Job ID = 4303035 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/SRR1163626.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: 00:04:47 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 256438 (1.19%) aligned 0 times 17820616 (82.85%) aligned exactly 1 time 3432555 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 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] 3667277 / 21253171 = 0.1726 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:44:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.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 @ Thu, 12 Dec 2019 00:44:34: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:44:34: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:44:41: 1000000 INFO @ Thu, 12 Dec 2019 00:44:47: 2000000 INFO @ Thu, 12 Dec 2019 00:44:54: 3000000 INFO @ Thu, 12 Dec 2019 00:45:00: 4000000 INFO @ Thu, 12 Dec 2019 00:45:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.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 @ Thu, 12 Dec 2019 00:45:04: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:45:04: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:45:07: 5000000 INFO @ Thu, 12 Dec 2019 00:45:10: 1000000 INFO @ Thu, 12 Dec 2019 00:45:14: 6000000 INFO @ Thu, 12 Dec 2019 00:45:17: 2000000 INFO @ Thu, 12 Dec 2019 00:45:20: 7000000 INFO @ Thu, 12 Dec 2019 00:45:23: 3000000 INFO @ Thu, 12 Dec 2019 00:45:27: 8000000 INFO @ Thu, 12 Dec 2019 00:45:30: 4000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:45:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.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 @ Thu, 12 Dec 2019 00:45:34: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:45:34: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:45:34: 9000000 INFO @ Thu, 12 Dec 2019 00:45:36: 5000000 INFO @ Thu, 12 Dec 2019 00:45:41: 10000000 INFO @ Thu, 12 Dec 2019 00:45:42: 1000000 INFO @ Thu, 12 Dec 2019 00:45:43: 6000000 INFO @ Thu, 12 Dec 2019 00:45:48: 11000000 INFO @ Thu, 12 Dec 2019 00:45:50: 7000000 INFO @ Thu, 12 Dec 2019 00:45:51: 2000000 INFO @ Thu, 12 Dec 2019 00:45:54: 12000000 INFO @ Thu, 12 Dec 2019 00:45:56: 8000000 INFO @ Thu, 12 Dec 2019 00:46:00: 3000000 INFO @ Thu, 12 Dec 2019 00:46:01: 13000000 INFO @ Thu, 12 Dec 2019 00:46:03: 9000000 INFO @ Thu, 12 Dec 2019 00:46:08: 4000000 INFO @ Thu, 12 Dec 2019 00:46:08: 14000000 INFO @ Thu, 12 Dec 2019 00:46:09: 10000000 INFO @ Thu, 12 Dec 2019 00:46:15: 15000000 INFO @ Thu, 12 Dec 2019 00:46:16: 11000000 INFO @ Thu, 12 Dec 2019 00:46:17: 5000000 INFO @ Thu, 12 Dec 2019 00:46:22: 16000000 INFO @ Thu, 12 Dec 2019 00:46:23: 12000000 INFO @ Thu, 12 Dec 2019 00:46:26: 6000000 INFO @ Thu, 12 Dec 2019 00:46:29: 17000000 INFO @ Thu, 12 Dec 2019 00:46:29: 13000000 INFO @ Thu, 12 Dec 2019 00:46:33: #1 tag size is determined as 42 bps INFO @ Thu, 12 Dec 2019 00:46:33: #1 tag size = 42 INFO @ Thu, 12 Dec 2019 00:46:33: #1 total tags in treatment: 17585894 INFO @ Thu, 12 Dec 2019 00:46:33: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:46:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:46:34: #1 tags after filtering in treatment: 17585894 INFO @ Thu, 12 Dec 2019 00:46:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:46:34: #1 finished! INFO @ Thu, 12 Dec 2019 00:46:34: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:46:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:46:34: 7000000 INFO @ Thu, 12 Dec 2019 00:46:35: #2 number of paired peaks: 215 WARNING @ Thu, 12 Dec 2019 00:46:35: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Thu, 12 Dec 2019 00:46:35: start model_add_line... INFO @ Thu, 12 Dec 2019 00:46:35: start X-correlation... INFO @ Thu, 12 Dec 2019 00:46:35: end of X-cor INFO @ Thu, 12 Dec 2019 00:46:35: #2 finished! INFO @ Thu, 12 Dec 2019 00:46:35: #2 predicted fragment length is 40 bps INFO @ Thu, 12 Dec 2019 00:46:35: #2 alternative fragment length(s) may be 1,40,95,589,591 bps INFO @ Thu, 12 Dec 2019 00:46:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.05_model.r WARNING @ Thu, 12 Dec 2019 00:46:35: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:46:35: #2 You may need to consider one of the other alternative d(s): 1,40,95,589,591 WARNING @ Thu, 12 Dec 2019 00:46:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:46:35: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:46:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:46:36: 14000000 INFO @ Thu, 12 Dec 2019 00:46:43: 8000000 INFO @ Thu, 12 Dec 2019 00:46:43: 15000000 INFO @ Thu, 12 Dec 2019 00:46:49: 16000000 INFO @ Thu, 12 Dec 2019 00:46:51: 9000000 INFO @ Thu, 12 Dec 2019 00:46:56: 17000000 INFO @ Thu, 12 Dec 2019 00:46:59: 10000000 INFO @ Thu, 12 Dec 2019 00:47:00: #1 tag size is determined as 42 bps INFO @ Thu, 12 Dec 2019 00:47:00: #1 tag size = 42 INFO @ Thu, 12 Dec 2019 00:47:00: #1 total tags in treatment: 17585894 INFO @ Thu, 12 Dec 2019 00:47:00: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:47:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:47:00: #1 tags after filtering in treatment: 17585894 INFO @ Thu, 12 Dec 2019 00:47:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:47:00: #1 finished! INFO @ Thu, 12 Dec 2019 00:47:00: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:47:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:47:02: #2 number of paired peaks: 215 WARNING @ Thu, 12 Dec 2019 00:47:02: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Thu, 12 Dec 2019 00:47:02: start model_add_line... INFO @ Thu, 12 Dec 2019 00:47:02: start X-correlation... INFO @ Thu, 12 Dec 2019 00:47:02: end of X-cor INFO @ Thu, 12 Dec 2019 00:47:02: #2 finished! INFO @ Thu, 12 Dec 2019 00:47:02: #2 predicted fragment length is 40 bps INFO @ Thu, 12 Dec 2019 00:47:02: #2 alternative fragment length(s) may be 1,40,95,589,591 bps INFO @ Thu, 12 Dec 2019 00:47:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.10_model.r WARNING @ Thu, 12 Dec 2019 00:47:02: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:47:02: #2 You may need to consider one of the other alternative d(s): 1,40,95,589,591 WARNING @ Thu, 12 Dec 2019 00:47:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:47:02: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:47:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:47:08: 11000000 INFO @ Thu, 12 Dec 2019 00:47:16: 12000000 INFO @ Thu, 12 Dec 2019 00:47:19: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:47:24: 13000000 INFO @ Thu, 12 Dec 2019 00:47:32: 14000000 INFO @ Thu, 12 Dec 2019 00:47:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:47:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:47:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.05_summits.bed INFO @ Thu, 12 Dec 2019 00:47:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (700 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:47:41: 15000000 INFO @ Thu, 12 Dec 2019 00:47:45: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:47:49: 16000000 INFO @ Thu, 12 Dec 2019 00:47:57: 17000000 INFO @ Thu, 12 Dec 2019 00:48:02: #1 tag size is determined as 42 bps INFO @ Thu, 12 Dec 2019 00:48:02: #1 tag size = 42 INFO @ Thu, 12 Dec 2019 00:48:02: #1 total tags in treatment: 17585894 INFO @ Thu, 12 Dec 2019 00:48:02: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:48:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:48:03: #1 tags after filtering in treatment: 17585894 INFO @ Thu, 12 Dec 2019 00:48:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:48:03: #1 finished! INFO @ Thu, 12 Dec 2019 00:48:03: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:48:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:48:04: #2 number of paired peaks: 215 WARNING @ Thu, 12 Dec 2019 00:48:04: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Thu, 12 Dec 2019 00:48:04: start model_add_line... INFO @ Thu, 12 Dec 2019 00:48:05: start X-correlation... INFO @ Thu, 12 Dec 2019 00:48:05: end of X-cor INFO @ Thu, 12 Dec 2019 00:48:05: #2 finished! INFO @ Thu, 12 Dec 2019 00:48:05: #2 predicted fragment length is 40 bps INFO @ Thu, 12 Dec 2019 00:48:05: #2 alternative fragment length(s) may be 1,40,95,589,591 bps INFO @ Thu, 12 Dec 2019 00:48:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.20_model.r WARNING @ Thu, 12 Dec 2019 00:48:05: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:48:05: #2 You may need to consider one of the other alternative d(s): 1,40,95,589,591 WARNING @ Thu, 12 Dec 2019 00:48:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:48:05: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:48:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:48:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:48:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:48:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.10_summits.bed INFO @ Thu, 12 Dec 2019 00:48:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (338 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:48:48: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:49:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:49:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:49:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466560/SRX466560.20_summits.bed INFO @ Thu, 12 Dec 2019 00:49:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (107 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。