Job ID = 2589955 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,961,902 reads read : 15,961,902 reads written : 15,961,902 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1163552.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: 00:03:44 15961902 reads; of these: 15961902 (100.00%) were unpaired; of these: 524889 (3.29%) aligned 0 times 13384425 (83.85%) aligned exactly 1 time 2052588 (12.86%) aligned >1 times 96.71% overall alignment rate Time searching: 00:03:44 Overall time: 00:03:44 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] 3251759 / 15437013 = 0.2106 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 18:59:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.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 18:59:28: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:59:28: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:59:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.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 18:59:29: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:59:29: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:59:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.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 18:59:30: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:59:30: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:59:35: 1000000 INFO @ Mon, 12 Aug 2019 18:59:38: 1000000 INFO @ Mon, 12 Aug 2019 18:59:39: 1000000 INFO @ Mon, 12 Aug 2019 18:59:43: 2000000 INFO @ Mon, 12 Aug 2019 18:59:47: 2000000 INFO @ Mon, 12 Aug 2019 18:59:47: 2000000 INFO @ Mon, 12 Aug 2019 18:59:51: 3000000 INFO @ Mon, 12 Aug 2019 18:59:56: 3000000 INFO @ Mon, 12 Aug 2019 18:59:57: 3000000 INFO @ Mon, 12 Aug 2019 18:59:59: 4000000 INFO @ Mon, 12 Aug 2019 19:00:05: 4000000 INFO @ Mon, 12 Aug 2019 19:00:06: 4000000 INFO @ Mon, 12 Aug 2019 19:00:06: 5000000 INFO @ Mon, 12 Aug 2019 19:00:14: 6000000 INFO @ Mon, 12 Aug 2019 19:00:14: 5000000 INFO @ Mon, 12 Aug 2019 19:00:15: 5000000 INFO @ Mon, 12 Aug 2019 19:00:21: 7000000 INFO @ Mon, 12 Aug 2019 19:00:23: 6000000 INFO @ Mon, 12 Aug 2019 19:00:24: 6000000 INFO @ Mon, 12 Aug 2019 19:00:29: 8000000 INFO @ Mon, 12 Aug 2019 19:00:32: 7000000 INFO @ Mon, 12 Aug 2019 19:00:32: 7000000 INFO @ Mon, 12 Aug 2019 19:00:36: 9000000 INFO @ Mon, 12 Aug 2019 19:00:40: 8000000 INFO @ Mon, 12 Aug 2019 19:00:41: 8000000 INFO @ Mon, 12 Aug 2019 19:00:43: 10000000 INFO @ Mon, 12 Aug 2019 19:00:49: 9000000 INFO @ Mon, 12 Aug 2019 19:00:49: 9000000 INFO @ Mon, 12 Aug 2019 19:00:50: 11000000 INFO @ Mon, 12 Aug 2019 19:00:58: 10000000 INFO @ Mon, 12 Aug 2019 19:00:58: 12000000 INFO @ Mon, 12 Aug 2019 19:00:58: 10000000 INFO @ Mon, 12 Aug 2019 19:00:59: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:00:59: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:00:59: #1 total tags in treatment: 12185254 INFO @ Mon, 12 Aug 2019 19:00:59: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:00:59: #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 19:00:59: #1 tags after filtering in treatment: 12185254 INFO @ Mon, 12 Aug 2019 19:00:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:00:59: #1 finished! INFO @ Mon, 12 Aug 2019 19:00:59: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:00:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:01:00: #2 number of paired peaks: 164 WARNING @ Mon, 12 Aug 2019 19:01:00: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Mon, 12 Aug 2019 19:01:00: start model_add_line... INFO @ Mon, 12 Aug 2019 19:01:01: start X-correlation... INFO @ Mon, 12 Aug 2019 19:01:01: end of X-cor INFO @ Mon, 12 Aug 2019 19:01:01: #2 finished! INFO @ Mon, 12 Aug 2019 19:01:01: #2 predicted fragment length is 51 bps INFO @ Mon, 12 Aug 2019 19:01:01: #2 alternative fragment length(s) may be 3,51,551 bps INFO @ Mon, 12 Aug 2019 19:01:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.05_model.r WARNING @ Mon, 12 Aug 2019 19:01:01: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:01:01: #2 You may need to consider one of the other alternative d(s): 3,51,551 WARNING @ Mon, 12 Aug 2019 19:01:01: #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 19:01:01: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:01:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:01:06: 11000000 INFO @ Mon, 12 Aug 2019 19:01:06: 11000000 INFO @ Mon, 12 Aug 2019 19:01:14: 12000000 INFO @ Mon, 12 Aug 2019 19:01:14: 12000000 INFO @ Mon, 12 Aug 2019 19:01:15: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:01:15: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:01:15: #1 total tags in treatment: 12185254 INFO @ Mon, 12 Aug 2019 19:01:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:01:15: #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 19:01:16: #1 tags after filtering in treatment: 12185254 INFO @ Mon, 12 Aug 2019 19:01:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:01:16: #1 finished! INFO @ Mon, 12 Aug 2019 19:01:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:01:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:01:16: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:01:16: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:01:16: #1 total tags in treatment: 12185254 INFO @ Mon, 12 Aug 2019 19:01:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:01:16: #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 19:01:16: #1 tags after filtering in treatment: 12185254 INFO @ Mon, 12 Aug 2019 19:01:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:01:16: #1 finished! INFO @ Mon, 12 Aug 2019 19:01:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:01:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:01:17: #2 number of paired peaks: 164 WARNING @ Mon, 12 Aug 2019 19:01:17: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Mon, 12 Aug 2019 19:01:17: start model_add_line... INFO @ Mon, 12 Aug 2019 19:01:17: start X-correlation... INFO @ Mon, 12 Aug 2019 19:01:17: end of X-cor INFO @ Mon, 12 Aug 2019 19:01:17: #2 finished! INFO @ Mon, 12 Aug 2019 19:01:17: #2 predicted fragment length is 51 bps INFO @ Mon, 12 Aug 2019 19:01:17: #2 alternative fragment length(s) may be 3,51,551 bps INFO @ Mon, 12 Aug 2019 19:01:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.20_model.r WARNING @ Mon, 12 Aug 2019 19:01:17: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:01:17: #2 You may need to consider one of the other alternative d(s): 3,51,551 WARNING @ Mon, 12 Aug 2019 19:01:17: #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 19:01:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:01:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:01:17: #2 number of paired peaks: 164 WARNING @ Mon, 12 Aug 2019 19:01:17: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Mon, 12 Aug 2019 19:01:17: start model_add_line... INFO @ Mon, 12 Aug 2019 19:01:17: start X-correlation... INFO @ Mon, 12 Aug 2019 19:01:17: end of X-cor INFO @ Mon, 12 Aug 2019 19:01:17: #2 finished! INFO @ Mon, 12 Aug 2019 19:01:17: #2 predicted fragment length is 51 bps INFO @ Mon, 12 Aug 2019 19:01:17: #2 alternative fragment length(s) may be 3,51,551 bps INFO @ Mon, 12 Aug 2019 19:01:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.10_model.r WARNING @ Mon, 12 Aug 2019 19:01:17: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:01:17: #2 You may need to consider one of the other alternative d(s): 3,51,551 WARNING @ Mon, 12 Aug 2019 19:01:17: #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 19:01:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:01:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:01:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:01:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:01:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:01:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.05_summits.bed INFO @ Mon, 12 Aug 2019 19:01:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (553 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:01:48: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:01:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:02:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:02:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:02:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.20_summits.bed INFO @ Mon, 12 Aug 2019 19:02:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (119 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:02:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:02:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:02:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466486/SRX466486.10_summits.bed INFO @ Mon, 12 Aug 2019 19:02:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (301 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。