Job ID = 1292939 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,967,421 reads read : 15,967,421 reads written : 15,967,421 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:19 15967421 reads; of these: 15967421 (100.00%) were unpaired; of these: 487929 (3.06%) aligned 0 times 13057758 (81.78%) aligned exactly 1 time 2421734 (15.17%) aligned >1 times 96.94% overall alignment rate Time searching: 00:04:20 Overall time: 00:04:20 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] 1447444 / 15479492 = 0.0935 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 21:16:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.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 21:16:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:16:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:16:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.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 21:16:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.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 21:16:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:16:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:16:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:16:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:17:06: 1000000 INFO @ Sun, 02 Jun 2019 21:17:07: 1000000 INFO @ Sun, 02 Jun 2019 21:17:07: 1000000 INFO @ Sun, 02 Jun 2019 21:17:16: 2000000 INFO @ Sun, 02 Jun 2019 21:17:16: 2000000 INFO @ Sun, 02 Jun 2019 21:17:16: 2000000 INFO @ Sun, 02 Jun 2019 21:17:25: 3000000 INFO @ Sun, 02 Jun 2019 21:17:25: 3000000 INFO @ Sun, 02 Jun 2019 21:17:25: 3000000 INFO @ Sun, 02 Jun 2019 21:17:35: 4000000 INFO @ Sun, 02 Jun 2019 21:17:35: 4000000 INFO @ Sun, 02 Jun 2019 21:17:35: 4000000 INFO @ Sun, 02 Jun 2019 21:17:44: 5000000 INFO @ Sun, 02 Jun 2019 21:17:44: 5000000 INFO @ Sun, 02 Jun 2019 21:17:44: 5000000 INFO @ Sun, 02 Jun 2019 21:17:53: 6000000 INFO @ Sun, 02 Jun 2019 21:17:54: 6000000 INFO @ Sun, 02 Jun 2019 21:17:54: 6000000 INFO @ Sun, 02 Jun 2019 21:18:02: 7000000 INFO @ Sun, 02 Jun 2019 21:18:03: 7000000 INFO @ Sun, 02 Jun 2019 21:18:03: 7000000 INFO @ Sun, 02 Jun 2019 21:18:11: 8000000 INFO @ Sun, 02 Jun 2019 21:18:12: 8000000 INFO @ Sun, 02 Jun 2019 21:18:12: 8000000 INFO @ Sun, 02 Jun 2019 21:18:20: 9000000 INFO @ Sun, 02 Jun 2019 21:18:22: 9000000 INFO @ Sun, 02 Jun 2019 21:18:22: 9000000 INFO @ Sun, 02 Jun 2019 21:18:29: 10000000 INFO @ Sun, 02 Jun 2019 21:18:31: 10000000 INFO @ Sun, 02 Jun 2019 21:18:31: 10000000 INFO @ Sun, 02 Jun 2019 21:18:38: 11000000 INFO @ Sun, 02 Jun 2019 21:18:40: 11000000 INFO @ Sun, 02 Jun 2019 21:18:40: 11000000 INFO @ Sun, 02 Jun 2019 21:18:47: 12000000 INFO @ Sun, 02 Jun 2019 21:18:50: 12000000 INFO @ Sun, 02 Jun 2019 21:18:50: 12000000 INFO @ Sun, 02 Jun 2019 21:18:56: 13000000 INFO @ Sun, 02 Jun 2019 21:18:59: 13000000 INFO @ Sun, 02 Jun 2019 21:18:59: 13000000 INFO @ Sun, 02 Jun 2019 21:19:05: 14000000 INFO @ Sun, 02 Jun 2019 21:19:06: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:19:06: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:19:06: #1 total tags in treatment: 14032048 INFO @ Sun, 02 Jun 2019 21:19:06: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:19:06: #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 21:19:06: #1 tags after filtering in treatment: 14032048 INFO @ Sun, 02 Jun 2019 21:19:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:19:06: #1 finished! INFO @ Sun, 02 Jun 2019 21:19:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:19:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:19:07: #2 number of paired peaks: 237 WARNING @ Sun, 02 Jun 2019 21:19:07: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Sun, 02 Jun 2019 21:19:07: start model_add_line... INFO @ Sun, 02 Jun 2019 21:19:07: start X-correlation... INFO @ Sun, 02 Jun 2019 21:19:07: end of X-cor INFO @ Sun, 02 Jun 2019 21:19:07: #2 finished! INFO @ Sun, 02 Jun 2019 21:19:07: #2 predicted fragment length is 55 bps INFO @ Sun, 02 Jun 2019 21:19:07: #2 alternative fragment length(s) may be 3,55,559,571 bps INFO @ Sun, 02 Jun 2019 21:19:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.10_model.r WARNING @ Sun, 02 Jun 2019 21:19:07: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:19:07: #2 You may need to consider one of the other alternative d(s): 3,55,559,571 WARNING @ Sun, 02 Jun 2019 21:19:07: #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 21:19:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:19:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:19:08: 14000000 INFO @ Sun, 02 Jun 2019 21:19:08: 14000000 INFO @ Sun, 02 Jun 2019 21:19:09: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:19:09: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:19:09: #1 total tags in treatment: 14032048 INFO @ Sun, 02 Jun 2019 21:19:09: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:19:09: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:19:09: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:19:09: #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 21:19:09: #1 total tags in treatment: 14032048 INFO @ Sun, 02 Jun 2019 21:19:09: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:19:09: #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 21:19:09: #1 tags after filtering in treatment: 14032048 INFO @ Sun, 02 Jun 2019 21:19:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:19:09: #1 finished! INFO @ Sun, 02 Jun 2019 21:19:09: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:19:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:19:09: #1 tags after filtering in treatment: 14032048 INFO @ Sun, 02 Jun 2019 21:19:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:19:09: #1 finished! INFO @ Sun, 02 Jun 2019 21:19:09: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:19:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:19:10: #2 number of paired peaks: 237 WARNING @ Sun, 02 Jun 2019 21:19:10: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Sun, 02 Jun 2019 21:19:10: start model_add_line... INFO @ Sun, 02 Jun 2019 21:19:10: #2 number of paired peaks: 237 WARNING @ Sun, 02 Jun 2019 21:19:10: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Sun, 02 Jun 2019 21:19:10: start model_add_line... INFO @ Sun, 02 Jun 2019 21:19:10: start X-correlation... INFO @ Sun, 02 Jun 2019 21:19:10: start X-correlation... INFO @ Sun, 02 Jun 2019 21:19:10: end of X-cor INFO @ Sun, 02 Jun 2019 21:19:10: #2 finished! INFO @ Sun, 02 Jun 2019 21:19:10: #2 predicted fragment length is 55 bps INFO @ Sun, 02 Jun 2019 21:19:10: #2 alternative fragment length(s) may be 3,55,559,571 bps INFO @ Sun, 02 Jun 2019 21:19:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.05_model.r INFO @ Sun, 02 Jun 2019 21:19:10: end of X-cor INFO @ Sun, 02 Jun 2019 21:19:10: #2 finished! INFO @ Sun, 02 Jun 2019 21:19:10: #2 predicted fragment length is 55 bps INFO @ Sun, 02 Jun 2019 21:19:10: #2 alternative fragment length(s) may be 3,55,559,571 bps INFO @ Sun, 02 Jun 2019 21:19:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.20_model.r WARNING @ Sun, 02 Jun 2019 21:19:10: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:19:10: #2 You may need to consider one of the other alternative d(s): 3,55,559,571 WARNING @ Sun, 02 Jun 2019 21:19:10: #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 21:19:10: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:19:10: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 02 Jun 2019 21:19:10: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:19:10: #2 You may need to consider one of the other alternative d(s): 3,55,559,571 WARNING @ Sun, 02 Jun 2019 21:19:10: #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 21:19:10: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:19:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:19:42: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:19:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:19:46: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:20:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:20:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:20:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.10_summits.bed INFO @ Sun, 02 Jun 2019 21:20:00: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (339 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:20:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:20:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:20:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.05_summits.bed INFO @ Sun, 02 Jun 2019 21:20:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (606 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:20:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:20:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:20:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020728/SRX5020728.20_summits.bed INFO @ Sun, 02 Jun 2019 21:20:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (156 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。