Job ID = 2590178 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,727,987 reads read : 10,727,987 reads written : 10,727,987 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1198598.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: 00:00:00 Multiseed full-index search: 00:02:10 10727987 reads; of these: 10727987 (100.00%) were unpaired; of these: 2100062 (19.58%) aligned 0 times 7379786 (68.79%) aligned exactly 1 time 1248139 (11.63%) aligned >1 times 80.42% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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] 1364280 / 8627925 = 0.1581 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 @ Mon, 12 Aug 2019 19:57:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.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 @ Mon, 12 Aug 2019 19:57:03: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:57:03: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:57:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.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 @ Mon, 12 Aug 2019 19:57:04: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:57:04: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:57:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.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 @ Mon, 12 Aug 2019 19:57:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:57:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:57:12: 1000000 INFO @ Mon, 12 Aug 2019 19:57:12: 1000000 INFO @ Mon, 12 Aug 2019 19:57:12: 1000000 INFO @ Mon, 12 Aug 2019 19:57:19: 2000000 INFO @ Mon, 12 Aug 2019 19:57:19: 2000000 INFO @ Mon, 12 Aug 2019 19:57:20: 2000000 INFO @ Mon, 12 Aug 2019 19:57:26: 3000000 INFO @ Mon, 12 Aug 2019 19:57:27: 3000000 INFO @ Mon, 12 Aug 2019 19:57:29: 3000000 INFO @ Mon, 12 Aug 2019 19:57:33: 4000000 INFO @ Mon, 12 Aug 2019 19:57:34: 4000000 INFO @ Mon, 12 Aug 2019 19:57:37: 4000000 INFO @ Mon, 12 Aug 2019 19:57:40: 5000000 INFO @ Mon, 12 Aug 2019 19:57:41: 5000000 INFO @ Mon, 12 Aug 2019 19:57:46: 5000000 INFO @ Mon, 12 Aug 2019 19:57:47: 6000000 INFO @ Mon, 12 Aug 2019 19:57:49: 6000000 INFO @ Mon, 12 Aug 2019 19:57:55: 7000000 INFO @ Mon, 12 Aug 2019 19:57:55: 6000000 INFO @ Mon, 12 Aug 2019 19:57:56: 7000000 INFO @ Mon, 12 Aug 2019 19:57:56: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:57:56: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:57:56: #1 total tags in treatment: 7263645 INFO @ Mon, 12 Aug 2019 19:57:56: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:57:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:57:57: #1 tags after filtering in treatment: 7263645 INFO @ Mon, 12 Aug 2019 19:57:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:57:57: #1 finished! INFO @ Mon, 12 Aug 2019 19:57:57: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:57:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:57:57: #2 number of paired peaks: 279 WARNING @ Mon, 12 Aug 2019 19:57:57: Fewer paired peaks (279) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 279 pairs to build model! INFO @ Mon, 12 Aug 2019 19:57:57: start model_add_line... INFO @ Mon, 12 Aug 2019 19:57:57: start X-correlation... INFO @ Mon, 12 Aug 2019 19:57:57: end of X-cor INFO @ Mon, 12 Aug 2019 19:57:57: #2 finished! INFO @ Mon, 12 Aug 2019 19:57:57: #2 predicted fragment length is 38 bps INFO @ Mon, 12 Aug 2019 19:57:57: #2 alternative fragment length(s) may be 4,38,437,461,578 bps INFO @ Mon, 12 Aug 2019 19:57:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.20_model.r WARNING @ Mon, 12 Aug 2019 19:57:57: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:57:57: #2 You may need to consider one of the other alternative d(s): 4,38,437,461,578 WARNING @ Mon, 12 Aug 2019 19:57:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:57:57: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:57:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:57:58: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:57:58: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:57:58: #1 total tags in treatment: 7263645 INFO @ Mon, 12 Aug 2019 19:57:58: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:57:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:57:58: #1 tags after filtering in treatment: 7263645 INFO @ Mon, 12 Aug 2019 19:57:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:57:58: #1 finished! INFO @ Mon, 12 Aug 2019 19:57:58: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:57:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:57:59: #2 number of paired peaks: 279 WARNING @ Mon, 12 Aug 2019 19:57:59: Fewer paired peaks (279) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 279 pairs to build model! INFO @ Mon, 12 Aug 2019 19:57:59: start model_add_line... INFO @ Mon, 12 Aug 2019 19:57:59: start X-correlation... INFO @ Mon, 12 Aug 2019 19:57:59: end of X-cor INFO @ Mon, 12 Aug 2019 19:57:59: #2 finished! INFO @ Mon, 12 Aug 2019 19:57:59: #2 predicted fragment length is 38 bps INFO @ Mon, 12 Aug 2019 19:57:59: #2 alternative fragment length(s) may be 4,38,437,461,578 bps INFO @ Mon, 12 Aug 2019 19:57:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.10_model.r WARNING @ Mon, 12 Aug 2019 19:57:59: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:57:59: #2 You may need to consider one of the other alternative d(s): 4,38,437,461,578 WARNING @ Mon, 12 Aug 2019 19:57:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:57:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:57:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:58:03: 7000000 INFO @ Mon, 12 Aug 2019 19:58:05: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:58:05: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:58:05: #1 total tags in treatment: 7263645 INFO @ Mon, 12 Aug 2019 19:58:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:58:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:58:05: #1 tags after filtering in treatment: 7263645 INFO @ Mon, 12 Aug 2019 19:58:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:58:05: #1 finished! INFO @ Mon, 12 Aug 2019 19:58:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:58:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:58:06: #2 number of paired peaks: 279 WARNING @ Mon, 12 Aug 2019 19:58:06: Fewer paired peaks (279) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 279 pairs to build model! INFO @ Mon, 12 Aug 2019 19:58:06: start model_add_line... INFO @ Mon, 12 Aug 2019 19:58:06: start X-correlation... INFO @ Mon, 12 Aug 2019 19:58:06: end of X-cor INFO @ Mon, 12 Aug 2019 19:58:06: #2 finished! INFO @ Mon, 12 Aug 2019 19:58:06: #2 predicted fragment length is 38 bps INFO @ Mon, 12 Aug 2019 19:58:06: #2 alternative fragment length(s) may be 4,38,437,461,578 bps INFO @ Mon, 12 Aug 2019 19:58:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.05_model.r WARNING @ Mon, 12 Aug 2019 19:58:06: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:58:06: #2 You may need to consider one of the other alternative d(s): 4,38,437,461,578 WARNING @ Mon, 12 Aug 2019 19:58:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:58:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:58:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:58:18: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:58:19: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:58:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:58:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:58:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:58:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.20_summits.bed INFO @ Mon, 12 Aug 2019 19:58:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (80 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:58:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:58:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:58:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.10_summits.bed INFO @ Mon, 12 Aug 2019 19:58:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (266 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:58:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:58:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:58:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495066/SRX495066.05_summits.bed INFO @ Mon, 12 Aug 2019 19:58:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (495 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。