Job ID = 2589968 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,509,609 reads read : 21,509,609 reads written : 21,509,609 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1163565.sra.cache’: 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: 00:04:11 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 256444 (1.19%) aligned 0 times 17820598 (82.85%) aligned exactly 1 time 3432567 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:04:11 Overall time: 00:04:11 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3666934 / 21253165 = 0.1725 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 19:03:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.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 19:03:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:03:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:03:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.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 19:03:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:03:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:03:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.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 19:03:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:03:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:03:56: 1000000 INFO @ Mon, 12 Aug 2019 19:03:56: 1000000 INFO @ Mon, 12 Aug 2019 19:03:58: 1000000 INFO @ Mon, 12 Aug 2019 19:04:02: 2000000 INFO @ Mon, 12 Aug 2019 19:04:03: 2000000 INFO @ Mon, 12 Aug 2019 19:04:04: 2000000 INFO @ Mon, 12 Aug 2019 19:04:09: 3000000 INFO @ Mon, 12 Aug 2019 19:04:09: 3000000 INFO @ Mon, 12 Aug 2019 19:04:11: 3000000 INFO @ Mon, 12 Aug 2019 19:04:15: 4000000 INFO @ Mon, 12 Aug 2019 19:04:16: 4000000 INFO @ Mon, 12 Aug 2019 19:04:17: 4000000 INFO @ Mon, 12 Aug 2019 19:04:21: 5000000 INFO @ Mon, 12 Aug 2019 19:04:22: 5000000 INFO @ Mon, 12 Aug 2019 19:04:24: 5000000 INFO @ Mon, 12 Aug 2019 19:04:27: 6000000 INFO @ Mon, 12 Aug 2019 19:04:29: 6000000 INFO @ Mon, 12 Aug 2019 19:04:30: 6000000 INFO @ Mon, 12 Aug 2019 19:04:33: 7000000 INFO @ Mon, 12 Aug 2019 19:04:35: 7000000 INFO @ Mon, 12 Aug 2019 19:04:37: 7000000 INFO @ Mon, 12 Aug 2019 19:04:40: 8000000 INFO @ Mon, 12 Aug 2019 19:04:42: 8000000 INFO @ Mon, 12 Aug 2019 19:04:43: 8000000 INFO @ Mon, 12 Aug 2019 19:04:46: 9000000 INFO @ Mon, 12 Aug 2019 19:04:48: 9000000 INFO @ Mon, 12 Aug 2019 19:04:50: 9000000 INFO @ Mon, 12 Aug 2019 19:04:52: 10000000 INFO @ Mon, 12 Aug 2019 19:04:55: 10000000 INFO @ Mon, 12 Aug 2019 19:04:57: 10000000 INFO @ Mon, 12 Aug 2019 19:04:58: 11000000 INFO @ Mon, 12 Aug 2019 19:05:01: 11000000 INFO @ Mon, 12 Aug 2019 19:05:03: 11000000 INFO @ Mon, 12 Aug 2019 19:05:04: 12000000 INFO @ Mon, 12 Aug 2019 19:05:08: 12000000 INFO @ Mon, 12 Aug 2019 19:05:10: 12000000 INFO @ Mon, 12 Aug 2019 19:05:10: 13000000 INFO @ Mon, 12 Aug 2019 19:05:15: 13000000 INFO @ Mon, 12 Aug 2019 19:05:16: 13000000 INFO @ Mon, 12 Aug 2019 19:05:17: 14000000 INFO @ Mon, 12 Aug 2019 19:05:21: 14000000 INFO @ Mon, 12 Aug 2019 19:05:23: 15000000 INFO @ Mon, 12 Aug 2019 19:05:23: 14000000 INFO @ Mon, 12 Aug 2019 19:05:28: 15000000 INFO @ Mon, 12 Aug 2019 19:05:29: 16000000 INFO @ Mon, 12 Aug 2019 19:05:29: 15000000 INFO @ Mon, 12 Aug 2019 19:05:34: 16000000 INFO @ Mon, 12 Aug 2019 19:05:35: 17000000 INFO @ Mon, 12 Aug 2019 19:05:36: 16000000 INFO @ Mon, 12 Aug 2019 19:05:39: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:05:39: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:05:39: #1 total tags in treatment: 17586231 INFO @ Mon, 12 Aug 2019 19:05:39: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:05:39: #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 19:05:39: #1 tags after filtering in treatment: 17586231 INFO @ Mon, 12 Aug 2019 19:05:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:05:39: #1 finished! INFO @ Mon, 12 Aug 2019 19:05:39: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:05:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:05:41: #2 number of paired peaks: 208 WARNING @ Mon, 12 Aug 2019 19:05:41: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Mon, 12 Aug 2019 19:05:41: start model_add_line... INFO @ Mon, 12 Aug 2019 19:05:41: start X-correlation... INFO @ Mon, 12 Aug 2019 19:05:41: 17000000 INFO @ Mon, 12 Aug 2019 19:05:41: end of X-cor INFO @ Mon, 12 Aug 2019 19:05:41: #2 finished! INFO @ Mon, 12 Aug 2019 19:05:41: #2 predicted fragment length is 42 bps INFO @ Mon, 12 Aug 2019 19:05:41: #2 alternative fragment length(s) may be 2,42,552,573,593 bps INFO @ Mon, 12 Aug 2019 19:05:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.10_model.r WARNING @ Mon, 12 Aug 2019 19:05:41: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:05:41: #2 You may need to consider one of the other alternative d(s): 2,42,552,573,593 WARNING @ Mon, 12 Aug 2019 19:05:41: #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 19:05:41: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:05:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:05:43: 17000000 INFO @ Mon, 12 Aug 2019 19:05:45: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:05:45: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:05:45: #1 total tags in treatment: 17586231 INFO @ Mon, 12 Aug 2019 19:05:45: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:05:45: #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 19:05:45: #1 tags after filtering in treatment: 17586231 INFO @ Mon, 12 Aug 2019 19:05:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:05:45: #1 finished! INFO @ Mon, 12 Aug 2019 19:05:45: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:05:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:05:47: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:05:47: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:05:47: #1 total tags in treatment: 17586231 INFO @ Mon, 12 Aug 2019 19:05:47: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:05:47: #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 19:05:47: #2 number of paired peaks: 208 WARNING @ Mon, 12 Aug 2019 19:05:47: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Mon, 12 Aug 2019 19:05:47: start model_add_line... INFO @ Mon, 12 Aug 2019 19:05:47: start X-correlation... INFO @ Mon, 12 Aug 2019 19:05:47: end of X-cor INFO @ Mon, 12 Aug 2019 19:05:47: #2 finished! INFO @ Mon, 12 Aug 2019 19:05:47: #2 predicted fragment length is 42 bps INFO @ Mon, 12 Aug 2019 19:05:47: #2 alternative fragment length(s) may be 2,42,552,573,593 bps INFO @ Mon, 12 Aug 2019 19:05:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.05_model.r INFO @ Mon, 12 Aug 2019 19:05:47: #1 tags after filtering in treatment: 17586231 INFO @ Mon, 12 Aug 2019 19:05:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:05:47: #1 finished! INFO @ Mon, 12 Aug 2019 19:05:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:05:47: #2 looking for paired plus/minus strand peaks... WARNING @ Mon, 12 Aug 2019 19:05:47: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:05:47: #2 You may need to consider one of the other alternative d(s): 2,42,552,573,593 WARNING @ Mon, 12 Aug 2019 19:05:47: #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 19:05:47: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:05:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:05:49: #2 number of paired peaks: 208 WARNING @ Mon, 12 Aug 2019 19:05:49: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Mon, 12 Aug 2019 19:05:49: start model_add_line... INFO @ Mon, 12 Aug 2019 19:05:49: start X-correlation... INFO @ Mon, 12 Aug 2019 19:05:49: end of X-cor INFO @ Mon, 12 Aug 2019 19:05:49: #2 finished! INFO @ Mon, 12 Aug 2019 19:05:49: #2 predicted fragment length is 42 bps INFO @ Mon, 12 Aug 2019 19:05:49: #2 alternative fragment length(s) may be 2,42,552,573,593 bps INFO @ Mon, 12 Aug 2019 19:05:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.20_model.r WARNING @ Mon, 12 Aug 2019 19:05:49: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:05:49: #2 You may need to consider one of the other alternative d(s): 2,42,552,573,593 WARNING @ Mon, 12 Aug 2019 19:05:49: #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 19:05:49: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:05:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:06:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:06:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:06:29: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:06:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:06:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:06:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.10_summits.bed INFO @ Mon, 12 Aug 2019 19:06:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (335 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:06:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:06:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:06:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.05_summits.bed INFO @ Mon, 12 Aug 2019 19:06:47: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (694 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:06:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:06:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:06:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466499/SRX466499.20_summits.bed INFO @ Mon, 12 Aug 2019 19:06:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (111 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。