Job ID = 1292797 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: 00:02:26 13809537 reads; of these: 13809537 (100.00%) were unpaired; of these: 2269458 (16.43%) aligned 0 times 9709618 (70.31%) aligned exactly 1 time 1830461 (13.26%) aligned >1 times 83.57% overall alignment rate Time searching: 00:02:26 Overall time: 00:02:26 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] 1987670 / 11540079 = 0.1722 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 20:33:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.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 20:33:16: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:33:16: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:33:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.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 20:33:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.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 20:33:16: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:33:16: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:33:16: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:33:16: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:33:24: 1000000 INFO @ Sun, 02 Jun 2019 20:33:24: 1000000 INFO @ Sun, 02 Jun 2019 20:33:25: 1000000 INFO @ Sun, 02 Jun 2019 20:33:32: 2000000 INFO @ Sun, 02 Jun 2019 20:33:32: 2000000 INFO @ Sun, 02 Jun 2019 20:33:33: 2000000 INFO @ Sun, 02 Jun 2019 20:33:39: 3000000 INFO @ Sun, 02 Jun 2019 20:33:39: 3000000 INFO @ Sun, 02 Jun 2019 20:33:41: 3000000 INFO @ Sun, 02 Jun 2019 20:33:46: 4000000 INFO @ Sun, 02 Jun 2019 20:33:46: 4000000 INFO @ Sun, 02 Jun 2019 20:33:49: 4000000 INFO @ Sun, 02 Jun 2019 20:33:54: 5000000 INFO @ Sun, 02 Jun 2019 20:33:54: 5000000 INFO @ Sun, 02 Jun 2019 20:33:57: 5000000 INFO @ Sun, 02 Jun 2019 20:34:01: 6000000 INFO @ Sun, 02 Jun 2019 20:34:01: 6000000 INFO @ Sun, 02 Jun 2019 20:34:05: 6000000 INFO @ Sun, 02 Jun 2019 20:34:08: 7000000 INFO @ Sun, 02 Jun 2019 20:34:08: 7000000 INFO @ Sun, 02 Jun 2019 20:34:13: 7000000 INFO @ Sun, 02 Jun 2019 20:34:16: 8000000 INFO @ Sun, 02 Jun 2019 20:34:16: 8000000 INFO @ Sun, 02 Jun 2019 20:34:21: 8000000 INFO @ Sun, 02 Jun 2019 20:34:23: 9000000 INFO @ Sun, 02 Jun 2019 20:34:23: 9000000 INFO @ Sun, 02 Jun 2019 20:34:27: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:34:27: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:34:27: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:34:27: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:34:27: #1 total tags in treatment: 9552409 INFO @ Sun, 02 Jun 2019 20:34:27: #1 total tags in treatment: 9552409 INFO @ Sun, 02 Jun 2019 20:34:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:34:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:34:27: #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 20:34:27: #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 20:34:28: #1 tags after filtering in treatment: 9552409 INFO @ Sun, 02 Jun 2019 20:34:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:34:28: #1 finished! INFO @ Sun, 02 Jun 2019 20:34:28: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:34:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:34:28: #1 tags after filtering in treatment: 9552409 INFO @ Sun, 02 Jun 2019 20:34:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:34:28: #1 finished! INFO @ Sun, 02 Jun 2019 20:34:28: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:34:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:34:28: #2 number of paired peaks: 282 WARNING @ Sun, 02 Jun 2019 20:34:28: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Sun, 02 Jun 2019 20:34:28: start model_add_line... INFO @ Sun, 02 Jun 2019 20:34:28: #2 number of paired peaks: 282 WARNING @ Sun, 02 Jun 2019 20:34:28: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Sun, 02 Jun 2019 20:34:28: start model_add_line... INFO @ Sun, 02 Jun 2019 20:34:28: start X-correlation... INFO @ Sun, 02 Jun 2019 20:34:28: start X-correlation... INFO @ Sun, 02 Jun 2019 20:34:29: end of X-cor INFO @ Sun, 02 Jun 2019 20:34:29: #2 finished! INFO @ Sun, 02 Jun 2019 20:34:29: #2 predicted fragment length is 39 bps INFO @ Sun, 02 Jun 2019 20:34:29: #2 alternative fragment length(s) may be 2,39,571,594 bps INFO @ Sun, 02 Jun 2019 20:34:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.10_model.r INFO @ Sun, 02 Jun 2019 20:34:29: end of X-cor INFO @ Sun, 02 Jun 2019 20:34:29: #2 finished! INFO @ Sun, 02 Jun 2019 20:34:29: #2 predicted fragment length is 39 bps INFO @ Sun, 02 Jun 2019 20:34:29: #2 alternative fragment length(s) may be 2,39,571,594 bps INFO @ Sun, 02 Jun 2019 20:34:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.05_model.r WARNING @ Sun, 02 Jun 2019 20:34:29: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:34:29: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:34:29: #2 You may need to consider one of the other alternative d(s): 2,39,571,594 WARNING @ Sun, 02 Jun 2019 20:34:29: #2 You may need to consider one of the other alternative d(s): 2,39,571,594 WARNING @ Sun, 02 Jun 2019 20:34:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Sun, 02 Jun 2019 20:34:29: #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 20:34:29: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:34:29: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:34:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:34:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:34:29: 9000000 INFO @ Sun, 02 Jun 2019 20:34:34: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:34:34: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:34:34: #1 total tags in treatment: 9552409 INFO @ Sun, 02 Jun 2019 20:34:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:34:34: #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 20:34:34: #1 tags after filtering in treatment: 9552409 INFO @ Sun, 02 Jun 2019 20:34:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:34:34: #1 finished! INFO @ Sun, 02 Jun 2019 20:34:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:34:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:34:35: #2 number of paired peaks: 282 WARNING @ Sun, 02 Jun 2019 20:34:35: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Sun, 02 Jun 2019 20:34:35: start model_add_line... INFO @ Sun, 02 Jun 2019 20:34:35: start X-correlation... INFO @ Sun, 02 Jun 2019 20:34:35: end of X-cor INFO @ Sun, 02 Jun 2019 20:34:35: #2 finished! INFO @ Sun, 02 Jun 2019 20:34:35: #2 predicted fragment length is 39 bps INFO @ Sun, 02 Jun 2019 20:34:35: #2 alternative fragment length(s) may be 2,39,571,594 bps INFO @ Sun, 02 Jun 2019 20:34:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.20_model.r WARNING @ Sun, 02 Jun 2019 20:34:35: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:34:35: #2 You may need to consider one of the other alternative d(s): 2,39,571,594 WARNING @ Sun, 02 Jun 2019 20:34:35: #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 20:34:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:34:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:34:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:34:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:35:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:35:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:35:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:35:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.10_summits.bed INFO @ Sun, 02 Jun 2019 20:35:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (288 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:35:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:35:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:35:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.05_summits.bed INFO @ Sun, 02 Jun 2019 20:35:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (582 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:35:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:35:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:35:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495045/SRX495045.20_summits.bed INFO @ Sun, 02 Jun 2019 20:35:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (92 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。