Job ID = 1293073 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,214,457 reads read : 28,428,914 reads written : 14,214,457 reads 0-length : 14,214,457 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: 00:03:52 14214457 reads; of these: 14214457 (100.00%) were unpaired; of these: 217916 (1.53%) aligned 0 times 11521183 (81.05%) aligned exactly 1 time 2475358 (17.41%) aligned >1 times 98.47% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 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] 1284840 / 13996541 = 0.0918 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 21:53:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.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 21:53:01: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:53:01: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:53:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.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 21:53:01: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:53:01: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:53:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.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 21:53:01: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:53:01: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:53:08: 1000000 INFO @ Sun, 02 Jun 2019 21:53:08: 1000000 INFO @ Sun, 02 Jun 2019 21:53:09: 1000000 INFO @ Sun, 02 Jun 2019 21:53:15: 2000000 INFO @ Sun, 02 Jun 2019 21:53:15: 2000000 INFO @ Sun, 02 Jun 2019 21:53:16: 2000000 INFO @ Sun, 02 Jun 2019 21:53:22: 3000000 INFO @ Sun, 02 Jun 2019 21:53:22: 3000000 INFO @ Sun, 02 Jun 2019 21:53:24: 3000000 INFO @ Sun, 02 Jun 2019 21:53:29: 4000000 INFO @ Sun, 02 Jun 2019 21:53:29: 4000000 INFO @ Sun, 02 Jun 2019 21:53:31: 4000000 INFO @ Sun, 02 Jun 2019 21:53:36: 5000000 INFO @ Sun, 02 Jun 2019 21:53:36: 5000000 INFO @ Sun, 02 Jun 2019 21:53:39: 5000000 INFO @ Sun, 02 Jun 2019 21:53:43: 6000000 INFO @ Sun, 02 Jun 2019 21:53:44: 6000000 INFO @ Sun, 02 Jun 2019 21:53:46: 6000000 INFO @ Sun, 02 Jun 2019 21:53:51: 7000000 INFO @ Sun, 02 Jun 2019 21:53:51: 7000000 INFO @ Sun, 02 Jun 2019 21:53:53: 7000000 INFO @ Sun, 02 Jun 2019 21:53:58: 8000000 INFO @ Sun, 02 Jun 2019 21:53:58: 8000000 INFO @ Sun, 02 Jun 2019 21:54:01: 8000000 INFO @ Sun, 02 Jun 2019 21:54:05: 9000000 INFO @ Sun, 02 Jun 2019 21:54:05: 9000000 INFO @ Sun, 02 Jun 2019 21:54:09: 9000000 INFO @ Sun, 02 Jun 2019 21:54:13: 10000000 INFO @ Sun, 02 Jun 2019 21:54:13: 10000000 INFO @ Sun, 02 Jun 2019 21:54:16: 10000000 INFO @ Sun, 02 Jun 2019 21:54:20: 11000000 INFO @ Sun, 02 Jun 2019 21:54:20: 11000000 INFO @ Sun, 02 Jun 2019 21:54:24: 11000000 INFO @ Sun, 02 Jun 2019 21:54:28: 12000000 INFO @ Sun, 02 Jun 2019 21:54:28: 12000000 INFO @ Sun, 02 Jun 2019 21:54:31: 12000000 INFO @ Sun, 02 Jun 2019 21:54:33: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:54:33: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:54:33: #1 total tags in treatment: 12711701 INFO @ Sun, 02 Jun 2019 21:54:33: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:54:33: #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 21:54:33: #1 tags after filtering in treatment: 12711701 INFO @ Sun, 02 Jun 2019 21:54:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:54:33: #1 finished! INFO @ Sun, 02 Jun 2019 21:54:33: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:54:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:54:34: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:54:34: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:54:34: #1 total tags in treatment: 12711701 INFO @ Sun, 02 Jun 2019 21:54:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:54:34: #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 21:54:34: #1 tags after filtering in treatment: 12711701 INFO @ Sun, 02 Jun 2019 21:54:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:54:34: #1 finished! INFO @ Sun, 02 Jun 2019 21:54:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:54:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:54:35: #2 number of paired peaks: 285 WARNING @ Sun, 02 Jun 2019 21:54:35: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Sun, 02 Jun 2019 21:54:35: start model_add_line... INFO @ Sun, 02 Jun 2019 21:54:35: start X-correlation... INFO @ Sun, 02 Jun 2019 21:54:35: end of X-cor INFO @ Sun, 02 Jun 2019 21:54:35: #2 finished! INFO @ Sun, 02 Jun 2019 21:54:35: #2 predicted fragment length is 52 bps INFO @ Sun, 02 Jun 2019 21:54:35: #2 alternative fragment length(s) may be 2,52,575 bps INFO @ Sun, 02 Jun 2019 21:54:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.10_model.r WARNING @ Sun, 02 Jun 2019 21:54:35: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:54:35: #2 You may need to consider one of the other alternative d(s): 2,52,575 WARNING @ Sun, 02 Jun 2019 21:54:35: #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 21:54:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:54:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:54:35: #2 number of paired peaks: 285 WARNING @ Sun, 02 Jun 2019 21:54:35: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Sun, 02 Jun 2019 21:54:35: start model_add_line... INFO @ Sun, 02 Jun 2019 21:54:35: start X-correlation... INFO @ Sun, 02 Jun 2019 21:54:35: end of X-cor INFO @ Sun, 02 Jun 2019 21:54:35: #2 finished! INFO @ Sun, 02 Jun 2019 21:54:35: #2 predicted fragment length is 52 bps INFO @ Sun, 02 Jun 2019 21:54:35: #2 alternative fragment length(s) may be 2,52,575 bps INFO @ Sun, 02 Jun 2019 21:54:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.20_model.r WARNING @ Sun, 02 Jun 2019 21:54:35: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:54:35: #2 You may need to consider one of the other alternative d(s): 2,52,575 WARNING @ Sun, 02 Jun 2019 21:54:35: #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 21:54:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:54:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:54:36: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:54:36: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:54:36: #1 total tags in treatment: 12711701 INFO @ Sun, 02 Jun 2019 21:54:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:54:36: #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 21:54:37: #1 tags after filtering in treatment: 12711701 INFO @ Sun, 02 Jun 2019 21:54:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:54:37: #1 finished! INFO @ Sun, 02 Jun 2019 21:54:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:54:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:54:38: #2 number of paired peaks: 285 WARNING @ Sun, 02 Jun 2019 21:54:38: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Sun, 02 Jun 2019 21:54:38: start model_add_line... INFO @ Sun, 02 Jun 2019 21:54:38: start X-correlation... INFO @ Sun, 02 Jun 2019 21:54:38: end of X-cor INFO @ Sun, 02 Jun 2019 21:54:38: #2 finished! INFO @ Sun, 02 Jun 2019 21:54:38: #2 predicted fragment length is 52 bps INFO @ Sun, 02 Jun 2019 21:54:38: #2 alternative fragment length(s) may be 2,52,575 bps INFO @ Sun, 02 Jun 2019 21:54:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.05_model.r WARNING @ Sun, 02 Jun 2019 21:54:38: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:54:38: #2 You may need to consider one of the other alternative d(s): 2,52,575 WARNING @ Sun, 02 Jun 2019 21:54:38: #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 21:54:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:54:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:55:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:55:08: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:55:10: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:55:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:55:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:55:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.10_summits.bed INFO @ Sun, 02 Jun 2019 21:55:24: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (401 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:55:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:55:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:55:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.20_summits.bed INFO @ Sun, 02 Jun 2019 21:55:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (184 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:55:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:55:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:55:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020835/SRX5020835.05_summits.bed INFO @ Sun, 02 Jun 2019 21:55:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (649 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。