Job ID = 6529994 SRX = SRX5827845 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: 00:17:11 75603991 reads; of these: 75603991 (100.00%) were unpaired; of these: 11900533 (15.74%) aligned 0 times 52734108 (69.75%) aligned exactly 1 time 10969350 (14.51%) aligned >1 times 84.26% overall alignment rate Time searching: 00:17:11 Overall time: 00:17:11 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 28 files... [bam_rmdupse_core] 40983209 / 63703458 = 0.6433 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 03:43:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.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 03:43:36: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:43:36: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:43:41: 1000000 INFO @ Tue, 30 Jun 2020 03:43:47: 2000000 INFO @ Tue, 30 Jun 2020 03:43:52: 3000000 INFO @ Tue, 30 Jun 2020 03:43:57: 4000000 INFO @ Tue, 30 Jun 2020 03:44:02: 5000000 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 03:44:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.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 03:44:06: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:44:06: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:44:07: 6000000 INFO @ Tue, 30 Jun 2020 03:44:12: 1000000 INFO @ Tue, 30 Jun 2020 03:44:13: 7000000 INFO @ Tue, 30 Jun 2020 03:44:17: 2000000 INFO @ Tue, 30 Jun 2020 03:44:19: 8000000 INFO @ Tue, 30 Jun 2020 03:44:23: 3000000 INFO @ Tue, 30 Jun 2020 03:44:24: 9000000 INFO @ Tue, 30 Jun 2020 03:44:29: 4000000 INFO @ Tue, 30 Jun 2020 03:44:30: 10000000 INFO @ Tue, 30 Jun 2020 03:44:34: 5000000 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 03:44:36: 11000000 INFO @ Tue, 30 Jun 2020 03:44:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.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 03:44:36: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:44:36: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:44:40: 6000000 INFO @ Tue, 30 Jun 2020 03:44:42: 12000000 INFO @ Tue, 30 Jun 2020 03:44:43: 1000000 INFO @ Tue, 30 Jun 2020 03:44:46: 7000000 INFO @ Tue, 30 Jun 2020 03:44:48: 13000000 INFO @ Tue, 30 Jun 2020 03:44:49: 2000000 INFO @ Tue, 30 Jun 2020 03:44:52: 8000000 INFO @ Tue, 30 Jun 2020 03:44:54: 14000000 INFO @ Tue, 30 Jun 2020 03:44:56: 3000000 INFO @ Tue, 30 Jun 2020 03:44:58: 9000000 INFO @ Tue, 30 Jun 2020 03:45:00: 15000000 INFO @ Tue, 30 Jun 2020 03:45:02: 4000000 INFO @ Tue, 30 Jun 2020 03:45:04: 10000000 INFO @ Tue, 30 Jun 2020 03:45:06: 16000000 INFO @ Tue, 30 Jun 2020 03:45:09: 5000000 INFO @ Tue, 30 Jun 2020 03:45:10: 11000000 INFO @ Tue, 30 Jun 2020 03:45:12: 17000000 INFO @ Tue, 30 Jun 2020 03:45:15: 6000000 INFO @ Tue, 30 Jun 2020 03:45:16: 12000000 INFO @ Tue, 30 Jun 2020 03:45:18: 18000000 INFO @ Tue, 30 Jun 2020 03:45:22: 7000000 INFO @ Tue, 30 Jun 2020 03:45:22: 13000000 INFO @ Tue, 30 Jun 2020 03:45:24: 19000000 INFO @ Tue, 30 Jun 2020 03:45:28: 14000000 INFO @ Tue, 30 Jun 2020 03:45:28: 8000000 INFO @ Tue, 30 Jun 2020 03:45:30: 20000000 INFO @ Tue, 30 Jun 2020 03:45:34: 15000000 INFO @ Tue, 30 Jun 2020 03:45:35: 9000000 INFO @ Tue, 30 Jun 2020 03:45:36: 21000000 INFO @ Tue, 30 Jun 2020 03:45:40: 16000000 INFO @ Tue, 30 Jun 2020 03:45:42: 10000000 INFO @ Tue, 30 Jun 2020 03:45:42: 22000000 INFO @ Tue, 30 Jun 2020 03:45:46: 17000000 INFO @ Tue, 30 Jun 2020 03:45:47: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:45:47: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:45:47: #1 total tags in treatment: 22720249 INFO @ Tue, 30 Jun 2020 03:45:47: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:45:47: #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 03:45:47: #1 tags after filtering in treatment: 22720249 INFO @ Tue, 30 Jun 2020 03:45:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:45:47: #1 finished! INFO @ Tue, 30 Jun 2020 03:45:47: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:45:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:45:48: 11000000 INFO @ Tue, 30 Jun 2020 03:45:49: #2 number of paired peaks: 585 WARNING @ Tue, 30 Jun 2020 03:45:49: Fewer paired peaks (585) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 585 pairs to build model! INFO @ Tue, 30 Jun 2020 03:45:49: start model_add_line... INFO @ Tue, 30 Jun 2020 03:45:49: start X-correlation... INFO @ Tue, 30 Jun 2020 03:45:49: end of X-cor INFO @ Tue, 30 Jun 2020 03:45:49: #2 finished! INFO @ Tue, 30 Jun 2020 03:45:49: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 03:45:49: #2 alternative fragment length(s) may be 1,31 bps INFO @ Tue, 30 Jun 2020 03:45:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.05_model.r WARNING @ Tue, 30 Jun 2020 03:45:49: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:45:49: #2 You may need to consider one of the other alternative d(s): 1,31 WARNING @ Tue, 30 Jun 2020 03:45:49: #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 03:45:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:45:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:45:52: 18000000 INFO @ Tue, 30 Jun 2020 03:45:55: 12000000 INFO @ Tue, 30 Jun 2020 03:45:59: 19000000 INFO @ Tue, 30 Jun 2020 03:46:02: 13000000 INFO @ Tue, 30 Jun 2020 03:46:05: 20000000 INFO @ Tue, 30 Jun 2020 03:46:08: 14000000 INFO @ Tue, 30 Jun 2020 03:46:11: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:46:15: 15000000 INFO @ Tue, 30 Jun 2020 03:46:18: 22000000 INFO @ Tue, 30 Jun 2020 03:46:22: 16000000 INFO @ Tue, 30 Jun 2020 03:46:22: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:46:22: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:46:22: #1 total tags in treatment: 22720249 INFO @ Tue, 30 Jun 2020 03:46:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:46:22: #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 03:46:23: #1 tags after filtering in treatment: 22720249 INFO @ Tue, 30 Jun 2020 03:46:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:46:23: #1 finished! INFO @ Tue, 30 Jun 2020 03:46:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:46:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:46:24: #2 number of paired peaks: 585 WARNING @ Tue, 30 Jun 2020 03:46:24: Fewer paired peaks (585) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 585 pairs to build model! INFO @ Tue, 30 Jun 2020 03:46:24: start model_add_line... INFO @ Tue, 30 Jun 2020 03:46:24: start X-correlation... INFO @ Tue, 30 Jun 2020 03:46:24: end of X-cor INFO @ Tue, 30 Jun 2020 03:46:24: #2 finished! INFO @ Tue, 30 Jun 2020 03:46:24: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 03:46:24: #2 alternative fragment length(s) may be 1,31 bps INFO @ Tue, 30 Jun 2020 03:46:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.10_model.r WARNING @ Tue, 30 Jun 2020 03:46:24: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:46:24: #2 You may need to consider one of the other alternative d(s): 1,31 WARNING @ Tue, 30 Jun 2020 03:46:24: #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 03:46:24: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:46:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:46:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:46:28: 17000000 INFO @ Tue, 30 Jun 2020 03:46:35: 18000000 INFO @ Tue, 30 Jun 2020 03:46:41: 19000000 INFO @ Tue, 30 Jun 2020 03:46:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:46:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:46:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.05_summits.bed INFO @ Tue, 30 Jun 2020 03:46:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:46:48: 20000000 INFO @ Tue, 30 Jun 2020 03:46:54: 21000000 INFO @ Tue, 30 Jun 2020 03:47:00: 22000000 INFO @ Tue, 30 Jun 2020 03:47:02: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:47:05: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:47:05: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:47:05: #1 total tags in treatment: 22720249 INFO @ Tue, 30 Jun 2020 03:47:05: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:47:05: #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 03:47:05: #1 tags after filtering in treatment: 22720249 INFO @ Tue, 30 Jun 2020 03:47:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:47:05: #1 finished! INFO @ Tue, 30 Jun 2020 03:47:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:47:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:47:07: #2 number of paired peaks: 585 WARNING @ Tue, 30 Jun 2020 03:47:07: Fewer paired peaks (585) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 585 pairs to build model! INFO @ Tue, 30 Jun 2020 03:47:07: start model_add_line... INFO @ Tue, 30 Jun 2020 03:47:07: start X-correlation... INFO @ Tue, 30 Jun 2020 03:47:07: end of X-cor INFO @ Tue, 30 Jun 2020 03:47:07: #2 finished! INFO @ Tue, 30 Jun 2020 03:47:07: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 03:47:07: #2 alternative fragment length(s) may be 1,31 bps INFO @ Tue, 30 Jun 2020 03:47:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.20_model.r WARNING @ Tue, 30 Jun 2020 03:47:07: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:47:07: #2 You may need to consider one of the other alternative d(s): 1,31 WARNING @ Tue, 30 Jun 2020 03:47:07: #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 03:47:07: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:47:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:47:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:47:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:47:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.10_summits.bed INFO @ Tue, 30 Jun 2020 03:47:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:47:43: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:48:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:48:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:48:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827845/SRX5827845.20_summits.bed INFO @ Tue, 30 Jun 2020 03:48:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling