Job ID = 1291782 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,580,230 reads read : 33,160,460 reads written : 16,580,230 reads 0-length : 16,580,230 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: 00:06:32 16580230 reads; of these: 16580230 (100.00%) were unpaired; of these: 296013 (1.79%) aligned 0 times 13442937 (81.08%) aligned exactly 1 time 2841280 (17.14%) aligned >1 times 98.21% overall alignment rate Time searching: 00:06:32 Overall time: 00:06:32 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] 2195948 / 16284217 = 0.1349 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 16:44:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.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 16:44:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:44:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:44:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.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 16:44:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:44:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:44:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.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 16:44:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:44:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:44:47: 1000000 INFO @ Sun, 02 Jun 2019 16:44:50: 1000000 INFO @ Sun, 02 Jun 2019 16:44:50: 1000000 INFO @ Sun, 02 Jun 2019 16:44:56: 2000000 INFO @ Sun, 02 Jun 2019 16:45:00: 2000000 INFO @ Sun, 02 Jun 2019 16:45:02: 2000000 INFO @ Sun, 02 Jun 2019 16:45:06: 3000000 INFO @ Sun, 02 Jun 2019 16:45:10: 3000000 INFO @ Sun, 02 Jun 2019 16:45:14: 3000000 INFO @ Sun, 02 Jun 2019 16:45:15: 4000000 INFO @ Sun, 02 Jun 2019 16:45:20: 4000000 INFO @ Sun, 02 Jun 2019 16:45:24: 5000000 INFO @ Sun, 02 Jun 2019 16:45:26: 4000000 INFO @ Sun, 02 Jun 2019 16:45:30: 5000000 INFO @ Sun, 02 Jun 2019 16:45:33: 6000000 INFO @ Sun, 02 Jun 2019 16:45:37: 5000000 INFO @ Sun, 02 Jun 2019 16:45:40: 6000000 INFO @ Sun, 02 Jun 2019 16:45:42: 7000000 INFO @ Sun, 02 Jun 2019 16:45:48: 6000000 INFO @ Sun, 02 Jun 2019 16:45:50: 7000000 INFO @ Sun, 02 Jun 2019 16:45:52: 8000000 INFO @ Sun, 02 Jun 2019 16:45:58: 7000000 INFO @ Sun, 02 Jun 2019 16:46:00: 8000000 INFO @ Sun, 02 Jun 2019 16:46:01: 9000000 INFO @ Sun, 02 Jun 2019 16:46:09: 8000000 INFO @ Sun, 02 Jun 2019 16:46:09: 9000000 INFO @ Sun, 02 Jun 2019 16:46:10: 10000000 INFO @ Sun, 02 Jun 2019 16:46:19: 10000000 INFO @ Sun, 02 Jun 2019 16:46:19: 11000000 INFO @ Sun, 02 Jun 2019 16:46:20: 9000000 INFO @ Sun, 02 Jun 2019 16:46:28: 12000000 INFO @ Sun, 02 Jun 2019 16:46:28: 11000000 INFO @ Sun, 02 Jun 2019 16:46:30: 10000000 INFO @ Sun, 02 Jun 2019 16:46:37: 13000000 INFO @ Sun, 02 Jun 2019 16:46:38: 12000000 INFO @ Sun, 02 Jun 2019 16:46:39: 11000000 INFO @ Sun, 02 Jun 2019 16:46:46: 14000000 INFO @ Sun, 02 Jun 2019 16:46:47: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 16:46:47: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 16:46:47: #1 total tags in treatment: 14088269 INFO @ Sun, 02 Jun 2019 16:46:47: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:46:47: #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 16:46:47: #1 tags after filtering in treatment: 14088269 INFO @ Sun, 02 Jun 2019 16:46:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:46:47: #1 finished! INFO @ Sun, 02 Jun 2019 16:46:47: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:46:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:46:47: 13000000 INFO @ Sun, 02 Jun 2019 16:46:49: #2 number of paired peaks: 232 WARNING @ Sun, 02 Jun 2019 16:46:49: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Sun, 02 Jun 2019 16:46:49: start model_add_line... INFO @ Sun, 02 Jun 2019 16:46:49: start X-correlation... INFO @ Sun, 02 Jun 2019 16:46:49: end of X-cor INFO @ Sun, 02 Jun 2019 16:46:49: #2 finished! INFO @ Sun, 02 Jun 2019 16:46:49: #2 predicted fragment length is 69 bps INFO @ Sun, 02 Jun 2019 16:46:49: #2 alternative fragment length(s) may be 3,69,576 bps INFO @ Sun, 02 Jun 2019 16:46:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.20_model.r WARNING @ Sun, 02 Jun 2019 16:46:49: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:46:49: #2 You may need to consider one of the other alternative d(s): 3,69,576 WARNING @ Sun, 02 Jun 2019 16:46:49: #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 16:46:49: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:46:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:46:49: 12000000 INFO @ Sun, 02 Jun 2019 16:46:57: 14000000 INFO @ Sun, 02 Jun 2019 16:46:58: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 16:46:58: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 16:46:58: #1 total tags in treatment: 14088269 INFO @ Sun, 02 Jun 2019 16:46:58: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:46:58: #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 16:46:58: #1 tags after filtering in treatment: 14088269 INFO @ Sun, 02 Jun 2019 16:46:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:46:58: #1 finished! INFO @ Sun, 02 Jun 2019 16:46:58: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:46:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:46:59: 13000000 INFO @ Sun, 02 Jun 2019 16:46:59: #2 number of paired peaks: 232 WARNING @ Sun, 02 Jun 2019 16:46:59: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Sun, 02 Jun 2019 16:46:59: start model_add_line... INFO @ Sun, 02 Jun 2019 16:46:59: start X-correlation... INFO @ Sun, 02 Jun 2019 16:46:59: end of X-cor INFO @ Sun, 02 Jun 2019 16:46:59: #2 finished! INFO @ Sun, 02 Jun 2019 16:46:59: #2 predicted fragment length is 69 bps INFO @ Sun, 02 Jun 2019 16:46:59: #2 alternative fragment length(s) may be 3,69,576 bps INFO @ Sun, 02 Jun 2019 16:46:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.05_model.r WARNING @ Sun, 02 Jun 2019 16:46:59: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:46:59: #2 You may need to consider one of the other alternative d(s): 3,69,576 WARNING @ Sun, 02 Jun 2019 16:46:59: #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 16:46:59: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:46:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:47:08: 14000000 INFO @ Sun, 02 Jun 2019 16:47:09: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 16:47:09: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 16:47:09: #1 total tags in treatment: 14088269 INFO @ Sun, 02 Jun 2019 16:47:09: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:47:09: #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 16:47:09: #1 tags after filtering in treatment: 14088269 INFO @ Sun, 02 Jun 2019 16:47:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:47:09: #1 finished! INFO @ Sun, 02 Jun 2019 16:47:09: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:47:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:47:10: #2 number of paired peaks: 232 WARNING @ Sun, 02 Jun 2019 16:47:10: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Sun, 02 Jun 2019 16:47:10: start model_add_line... INFO @ Sun, 02 Jun 2019 16:47:11: start X-correlation... INFO @ Sun, 02 Jun 2019 16:47:11: end of X-cor INFO @ Sun, 02 Jun 2019 16:47:11: #2 finished! INFO @ Sun, 02 Jun 2019 16:47:11: #2 predicted fragment length is 69 bps INFO @ Sun, 02 Jun 2019 16:47:11: #2 alternative fragment length(s) may be 3,69,576 bps INFO @ Sun, 02 Jun 2019 16:47:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.10_model.r WARNING @ Sun, 02 Jun 2019 16:47:11: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:47:11: #2 You may need to consider one of the other alternative d(s): 3,69,576 WARNING @ Sun, 02 Jun 2019 16:47:11: #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 16:47:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:47:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:47:24: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:47:34: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:47:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:47:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:47:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.20_summits.bed INFO @ Sun, 02 Jun 2019 16:47:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (199 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:47:47: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:47:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:47:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:47:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.05_summits.bed INFO @ Sun, 02 Jun 2019 16:47:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (652 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:48:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:48:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:48:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2543053/SRX2543053.10_summits.bed INFO @ Sun, 02 Jun 2019 16:48:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (401 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。