Job ID = 1293090 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,177,705 reads read : 50,355,410 reads written : 25,177,705 reads 0-length : 25,177,705 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: 00:07:46 25177705 reads; of these: 25177705 (100.00%) were unpaired; of these: 1802556 (7.16%) aligned 0 times 19825189 (78.74%) aligned exactly 1 time 3549960 (14.10%) aligned >1 times 92.84% overall alignment rate Time searching: 00:07:46 Overall time: 00:07:46 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 12 files... [bam_rmdupse_core] 7739252 / 23375149 = 0.3311 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 22:01:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.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 22:01:51: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:01:51: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:01:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.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 22:01:51: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:01:51: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:01:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.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 22:01:51: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:01:51: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:02:01: 1000000 INFO @ Sun, 02 Jun 2019 22:02:01: 1000000 INFO @ Sun, 02 Jun 2019 22:02:02: 1000000 INFO @ Sun, 02 Jun 2019 22:02:10: 2000000 INFO @ Sun, 02 Jun 2019 22:02:10: 2000000 INFO @ Sun, 02 Jun 2019 22:02:13: 2000000 INFO @ Sun, 02 Jun 2019 22:02:19: 3000000 INFO @ Sun, 02 Jun 2019 22:02:19: 3000000 INFO @ Sun, 02 Jun 2019 22:02:24: 3000000 INFO @ Sun, 02 Jun 2019 22:02:28: 4000000 INFO @ Sun, 02 Jun 2019 22:02:28: 4000000 INFO @ Sun, 02 Jun 2019 22:02:34: 4000000 INFO @ Sun, 02 Jun 2019 22:02:37: 5000000 INFO @ Sun, 02 Jun 2019 22:02:37: 5000000 INFO @ Sun, 02 Jun 2019 22:02:44: 5000000 INFO @ Sun, 02 Jun 2019 22:02:46: 6000000 INFO @ Sun, 02 Jun 2019 22:02:46: 6000000 INFO @ Sun, 02 Jun 2019 22:02:54: 6000000 INFO @ Sun, 02 Jun 2019 22:02:54: 7000000 INFO @ Sun, 02 Jun 2019 22:02:54: 7000000 INFO @ Sun, 02 Jun 2019 22:03:03: 8000000 INFO @ Sun, 02 Jun 2019 22:03:03: 8000000 INFO @ Sun, 02 Jun 2019 22:03:04: 7000000 INFO @ Sun, 02 Jun 2019 22:03:12: 9000000 INFO @ Sun, 02 Jun 2019 22:03:13: 9000000 INFO @ Sun, 02 Jun 2019 22:03:14: 8000000 INFO @ Sun, 02 Jun 2019 22:03:21: 10000000 INFO @ Sun, 02 Jun 2019 22:03:21: 10000000 INFO @ Sun, 02 Jun 2019 22:03:23: 9000000 INFO @ Sun, 02 Jun 2019 22:03:30: 11000000 INFO @ Sun, 02 Jun 2019 22:03:30: 11000000 INFO @ Sun, 02 Jun 2019 22:03:33: 10000000 INFO @ Sun, 02 Jun 2019 22:03:38: 12000000 INFO @ Sun, 02 Jun 2019 22:03:39: 12000000 INFO @ Sun, 02 Jun 2019 22:03:43: 11000000 INFO @ Sun, 02 Jun 2019 22:03:47: 13000000 INFO @ Sun, 02 Jun 2019 22:03:48: 13000000 INFO @ Sun, 02 Jun 2019 22:03:53: 12000000 INFO @ Sun, 02 Jun 2019 22:03:56: 14000000 INFO @ Sun, 02 Jun 2019 22:03:57: 14000000 INFO @ Sun, 02 Jun 2019 22:04:03: 13000000 INFO @ Sun, 02 Jun 2019 22:04:05: 15000000 INFO @ Sun, 02 Jun 2019 22:04:07: 15000000 INFO @ Sun, 02 Jun 2019 22:04:11: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:04:11: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:04:11: #1 total tags in treatment: 15635897 INFO @ Sun, 02 Jun 2019 22:04:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:04:11: #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 22:04:12: #1 tags after filtering in treatment: 15635897 INFO @ Sun, 02 Jun 2019 22:04:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:04:12: #1 finished! INFO @ Sun, 02 Jun 2019 22:04:12: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:04:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:04:13: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:04:13: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:04:13: #1 total tags in treatment: 15635897 INFO @ Sun, 02 Jun 2019 22:04:13: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:04:13: #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 22:04:13: 14000000 INFO @ Sun, 02 Jun 2019 22:04:13: #1 tags after filtering in treatment: 15635897 INFO @ Sun, 02 Jun 2019 22:04:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:04:13: #1 finished! INFO @ Sun, 02 Jun 2019 22:04:13: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:04:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:04:13: #2 number of paired peaks: 200 WARNING @ Sun, 02 Jun 2019 22:04:13: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Sun, 02 Jun 2019 22:04:13: start model_add_line... INFO @ Sun, 02 Jun 2019 22:04:13: start X-correlation... INFO @ Sun, 02 Jun 2019 22:04:13: end of X-cor INFO @ Sun, 02 Jun 2019 22:04:13: #2 finished! INFO @ Sun, 02 Jun 2019 22:04:13: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 22:04:13: #2 alternative fragment length(s) may be 2,49,579 bps INFO @ Sun, 02 Jun 2019 22:04:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.05_model.r WARNING @ Sun, 02 Jun 2019 22:04:13: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:04:13: #2 You may need to consider one of the other alternative d(s): 2,49,579 WARNING @ Sun, 02 Jun 2019 22:04:13: #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 22:04:13: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:04:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:04:14: #2 number of paired peaks: 200 WARNING @ Sun, 02 Jun 2019 22:04:14: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Sun, 02 Jun 2019 22:04:14: start model_add_line... INFO @ Sun, 02 Jun 2019 22:04:14: start X-correlation... INFO @ Sun, 02 Jun 2019 22:04:15: end of X-cor INFO @ Sun, 02 Jun 2019 22:04:15: #2 finished! INFO @ Sun, 02 Jun 2019 22:04:15: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 22:04:15: #2 alternative fragment length(s) may be 2,49,579 bps INFO @ Sun, 02 Jun 2019 22:04:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.20_model.r WARNING @ Sun, 02 Jun 2019 22:04:15: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:04:15: #2 You may need to consider one of the other alternative d(s): 2,49,579 WARNING @ Sun, 02 Jun 2019 22:04:15: #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 22:04:15: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:04:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:04:24: 15000000 INFO @ Sun, 02 Jun 2019 22:04:31: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:04:31: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:04:31: #1 total tags in treatment: 15635897 INFO @ Sun, 02 Jun 2019 22:04:31: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:04:31: #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 22:04:31: #1 tags after filtering in treatment: 15635897 INFO @ Sun, 02 Jun 2019 22:04:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:04:31: #1 finished! INFO @ Sun, 02 Jun 2019 22:04:31: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:04:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:04:32: #2 number of paired peaks: 200 WARNING @ Sun, 02 Jun 2019 22:04:32: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Sun, 02 Jun 2019 22:04:32: start model_add_line... INFO @ Sun, 02 Jun 2019 22:04:32: start X-correlation... INFO @ Sun, 02 Jun 2019 22:04:32: end of X-cor INFO @ Sun, 02 Jun 2019 22:04:32: #2 finished! INFO @ Sun, 02 Jun 2019 22:04:32: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 22:04:32: #2 alternative fragment length(s) may be 2,49,579 bps INFO @ Sun, 02 Jun 2019 22:04:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.10_model.r WARNING @ Sun, 02 Jun 2019 22:04:32: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:04:32: #2 You may need to consider one of the other alternative d(s): 2,49,579 WARNING @ Sun, 02 Jun 2019 22:04:32: #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 22:04:32: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:04:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:04:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:04:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:05:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:05:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:05:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.05_summits.bed INFO @ Sun, 02 Jun 2019 22:05:13: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (801 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:05:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:05:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:05:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.20_summits.bed INFO @ Sun, 02 Jun 2019 22:05:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (122 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:05:15: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:05:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:05:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:05:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5073498/SRX5073498.10_summits.bed INFO @ Sun, 02 Jun 2019 22:05:35: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (327 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。