Job ID = 4303045 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,047,878 reads read : 16,047,878 reads written : 16,047,878 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1198442.sra.cache’: 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: 00:00:01 Multiseed full-index search: 00:03:04 16047878 reads; of these: 16047878 (100.00%) were unpaired; of these: 1452017 (9.05%) aligned 0 times 12365357 (77.05%) aligned exactly 1 time 2230504 (13.90%) aligned >1 times 90.95% overall alignment rate Time searching: 00:03:05 Overall time: 00:03:05 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] 1645383 / 14595861 = 0.1127 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:42:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.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 @ Thu, 12 Dec 2019 00:42:03: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:42:03: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:42:10: 1000000 INFO @ Thu, 12 Dec 2019 00:42:17: 2000000 INFO @ Thu, 12 Dec 2019 00:42:25: 3000000 INFO @ Thu, 12 Dec 2019 00:42:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.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 @ Thu, 12 Dec 2019 00:42:32: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:42:32: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:42:33: 4000000 INFO @ Thu, 12 Dec 2019 00:42:40: 1000000 INFO @ Thu, 12 Dec 2019 00:42:40: 5000000 INFO @ Thu, 12 Dec 2019 00:42:47: 2000000 INFO @ Thu, 12 Dec 2019 00:42:48: 6000000 INFO @ Thu, 12 Dec 2019 00:42:55: 3000000 INFO @ Thu, 12 Dec 2019 00:42:55: 7000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:43:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.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 @ Thu, 12 Dec 2019 00:43:02: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:43:02: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:43:03: 4000000 INFO @ Thu, 12 Dec 2019 00:43:03: 8000000 INFO @ Thu, 12 Dec 2019 00:43:10: 1000000 INFO @ Thu, 12 Dec 2019 00:43:11: 5000000 INFO @ Thu, 12 Dec 2019 00:43:11: 9000000 INFO @ Thu, 12 Dec 2019 00:43:18: 2000000 INFO @ Thu, 12 Dec 2019 00:43:19: 6000000 INFO @ Thu, 12 Dec 2019 00:43:19: 10000000 INFO @ Thu, 12 Dec 2019 00:43:27: 3000000 INFO @ Thu, 12 Dec 2019 00:43:27: 11000000 INFO @ Thu, 12 Dec 2019 00:43:27: 7000000 INFO @ Thu, 12 Dec 2019 00:43:35: 4000000 INFO @ Thu, 12 Dec 2019 00:43:35: 12000000 INFO @ Thu, 12 Dec 2019 00:43:35: 8000000 INFO @ Thu, 12 Dec 2019 00:43:42: #1 tag size is determined as 42 bps INFO @ Thu, 12 Dec 2019 00:43:42: #1 tag size = 42 INFO @ Thu, 12 Dec 2019 00:43:42: #1 total tags in treatment: 12950478 INFO @ Thu, 12 Dec 2019 00:43:42: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:43:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:43:42: #1 tags after filtering in treatment: 12950478 INFO @ Thu, 12 Dec 2019 00:43:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:43:42: #1 finished! INFO @ Thu, 12 Dec 2019 00:43:42: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:43:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:43:43: 5000000 INFO @ Thu, 12 Dec 2019 00:43:43: #2 number of paired peaks: 264 WARNING @ Thu, 12 Dec 2019 00:43:43: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Thu, 12 Dec 2019 00:43:43: start model_add_line... INFO @ Thu, 12 Dec 2019 00:43:43: start X-correlation... INFO @ Thu, 12 Dec 2019 00:43:43: end of X-cor INFO @ Thu, 12 Dec 2019 00:43:43: #2 finished! INFO @ Thu, 12 Dec 2019 00:43:43: #2 predicted fragment length is 39 bps INFO @ Thu, 12 Dec 2019 00:43:43: #2 alternative fragment length(s) may be 2,39 bps INFO @ Thu, 12 Dec 2019 00:43:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.05_model.r WARNING @ Thu, 12 Dec 2019 00:43:43: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:43:43: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Thu, 12 Dec 2019 00:43:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:43:43: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:43:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:43:44: 9000000 INFO @ Thu, 12 Dec 2019 00:43:51: 6000000 INFO @ Thu, 12 Dec 2019 00:43:52: 10000000 INFO @ Thu, 12 Dec 2019 00:44:00: 7000000 INFO @ Thu, 12 Dec 2019 00:44:00: 11000000 INFO @ Thu, 12 Dec 2019 00:44:05: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:44:08: 8000000 INFO @ Thu, 12 Dec 2019 00:44:08: 12000000 INFO @ Thu, 12 Dec 2019 00:44:16: #1 tag size is determined as 42 bps INFO @ Thu, 12 Dec 2019 00:44:16: #1 tag size = 42 INFO @ Thu, 12 Dec 2019 00:44:16: #1 total tags in treatment: 12950478 INFO @ Thu, 12 Dec 2019 00:44:16: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:44:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:44:16: 9000000 INFO @ Thu, 12 Dec 2019 00:44:16: #1 tags after filtering in treatment: 12950478 INFO @ Thu, 12 Dec 2019 00:44:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:44:16: #1 finished! INFO @ Thu, 12 Dec 2019 00:44:16: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:44:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:44:17: #2 number of paired peaks: 264 WARNING @ Thu, 12 Dec 2019 00:44:17: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Thu, 12 Dec 2019 00:44:17: start model_add_line... INFO @ Thu, 12 Dec 2019 00:44:17: start X-correlation... INFO @ Thu, 12 Dec 2019 00:44:17: end of X-cor INFO @ Thu, 12 Dec 2019 00:44:17: #2 finished! INFO @ Thu, 12 Dec 2019 00:44:17: #2 predicted fragment length is 39 bps INFO @ Thu, 12 Dec 2019 00:44:17: #2 alternative fragment length(s) may be 2,39 bps INFO @ Thu, 12 Dec 2019 00:44:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.10_model.r WARNING @ Thu, 12 Dec 2019 00:44:17: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:44:17: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Thu, 12 Dec 2019 00:44:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:44:17: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:44:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:44:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:44:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:44:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.05_summits.bed INFO @ Thu, 12 Dec 2019 00:44:18: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (619 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:44:24: 10000000 INFO @ Thu, 12 Dec 2019 00:44:32: 11000000 INFO @ Thu, 12 Dec 2019 00:44:39: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:44:40: 12000000 INFO @ Thu, 12 Dec 2019 00:44:47: #1 tag size is determined as 42 bps INFO @ Thu, 12 Dec 2019 00:44:47: #1 tag size = 42 INFO @ Thu, 12 Dec 2019 00:44:47: #1 total tags in treatment: 12950478 INFO @ Thu, 12 Dec 2019 00:44:47: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:44:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:44:47: #1 tags after filtering in treatment: 12950478 INFO @ Thu, 12 Dec 2019 00:44:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:44:47: #1 finished! INFO @ Thu, 12 Dec 2019 00:44:47: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:44:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:44:48: #2 number of paired peaks: 264 WARNING @ Thu, 12 Dec 2019 00:44:48: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Thu, 12 Dec 2019 00:44:48: start model_add_line... INFO @ Thu, 12 Dec 2019 00:44:48: start X-correlation... INFO @ Thu, 12 Dec 2019 00:44:48: end of X-cor INFO @ Thu, 12 Dec 2019 00:44:48: #2 finished! INFO @ Thu, 12 Dec 2019 00:44:48: #2 predicted fragment length is 39 bps INFO @ Thu, 12 Dec 2019 00:44:48: #2 alternative fragment length(s) may be 2,39 bps INFO @ Thu, 12 Dec 2019 00:44:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.20_model.r WARNING @ Thu, 12 Dec 2019 00:44:48: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:44:48: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Thu, 12 Dec 2019 00:44:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:44:48: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:44:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:44:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:44:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:44:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.10_summits.bed INFO @ Thu, 12 Dec 2019 00:44:51: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (363 records, 4 fields): 297 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:45:09: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:45:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:45:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:45:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494910/SRX494910.20_summits.bed INFO @ Thu, 12 Dec 2019 00:45:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (117 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。