Job ID = 1291692 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,221,757 reads read : 20,221,757 reads written : 20,221,757 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:04:50 20221757 reads; of these: 20221757 (100.00%) were unpaired; of these: 1113922 (5.51%) aligned 0 times 16221511 (80.22%) aligned exactly 1 time 2886324 (14.27%) aligned >1 times 94.49% overall alignment rate Time searching: 00:04:50 Overall time: 00:04:50 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] 1960616 / 19107835 = 0.1026 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 @ Sun, 02 Jun 2019 16:27:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.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 @ Sun, 02 Jun 2019 16:27:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:27:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:27:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.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 @ Sun, 02 Jun 2019 16:27:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:27:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:27:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.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 @ Sun, 02 Jun 2019 16:27:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:27:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:27:58: 1000000 INFO @ Sun, 02 Jun 2019 16:27:59: 1000000 INFO @ Sun, 02 Jun 2019 16:27:59: 1000000 INFO @ Sun, 02 Jun 2019 16:28:05: 2000000 INFO @ Sun, 02 Jun 2019 16:28:08: 2000000 INFO @ Sun, 02 Jun 2019 16:28:08: 2000000 INFO @ Sun, 02 Jun 2019 16:28:12: 3000000 INFO @ Sun, 02 Jun 2019 16:28:16: 3000000 INFO @ Sun, 02 Jun 2019 16:28:16: 3000000 INFO @ Sun, 02 Jun 2019 16:28:19: 4000000 INFO @ Sun, 02 Jun 2019 16:28:23: 4000000 INFO @ Sun, 02 Jun 2019 16:28:24: 4000000 INFO @ Sun, 02 Jun 2019 16:28:27: 5000000 INFO @ Sun, 02 Jun 2019 16:28:31: 5000000 INFO @ Sun, 02 Jun 2019 16:28:32: 5000000 INFO @ Sun, 02 Jun 2019 16:28:34: 6000000 INFO @ Sun, 02 Jun 2019 16:28:39: 6000000 INFO @ Sun, 02 Jun 2019 16:28:40: 6000000 INFO @ Sun, 02 Jun 2019 16:28:41: 7000000 INFO @ Sun, 02 Jun 2019 16:28:46: 7000000 INFO @ Sun, 02 Jun 2019 16:28:48: 7000000 INFO @ Sun, 02 Jun 2019 16:28:49: 8000000 INFO @ Sun, 02 Jun 2019 16:28:54: 8000000 INFO @ Sun, 02 Jun 2019 16:28:55: 8000000 INFO @ Sun, 02 Jun 2019 16:28:56: 9000000 INFO @ Sun, 02 Jun 2019 16:29:01: 9000000 INFO @ Sun, 02 Jun 2019 16:29:03: 9000000 INFO @ Sun, 02 Jun 2019 16:29:03: 10000000 INFO @ Sun, 02 Jun 2019 16:29:09: 10000000 INFO @ Sun, 02 Jun 2019 16:29:10: 11000000 INFO @ Sun, 02 Jun 2019 16:29:11: 10000000 INFO @ Sun, 02 Jun 2019 16:29:16: 11000000 INFO @ Sun, 02 Jun 2019 16:29:18: 12000000 INFO @ Sun, 02 Jun 2019 16:29:19: 11000000 INFO @ Sun, 02 Jun 2019 16:29:24: 12000000 INFO @ Sun, 02 Jun 2019 16:29:25: 13000000 INFO @ Sun, 02 Jun 2019 16:29:27: 12000000 INFO @ Sun, 02 Jun 2019 16:29:31: 13000000 INFO @ Sun, 02 Jun 2019 16:29:32: 14000000 INFO @ Sun, 02 Jun 2019 16:29:34: 13000000 INFO @ Sun, 02 Jun 2019 16:29:39: 14000000 INFO @ Sun, 02 Jun 2019 16:29:39: 15000000 INFO @ Sun, 02 Jun 2019 16:29:42: 14000000 INFO @ Sun, 02 Jun 2019 16:29:46: 15000000 INFO @ Sun, 02 Jun 2019 16:29:46: 16000000 INFO @ Sun, 02 Jun 2019 16:29:50: 15000000 INFO @ Sun, 02 Jun 2019 16:29:54: 17000000 INFO @ Sun, 02 Jun 2019 16:29:54: 16000000 INFO @ Sun, 02 Jun 2019 16:29:55: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:29:55: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:29:55: #1 total tags in treatment: 17147219 INFO @ Sun, 02 Jun 2019 16:29:55: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:29:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:29:55: #1 tags after filtering in treatment: 17147219 INFO @ Sun, 02 Jun 2019 16:29:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:29:55: #1 finished! INFO @ Sun, 02 Jun 2019 16:29:55: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:29:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:29:57: #2 number of paired peaks: 225 WARNING @ Sun, 02 Jun 2019 16:29:57: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Sun, 02 Jun 2019 16:29:57: start model_add_line... INFO @ Sun, 02 Jun 2019 16:29:57: start X-correlation... INFO @ Sun, 02 Jun 2019 16:29:57: end of X-cor INFO @ Sun, 02 Jun 2019 16:29:57: #2 finished! INFO @ Sun, 02 Jun 2019 16:29:57: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 16:29:57: #2 alternative fragment length(s) may be 1,47,542,569,588 bps INFO @ Sun, 02 Jun 2019 16:29:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.05_model.r WARNING @ Sun, 02 Jun 2019 16:29:57: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:29:57: #2 You may need to consider one of the other alternative d(s): 1,47,542,569,588 WARNING @ Sun, 02 Jun 2019 16:29:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 16:29:57: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:29:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:29:58: 16000000 INFO @ Sun, 02 Jun 2019 16:30:01: 17000000 INFO @ Sun, 02 Jun 2019 16:30:02: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:30:02: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:30:02: #1 total tags in treatment: 17147219 INFO @ Sun, 02 Jun 2019 16:30:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:30:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:30:03: #1 tags after filtering in treatment: 17147219 INFO @ Sun, 02 Jun 2019 16:30:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:30:03: #1 finished! INFO @ Sun, 02 Jun 2019 16:30:03: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:30:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:30:04: #2 number of paired peaks: 225 WARNING @ Sun, 02 Jun 2019 16:30:04: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Sun, 02 Jun 2019 16:30:04: start model_add_line... INFO @ Sun, 02 Jun 2019 16:30:04: start X-correlation... INFO @ Sun, 02 Jun 2019 16:30:04: end of X-cor INFO @ Sun, 02 Jun 2019 16:30:04: #2 finished! INFO @ Sun, 02 Jun 2019 16:30:04: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 16:30:04: #2 alternative fragment length(s) may be 1,47,542,569,588 bps INFO @ Sun, 02 Jun 2019 16:30:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.20_model.r WARNING @ Sun, 02 Jun 2019 16:30:04: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:30:04: #2 You may need to consider one of the other alternative d(s): 1,47,542,569,588 WARNING @ Sun, 02 Jun 2019 16:30:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 16:30:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:30:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:30:06: 17000000 INFO @ Sun, 02 Jun 2019 16:30:08: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:30:08: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:30:08: #1 total tags in treatment: 17147219 INFO @ Sun, 02 Jun 2019 16:30:08: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:30:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:30:08: #1 tags after filtering in treatment: 17147219 INFO @ Sun, 02 Jun 2019 16:30:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:30:08: #1 finished! INFO @ Sun, 02 Jun 2019 16:30:08: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:30:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:30:09: #2 number of paired peaks: 225 WARNING @ Sun, 02 Jun 2019 16:30:09: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Sun, 02 Jun 2019 16:30:09: start model_add_line... INFO @ Sun, 02 Jun 2019 16:30:10: start X-correlation... INFO @ Sun, 02 Jun 2019 16:30:10: end of X-cor INFO @ Sun, 02 Jun 2019 16:30:10: #2 finished! INFO @ Sun, 02 Jun 2019 16:30:10: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 16:30:10: #2 alternative fragment length(s) may be 1,47,542,569,588 bps INFO @ Sun, 02 Jun 2019 16:30:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.10_model.r WARNING @ Sun, 02 Jun 2019 16:30:10: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:30:10: #2 You may need to consider one of the other alternative d(s): 1,47,542,569,588 WARNING @ Sun, 02 Jun 2019 16:30:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 16:30:10: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:30:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:30:40: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:30:47: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:30:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:31:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:31:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:31:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.05_summits.bed INFO @ Sun, 02 Jun 2019 16:31:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (665 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:31:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:31:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:31:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.20_summits.bed INFO @ Sun, 02 Jun 2019 16:31:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (152 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:31:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:31:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:31:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX216763/SRX216763.10_summits.bed INFO @ Sun, 02 Jun 2019 16:31:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (436 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。