Job ID = 1292813 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,809,537 reads read : 13,809,537 reads written : 13,809,537 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: 00:02:37 13809537 reads; of these: 13809537 (100.00%) were unpaired; of these: 2269442 (16.43%) aligned 0 times 9709671 (70.31%) aligned exactly 1 time 1830424 (13.25%) aligned >1 times 83.57% overall alignment rate Time searching: 00:02:37 Overall time: 00:02:37 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_rmdupse_core] 1988102 / 11540095 = 0.1723 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 20:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.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 20:42:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:42:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.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 20:42:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:42:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.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 20:42:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:42:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:42:24: 1000000 INFO @ Sun, 02 Jun 2019 20:42:25: 1000000 INFO @ Sun, 02 Jun 2019 20:42:25: 1000000 INFO @ Sun, 02 Jun 2019 20:42:31: 2000000 INFO @ Sun, 02 Jun 2019 20:42:32: 2000000 INFO @ Sun, 02 Jun 2019 20:42:33: 2000000 INFO @ Sun, 02 Jun 2019 20:42:37: 3000000 INFO @ Sun, 02 Jun 2019 20:42:39: 3000000 INFO @ Sun, 02 Jun 2019 20:42:41: 3000000 INFO @ Sun, 02 Jun 2019 20:42:44: 4000000 INFO @ Sun, 02 Jun 2019 20:42:46: 4000000 INFO @ Sun, 02 Jun 2019 20:42:49: 4000000 INFO @ Sun, 02 Jun 2019 20:42:50: 5000000 INFO @ Sun, 02 Jun 2019 20:42:53: 5000000 INFO @ Sun, 02 Jun 2019 20:42:56: 5000000 INFO @ Sun, 02 Jun 2019 20:42:57: 6000000 INFO @ Sun, 02 Jun 2019 20:43:00: 6000000 INFO @ Sun, 02 Jun 2019 20:43:04: 7000000 INFO @ Sun, 02 Jun 2019 20:43:04: 6000000 INFO @ Sun, 02 Jun 2019 20:43:07: 7000000 INFO @ Sun, 02 Jun 2019 20:43:10: 8000000 INFO @ Sun, 02 Jun 2019 20:43:12: 7000000 INFO @ Sun, 02 Jun 2019 20:43:14: 8000000 INFO @ Sun, 02 Jun 2019 20:43:17: 9000000 INFO @ Sun, 02 Jun 2019 20:43:20: 8000000 INFO @ Sun, 02 Jun 2019 20:43:20: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:43:20: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:43:20: #1 total tags in treatment: 9551993 INFO @ Sun, 02 Jun 2019 20:43:20: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:43:20: #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 20:43:21: #1 tags after filtering in treatment: 9551993 INFO @ Sun, 02 Jun 2019 20:43:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:43:21: #1 finished! INFO @ Sun, 02 Jun 2019 20:43:21: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:43:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:43:22: #2 number of paired peaks: 297 WARNING @ Sun, 02 Jun 2019 20:43:22: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Sun, 02 Jun 2019 20:43:22: start model_add_line... INFO @ Sun, 02 Jun 2019 20:43:22: 9000000 INFO @ Sun, 02 Jun 2019 20:43:22: start X-correlation... INFO @ Sun, 02 Jun 2019 20:43:22: end of X-cor INFO @ Sun, 02 Jun 2019 20:43:22: #2 finished! INFO @ Sun, 02 Jun 2019 20:43:22: #2 predicted fragment length is 40 bps INFO @ Sun, 02 Jun 2019 20:43:22: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sun, 02 Jun 2019 20:43:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.05_model.r WARNING @ Sun, 02 Jun 2019 20:43:22: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:43:22: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sun, 02 Jun 2019 20:43:22: #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 20:43:22: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:43:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:43:26: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:43:26: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:43:26: #1 total tags in treatment: 9551993 INFO @ Sun, 02 Jun 2019 20:43:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:43:26: #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 20:43:26: #1 tags after filtering in treatment: 9551993 INFO @ Sun, 02 Jun 2019 20:43:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:43:26: #1 finished! INFO @ Sun, 02 Jun 2019 20:43:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:43:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:43:27: #2 number of paired peaks: 297 WARNING @ Sun, 02 Jun 2019 20:43:27: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Sun, 02 Jun 2019 20:43:27: start model_add_line... INFO @ Sun, 02 Jun 2019 20:43:27: start X-correlation... INFO @ Sun, 02 Jun 2019 20:43:27: end of X-cor INFO @ Sun, 02 Jun 2019 20:43:27: #2 finished! INFO @ Sun, 02 Jun 2019 20:43:27: #2 predicted fragment length is 40 bps INFO @ Sun, 02 Jun 2019 20:43:27: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sun, 02 Jun 2019 20:43:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.10_model.r WARNING @ Sun, 02 Jun 2019 20:43:27: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:43:27: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sun, 02 Jun 2019 20:43:27: #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 20:43:27: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:43:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:43:27: 9000000 INFO @ Sun, 02 Jun 2019 20:43:32: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:43:32: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:43:32: #1 total tags in treatment: 9551993 INFO @ Sun, 02 Jun 2019 20:43:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:43:32: #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 20:43:32: #1 tags after filtering in treatment: 9551993 INFO @ Sun, 02 Jun 2019 20:43:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:43:32: #1 finished! INFO @ Sun, 02 Jun 2019 20:43:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:43:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:43:33: #2 number of paired peaks: 297 WARNING @ Sun, 02 Jun 2019 20:43:33: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Sun, 02 Jun 2019 20:43:33: start model_add_line... INFO @ Sun, 02 Jun 2019 20:43:33: start X-correlation... INFO @ Sun, 02 Jun 2019 20:43:33: end of X-cor INFO @ Sun, 02 Jun 2019 20:43:33: #2 finished! INFO @ Sun, 02 Jun 2019 20:43:33: #2 predicted fragment length is 40 bps INFO @ Sun, 02 Jun 2019 20:43:33: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sun, 02 Jun 2019 20:43:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.20_model.r WARNING @ Sun, 02 Jun 2019 20:43:33: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:43:33: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sun, 02 Jun 2019 20:43:33: #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 20:43:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:43:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:43:47: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:43:52: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:43:58: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:44:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:44:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:44:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.05_summits.bed INFO @ Sun, 02 Jun 2019 20:44:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (590 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:44:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:44:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:44:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.10_summits.bed INFO @ Sun, 02 Jun 2019 20:44:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (282 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:44:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:44:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:44:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495058/SRX495058.20_summits.bed INFO @ Sun, 02 Jun 2019 20:44:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (100 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。