Job ID = 2590160 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,434,363 reads read : 24,434,363 reads written : 24,434,363 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:06:15 24434363 reads; of these: 24434363 (100.00%) were unpaired; of these: 3205471 (13.12%) aligned 0 times 17392824 (71.18%) aligned exactly 1 time 3836068 (15.70%) aligned >1 times 86.88% overall alignment rate Time searching: 00:06:15 Overall time: 00:06:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 2472936 / 21228892 = 0.1165 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 12 Aug 2019 20:12:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 12 Aug 2019 20:12:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:12:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:12:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 12 Aug 2019 20:12:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:12:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:12:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 12 Aug 2019 20:12:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:12:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:12:23: 1000000 INFO @ Mon, 12 Aug 2019 20:12:24: 1000000 INFO @ Mon, 12 Aug 2019 20:12:26: 1000000 INFO @ Mon, 12 Aug 2019 20:12:29: 2000000 INFO @ Mon, 12 Aug 2019 20:12:30: 2000000 INFO @ Mon, 12 Aug 2019 20:12:34: 2000000 INFO @ Mon, 12 Aug 2019 20:12:36: 3000000 INFO @ Mon, 12 Aug 2019 20:12:37: 3000000 INFO @ Mon, 12 Aug 2019 20:12:41: 3000000 INFO @ Mon, 12 Aug 2019 20:12:42: 4000000 INFO @ Mon, 12 Aug 2019 20:12:43: 4000000 INFO @ Mon, 12 Aug 2019 20:12:48: 4000000 INFO @ Mon, 12 Aug 2019 20:12:48: 5000000 INFO @ Mon, 12 Aug 2019 20:12:49: 5000000 INFO @ Mon, 12 Aug 2019 20:12:55: 5000000 INFO @ Mon, 12 Aug 2019 20:12:55: 6000000 INFO @ Mon, 12 Aug 2019 20:12:56: 6000000 INFO @ Mon, 12 Aug 2019 20:13:01: 7000000 INFO @ Mon, 12 Aug 2019 20:13:02: 6000000 INFO @ Mon, 12 Aug 2019 20:13:02: 7000000 INFO @ Mon, 12 Aug 2019 20:13:08: 8000000 INFO @ Mon, 12 Aug 2019 20:13:09: 7000000 INFO @ Mon, 12 Aug 2019 20:13:09: 8000000 INFO @ Mon, 12 Aug 2019 20:13:14: 9000000 INFO @ Mon, 12 Aug 2019 20:13:15: 9000000 INFO @ Mon, 12 Aug 2019 20:13:16: 8000000 INFO @ Mon, 12 Aug 2019 20:13:21: 10000000 INFO @ Mon, 12 Aug 2019 20:13:22: 10000000 INFO @ Mon, 12 Aug 2019 20:13:24: 9000000 INFO @ Mon, 12 Aug 2019 20:13:27: 11000000 INFO @ Mon, 12 Aug 2019 20:13:28: 11000000 INFO @ Mon, 12 Aug 2019 20:13:32: 10000000 INFO @ Mon, 12 Aug 2019 20:13:34: 12000000 INFO @ Mon, 12 Aug 2019 20:13:35: 12000000 INFO @ Mon, 12 Aug 2019 20:13:40: 11000000 INFO @ Mon, 12 Aug 2019 20:13:40: 13000000 INFO @ Mon, 12 Aug 2019 20:13:41: 13000000 INFO @ Mon, 12 Aug 2019 20:13:47: 14000000 INFO @ Mon, 12 Aug 2019 20:13:47: 12000000 INFO @ Mon, 12 Aug 2019 20:13:48: 14000000 INFO @ Mon, 12 Aug 2019 20:13:53: 15000000 INFO @ Mon, 12 Aug 2019 20:13:54: 15000000 INFO @ Mon, 12 Aug 2019 20:13:55: 13000000 INFO @ Mon, 12 Aug 2019 20:14:00: 16000000 INFO @ Mon, 12 Aug 2019 20:14:01: 16000000 INFO @ Mon, 12 Aug 2019 20:14:03: 14000000 INFO @ Mon, 12 Aug 2019 20:14:06: 17000000 INFO @ Mon, 12 Aug 2019 20:14:07: 17000000 INFO @ Mon, 12 Aug 2019 20:14:11: 15000000 INFO @ Mon, 12 Aug 2019 20:14:13: 18000000 INFO @ Mon, 12 Aug 2019 20:14:13: 18000000 INFO @ Mon, 12 Aug 2019 20:14:18: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:14:18: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:14:18: #1 total tags in treatment: 18755956 INFO @ Mon, 12 Aug 2019 20:14:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:14:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:14:18: #1 tags after filtering in treatment: 18755956 INFO @ Mon, 12 Aug 2019 20:14:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:14:18: #1 finished! INFO @ Mon, 12 Aug 2019 20:14:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:14:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:14:19: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:14:19: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:14:19: #1 total tags in treatment: 18755956 INFO @ Mon, 12 Aug 2019 20:14:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:14:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:14:19: 16000000 INFO @ Mon, 12 Aug 2019 20:14:19: #1 tags after filtering in treatment: 18755956 INFO @ Mon, 12 Aug 2019 20:14:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:14:19: #1 finished! INFO @ Mon, 12 Aug 2019 20:14:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:14:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:14:20: #2 number of paired peaks: 252 WARNING @ Mon, 12 Aug 2019 20:14:20: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Mon, 12 Aug 2019 20:14:20: start model_add_line... INFO @ Mon, 12 Aug 2019 20:14:20: start X-correlation... INFO @ Mon, 12 Aug 2019 20:14:20: end of X-cor INFO @ Mon, 12 Aug 2019 20:14:20: #2 finished! INFO @ Mon, 12 Aug 2019 20:14:20: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 20:14:20: #2 alternative fragment length(s) may be 1,12,36,46,536,553 bps INFO @ Mon, 12 Aug 2019 20:14:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.05_model.r WARNING @ Mon, 12 Aug 2019 20:14:20: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:14:20: #2 You may need to consider one of the other alternative d(s): 1,12,36,46,536,553 WARNING @ Mon, 12 Aug 2019 20:14:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:14:20: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:14:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:14:21: #2 number of paired peaks: 252 WARNING @ Mon, 12 Aug 2019 20:14:21: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Mon, 12 Aug 2019 20:14:21: start model_add_line... INFO @ Mon, 12 Aug 2019 20:14:21: start X-correlation... INFO @ Mon, 12 Aug 2019 20:14:21: end of X-cor INFO @ Mon, 12 Aug 2019 20:14:21: #2 finished! INFO @ Mon, 12 Aug 2019 20:14:21: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 20:14:21: #2 alternative fragment length(s) may be 1,12,36,46,536,553 bps INFO @ Mon, 12 Aug 2019 20:14:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.10_model.r WARNING @ Mon, 12 Aug 2019 20:14:21: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:14:21: #2 You may need to consider one of the other alternative d(s): 1,12,36,46,536,553 WARNING @ Mon, 12 Aug 2019 20:14:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:14:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:14:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:14:26: 17000000 INFO @ Mon, 12 Aug 2019 20:14:34: 18000000 INFO @ Mon, 12 Aug 2019 20:14:40: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:14:40: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:14:40: #1 total tags in treatment: 18755956 INFO @ Mon, 12 Aug 2019 20:14:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:14:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:14:41: #1 tags after filtering in treatment: 18755956 INFO @ Mon, 12 Aug 2019 20:14:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:14:41: #1 finished! INFO @ Mon, 12 Aug 2019 20:14:41: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:14:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:14:42: #2 number of paired peaks: 252 WARNING @ Mon, 12 Aug 2019 20:14:42: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Mon, 12 Aug 2019 20:14:42: start model_add_line... INFO @ Mon, 12 Aug 2019 20:14:43: start X-correlation... INFO @ Mon, 12 Aug 2019 20:14:43: end of X-cor INFO @ Mon, 12 Aug 2019 20:14:43: #2 finished! INFO @ Mon, 12 Aug 2019 20:14:43: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 20:14:43: #2 alternative fragment length(s) may be 1,12,36,46,536,553 bps INFO @ Mon, 12 Aug 2019 20:14:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.20_model.r WARNING @ Mon, 12 Aug 2019 20:14:43: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:14:43: #2 You may need to consider one of the other alternative d(s): 1,12,36,46,536,553 WARNING @ Mon, 12 Aug 2019 20:14:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:14:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:14:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:15:01: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:15:02: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:15:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:15:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:15:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.05_summits.bed INFO @ Mon, 12 Aug 2019 20:15:20: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:15:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:15:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:15:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.10_summits.bed INFO @ Mon, 12 Aug 2019 20:15:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:15:24: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:15:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:15:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:15:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495030/SRX495030.20_summits.bed INFO @ Mon, 12 Aug 2019 20:15:43: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。