17000000 INFO @ Tue, 30 Jun 2020 03:21:49: 13000000 INFO @ Tue, 30 Jun 2020 03:21:51: 23000000 INFO @ Tue, 30 Jun 2020 03:21:52: 18000000 INFO @ Tue, 30 Jun 2020 03:21:55: 14000000 INFO @ Tue, 30 Jun 2020 03:21:57: 24000000 INFO @ Tue, 30 Jun 2020 03:21:59: 19000000 INFO @ Tue, 30 Jun 2020 03:22:02: 15000000 INFO @ Tue, 30 Jun 2020 03:22:04: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:22:04: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:22:04: #1 total tags in treatment: 24993768 INFO @ Tue, 30 Jun 2020 03:22:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:22:04: #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 03:22:05: #1 tags after filtering in treatment: 24993768 INFO @ Tue, 30 Jun 2020 03:22:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:22:05: #1 finished! INFO @ Tue, 30 Jun 2020 03:22:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:22:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:22:06: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:22:07: #2 number of paired peaks: 468 WARNING @ Tue, 30 Jun 2020 03:22:07: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Tue, 30 Jun 2020 03:22:07: start model_add_line... INFO @ Tue, 30 Jun 2020 03:22:07: start X-correlation... INFO @ Tue, 30 Jun 2020 03:22:07: end of X-cor INFO @ Tue, 30 Jun 2020 03:22:07: #2 finished! INFO @ Tue, 30 Jun 2020 03:22:07: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 03:22:07: #2 alternative fragment length(s) may be 2 bps INFO @ Tue, 30 Jun 2020 03:22:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.05_model.r WARNING @ Tue, 30 Jun 2020 03:22:07: #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 03:22:07: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Tue, 30 Jun 2020 03:22:07: #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 03:22:07: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:22:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:22:08: 16000000 INFO @ Tue, 30 Jun 2020 03:22:13: 21000000 INFO @ Tue, 30 Jun 2020 03:22:15: 17000000 INFO @ Tue, 30 Jun 2020 03:22:20: 22000000 INFO @ Tue, 30 Jun 2020 03:22:21: 18000000 INFO @ Tue, 30 Jun 2020 03:22:26: 23000000 INFO @ Tue, 30 Jun 2020 03:22:28: 19000000 INFO @ Tue, 30 Jun 2020 03:22:33: 24000000 INFO @ Tue, 30 Jun 2020 03:22:35: 20000000 INFO @ Tue, 30 Jun 2020 03:22:40: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:22:40: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:22:40: #1 total tags in treatment: 24993768 INFO @ Tue, 30 Jun 2020 03:22:40: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:22:40: #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 03:22:40: #1 tags after filtering in treatment: 24993768 INFO @ Tue, 30 Jun 2020 03:22:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:22:40: #1 finished! INFO @ Tue, 30 Jun 2020 03:22:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:22:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:22:41: 21000000 INFO @ Tue, 30 Jun 2020 03:22:42: #2 number of paired peaks: 468 WARNING @ Tue, 30 Jun 2020 03:22:42: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Tue, 30 Jun 2020 03:22:42: start model_add_line... INFO @ Tue, 30 Jun 2020 03:22:42: start X-correlation... INFO @ Tue, 30 Jun 2020 03:22:42: end of X-cor INFO @ Tue, 30 Jun 2020 03:22:42: #2 finished! INFO @ Tue, 30 Jun 2020 03:22:42: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 03:22:42: #2 alternative fragment length(s) may be 2 bps INFO @ Tue, 30 Jun 2020 03:22:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.10_model.r WARNING @ Tue, 30 Jun 2020 03:22:42: #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 03:22:42: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Tue, 30 Jun 2020 03:22:42: #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 03:22:42: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:22:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:22:47: 22000000 INFO @ Tue, 30 Jun 2020 03:22:48: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:22:53: 23000000 INFO @ Tue, 30 Jun 2020 03:23:00: 24000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:23:06: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:23:06: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:23:06: #1 total tags in treatment: 24993768 INFO @ Tue, 30 Jun 2020 03:23:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:23:06: #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 03:23:07: #1 tags after filtering in treatment: 24993768 INFO @ Tue, 30 Jun 2020 03:23:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:23:07: #1 finished! INFO @ Tue, 30 Jun 2020 03:23:07: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:23:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:23:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:23:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:23:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.05_summits.bed INFO @ Tue, 30 Jun 2020 03:23:08: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:23:08: #2 number of paired peaks: 468 WARNING @ Tue, 30 Jun 2020 03:23:08: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Tue, 30 Jun 2020 03:23:08: start model_add_line... INFO @ Tue, 30 Jun 2020 03:23:08: start X-correlation... INFO @ Tue, 30 Jun 2020 03:23:08: end of X-cor INFO @ Tue, 30 Jun 2020 03:23:08: #2 finished! INFO @ Tue, 30 Jun 2020 03:23:08: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 03:23:08: #2 alternative fragment length(s) may be 2 bps INFO @ Tue, 30 Jun 2020 03:23:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.20_model.r WARNING @ Tue, 30 Jun 2020 03:23:08: #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 03:23:08: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Tue, 30 Jun 2020 03:23:08: #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 03:23:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:23:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:23:23: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:23:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:23:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:23:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.10_summits.bed INFO @ Tue, 30 Jun 2020 03:23:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:23:49: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:24:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:24:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:24:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5416216/SRX5416216.20_summits.bed INFO @ Tue, 30 Jun 2020 03:24:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling