Job ID = 1293043 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,511,327 reads read : 25,022,654 reads written : 12,511,327 reads 0-length : 12,511,327 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: 00:05:12 12511327 reads; of these: 12511327 (100.00%) were unpaired; of these: 967286 (7.73%) aligned 0 times 9605634 (76.78%) aligned exactly 1 time 1938407 (15.49%) aligned >1 times 92.27% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 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] 994082 / 11544041 = 0.0861 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 21:41:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.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 21:41:51: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:41:51: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:41:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.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 21:41:51: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:41:51: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:41:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.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 21:41:51: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:41:51: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:42:01: 1000000 INFO @ Sun, 02 Jun 2019 21:42:02: 1000000 INFO @ Sun, 02 Jun 2019 21:42:02: 1000000 INFO @ Sun, 02 Jun 2019 21:42:10: 2000000 INFO @ Sun, 02 Jun 2019 21:42:12: 2000000 INFO @ Sun, 02 Jun 2019 21:42:12: 2000000 INFO @ Sun, 02 Jun 2019 21:42:19: 3000000 INFO @ Sun, 02 Jun 2019 21:42:22: 3000000 INFO @ Sun, 02 Jun 2019 21:42:22: 3000000 INFO @ Sun, 02 Jun 2019 21:42:28: 4000000 INFO @ Sun, 02 Jun 2019 21:42:32: 4000000 INFO @ Sun, 02 Jun 2019 21:42:32: 4000000 INFO @ Sun, 02 Jun 2019 21:42:37: 5000000 INFO @ Sun, 02 Jun 2019 21:42:42: 5000000 INFO @ Sun, 02 Jun 2019 21:42:42: 5000000 INFO @ Sun, 02 Jun 2019 21:42:45: 6000000 INFO @ Sun, 02 Jun 2019 21:42:52: 6000000 INFO @ Sun, 02 Jun 2019 21:42:52: 6000000 INFO @ Sun, 02 Jun 2019 21:42:54: 7000000 INFO @ Sun, 02 Jun 2019 21:43:02: 7000000 INFO @ Sun, 02 Jun 2019 21:43:02: 7000000 INFO @ Sun, 02 Jun 2019 21:43:03: 8000000 INFO @ Sun, 02 Jun 2019 21:43:11: 9000000 INFO @ Sun, 02 Jun 2019 21:43:12: 8000000 INFO @ Sun, 02 Jun 2019 21:43:12: 8000000 INFO @ Sun, 02 Jun 2019 21:43:20: 10000000 INFO @ Sun, 02 Jun 2019 21:43:22: 9000000 INFO @ Sun, 02 Jun 2019 21:43:22: 9000000 INFO @ Sun, 02 Jun 2019 21:43:25: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 21:43:25: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 21:43:25: #1 total tags in treatment: 10549959 INFO @ Sun, 02 Jun 2019 21:43:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:43:25: #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 21:43:25: #1 tags after filtering in treatment: 10549959 INFO @ Sun, 02 Jun 2019 21:43:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:43:25: #1 finished! INFO @ Sun, 02 Jun 2019 21:43:25: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:43:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:43:26: #2 number of paired peaks: 312 WARNING @ Sun, 02 Jun 2019 21:43:26: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Sun, 02 Jun 2019 21:43:26: start model_add_line... INFO @ Sun, 02 Jun 2019 21:43:26: start X-correlation... INFO @ Sun, 02 Jun 2019 21:43:26: end of X-cor INFO @ Sun, 02 Jun 2019 21:43:26: #2 finished! INFO @ Sun, 02 Jun 2019 21:43:26: #2 predicted fragment length is 65 bps INFO @ Sun, 02 Jun 2019 21:43:26: #2 alternative fragment length(s) may be 4,65 bps INFO @ Sun, 02 Jun 2019 21:43:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.10_model.r WARNING @ Sun, 02 Jun 2019 21:43:26: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:43:26: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Sun, 02 Jun 2019 21:43:26: #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 21:43:26: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:43:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:43:32: 10000000 INFO @ Sun, 02 Jun 2019 21:43:32: 10000000 INFO @ Sun, 02 Jun 2019 21:43:37: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 21:43:37: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 21:43:37: #1 total tags in treatment: 10549959 INFO @ Sun, 02 Jun 2019 21:43:37: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:43:37: #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 21:43:37: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 21:43:37: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 21:43:37: #1 total tags in treatment: 10549959 INFO @ Sun, 02 Jun 2019 21:43:37: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:43:37: #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 21:43:38: #1 tags after filtering in treatment: 10549959 INFO @ Sun, 02 Jun 2019 21:43:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:43:38: #1 finished! INFO @ Sun, 02 Jun 2019 21:43:38: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:43:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:43:38: #1 tags after filtering in treatment: 10549959 INFO @ Sun, 02 Jun 2019 21:43:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:43:38: #1 finished! INFO @ Sun, 02 Jun 2019 21:43:38: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:43:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:43:39: #2 number of paired peaks: 312 WARNING @ Sun, 02 Jun 2019 21:43:39: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Sun, 02 Jun 2019 21:43:39: start model_add_line... INFO @ Sun, 02 Jun 2019 21:43:39: #2 number of paired peaks: 312 WARNING @ Sun, 02 Jun 2019 21:43:39: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Sun, 02 Jun 2019 21:43:39: start model_add_line... INFO @ Sun, 02 Jun 2019 21:43:39: start X-correlation... INFO @ Sun, 02 Jun 2019 21:43:39: end of X-cor INFO @ Sun, 02 Jun 2019 21:43:39: #2 finished! INFO @ Sun, 02 Jun 2019 21:43:39: #2 predicted fragment length is 65 bps INFO @ Sun, 02 Jun 2019 21:43:39: #2 alternative fragment length(s) may be 4,65 bps INFO @ Sun, 02 Jun 2019 21:43:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.20_model.r WARNING @ Sun, 02 Jun 2019 21:43:39: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:43:39: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Sun, 02 Jun 2019 21:43:39: #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 21:43:39: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:43:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:43:39: start X-correlation... INFO @ Sun, 02 Jun 2019 21:43:39: end of X-cor INFO @ Sun, 02 Jun 2019 21:43:39: #2 finished! INFO @ Sun, 02 Jun 2019 21:43:39: #2 predicted fragment length is 65 bps INFO @ Sun, 02 Jun 2019 21:43:39: #2 alternative fragment length(s) may be 4,65 bps INFO @ Sun, 02 Jun 2019 21:43:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.05_model.r WARNING @ Sun, 02 Jun 2019 21:43:39: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:43:39: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Sun, 02 Jun 2019 21:43:39: #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 21:43:39: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:43:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:43:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:44:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:44:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:44:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:44:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:44:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.10_summits.bed INFO @ Sun, 02 Jun 2019 21:44:08: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (412 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:44:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:44:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:44:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.05_summits.bed INFO @ Sun, 02 Jun 2019 21:44:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (558 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:44:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:44:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:44:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020807/SRX5020807.20_summits.bed INFO @ Sun, 02 Jun 2019 21:44:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (213 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。