Job ID = 1291874 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,861,456 reads read : 12,861,456 reads written : 12,861,456 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: 00:03:36 12861456 reads; of these: 12861456 (100.00%) were unpaired; of these: 390031 (3.03%) aligned 0 times 10387334 (80.76%) aligned exactly 1 time 2084091 (16.20%) aligned >1 times 96.97% overall alignment rate Time searching: 00:03:36 Overall time: 00:03:36 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] 875619 / 12471425 = 0.0702 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 17:02:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.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 17:02:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:02:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:02:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.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 17:02:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:02:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:02:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.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 17:02:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:02:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:02:36: 1000000 INFO @ Sun, 02 Jun 2019 17:02:36: 1000000 INFO @ Sun, 02 Jun 2019 17:02:37: 1000000 INFO @ Sun, 02 Jun 2019 17:02:45: 2000000 INFO @ Sun, 02 Jun 2019 17:02:45: 2000000 INFO @ Sun, 02 Jun 2019 17:02:48: 2000000 INFO @ Sun, 02 Jun 2019 17:02:54: 3000000 INFO @ Sun, 02 Jun 2019 17:02:55: 3000000 INFO @ Sun, 02 Jun 2019 17:02:59: 3000000 INFO @ Sun, 02 Jun 2019 17:03:04: 4000000 INFO @ Sun, 02 Jun 2019 17:03:05: 4000000 INFO @ Sun, 02 Jun 2019 17:03:10: 4000000 INFO @ Sun, 02 Jun 2019 17:03:13: 5000000 INFO @ Sun, 02 Jun 2019 17:03:16: 5000000 INFO @ Sun, 02 Jun 2019 17:03:21: 5000000 INFO @ Sun, 02 Jun 2019 17:03:23: 6000000 INFO @ Sun, 02 Jun 2019 17:03:26: 6000000 INFO @ Sun, 02 Jun 2019 17:03:32: 6000000 INFO @ Sun, 02 Jun 2019 17:03:32: 7000000 INFO @ Sun, 02 Jun 2019 17:03:36: 7000000 INFO @ Sun, 02 Jun 2019 17:03:42: 8000000 INFO @ Sun, 02 Jun 2019 17:03:43: 7000000 INFO @ Sun, 02 Jun 2019 17:03:47: 8000000 INFO @ Sun, 02 Jun 2019 17:03:52: 9000000 INFO @ Sun, 02 Jun 2019 17:03:55: 8000000 INFO @ Sun, 02 Jun 2019 17:03:56: 9000000 INFO @ Sun, 02 Jun 2019 17:04:01: 10000000 INFO @ Sun, 02 Jun 2019 17:04:06: 9000000 INFO @ Sun, 02 Jun 2019 17:04:06: 10000000 INFO @ Sun, 02 Jun 2019 17:04:11: 11000000 INFO @ Sun, 02 Jun 2019 17:04:16: 11000000 INFO @ Sun, 02 Jun 2019 17:04:16: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:04:16: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:04:16: #1 total tags in treatment: 11595806 INFO @ Sun, 02 Jun 2019 17:04:16: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:04:16: #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 17:04:16: #1 tags after filtering in treatment: 11595806 INFO @ Sun, 02 Jun 2019 17:04:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:04:16: #1 finished! INFO @ Sun, 02 Jun 2019 17:04:16: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:04:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:04:17: 10000000 INFO @ Sun, 02 Jun 2019 17:04:18: #2 number of paired peaks: 309 WARNING @ Sun, 02 Jun 2019 17:04:18: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sun, 02 Jun 2019 17:04:18: start model_add_line... INFO @ Sun, 02 Jun 2019 17:04:18: start X-correlation... INFO @ Sun, 02 Jun 2019 17:04:18: end of X-cor INFO @ Sun, 02 Jun 2019 17:04:18: #2 finished! INFO @ Sun, 02 Jun 2019 17:04:18: #2 predicted fragment length is 53 bps INFO @ Sun, 02 Jun 2019 17:04:18: #2 alternative fragment length(s) may be 2,53,571 bps INFO @ Sun, 02 Jun 2019 17:04:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.20_model.r WARNING @ Sun, 02 Jun 2019 17:04:18: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:04:18: #2 You may need to consider one of the other alternative d(s): 2,53,571 WARNING @ Sun, 02 Jun 2019 17:04:18: #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 17:04:18: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:04:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:04:21: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:04:21: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:04:21: #1 total tags in treatment: 11595806 INFO @ Sun, 02 Jun 2019 17:04:21: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:04:21: #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 17:04:22: #1 tags after filtering in treatment: 11595806 INFO @ Sun, 02 Jun 2019 17:04:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:04:22: #1 finished! INFO @ Sun, 02 Jun 2019 17:04:22: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:04:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:04:23: #2 number of paired peaks: 309 WARNING @ Sun, 02 Jun 2019 17:04:23: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sun, 02 Jun 2019 17:04:23: start model_add_line... INFO @ Sun, 02 Jun 2019 17:04:23: start X-correlation... INFO @ Sun, 02 Jun 2019 17:04:23: end of X-cor INFO @ Sun, 02 Jun 2019 17:04:23: #2 finished! INFO @ Sun, 02 Jun 2019 17:04:23: #2 predicted fragment length is 53 bps INFO @ Sun, 02 Jun 2019 17:04:23: #2 alternative fragment length(s) may be 2,53,571 bps INFO @ Sun, 02 Jun 2019 17:04:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.10_model.r WARNING @ Sun, 02 Jun 2019 17:04:23: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:04:23: #2 You may need to consider one of the other alternative d(s): 2,53,571 WARNING @ Sun, 02 Jun 2019 17:04:23: #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 17:04:23: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:04:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:04:28: 11000000 INFO @ Sun, 02 Jun 2019 17:04:34: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:04:34: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:04:34: #1 total tags in treatment: 11595806 INFO @ Sun, 02 Jun 2019 17:04:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:04:34: #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 17:04:34: #1 tags after filtering in treatment: 11595806 INFO @ Sun, 02 Jun 2019 17:04:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:04:34: #1 finished! INFO @ Sun, 02 Jun 2019 17:04:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:04:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:04:35: #2 number of paired peaks: 309 WARNING @ Sun, 02 Jun 2019 17:04:35: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sun, 02 Jun 2019 17:04:35: start model_add_line... INFO @ Sun, 02 Jun 2019 17:04:35: start X-correlation... INFO @ Sun, 02 Jun 2019 17:04:35: end of X-cor INFO @ Sun, 02 Jun 2019 17:04:35: #2 finished! INFO @ Sun, 02 Jun 2019 17:04:35: #2 predicted fragment length is 53 bps INFO @ Sun, 02 Jun 2019 17:04:35: #2 alternative fragment length(s) may be 2,53,571 bps INFO @ Sun, 02 Jun 2019 17:04:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.05_model.r WARNING @ Sun, 02 Jun 2019 17:04:35: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:04:35: #2 You may need to consider one of the other alternative d(s): 2,53,571 WARNING @ Sun, 02 Jun 2019 17:04:35: #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 17:04:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:04:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:04:49: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:04:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:05:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:05:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:05:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.20_summits.bed INFO @ Sun, 02 Jun 2019 17:05:05: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (168 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:05:06: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:05:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:05:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:05:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.10_summits.bed INFO @ Sun, 02 Jun 2019 17:05:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (375 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:05:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:05:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:05:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257709/SRX257709.05_summits.bed INFO @ Sun, 02 Jun 2019 17:05:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (578 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。