Job ID = 1292478 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,803,024 reads read : 11,803,024 reads written : 11,803,024 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: 00:03:44 11803024 reads; of these: 11803024 (100.00%) were unpaired; of these: 352865 (2.99%) aligned 0 times 8195820 (69.44%) aligned exactly 1 time 3254339 (27.57%) aligned >1 times 97.01% 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] 2408892 / 11450159 = 0.2104 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 19:12:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.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 19:12:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:12:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:12:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.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 19:12:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:12:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:12:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.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 19:12:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:12:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:12:13: 1000000 INFO @ Sun, 02 Jun 2019 19:12:13: 1000000 INFO @ Sun, 02 Jun 2019 19:12:14: 1000000 INFO @ Sun, 02 Jun 2019 19:12:21: 2000000 INFO @ Sun, 02 Jun 2019 19:12:21: 2000000 INFO @ Sun, 02 Jun 2019 19:12:23: 2000000 INFO @ Sun, 02 Jun 2019 19:12:29: 3000000 INFO @ Sun, 02 Jun 2019 19:12:29: 3000000 INFO @ Sun, 02 Jun 2019 19:12:33: 3000000 INFO @ Sun, 02 Jun 2019 19:12:36: 4000000 INFO @ Sun, 02 Jun 2019 19:12:36: 4000000 INFO @ Sun, 02 Jun 2019 19:12:42: 4000000 INFO @ Sun, 02 Jun 2019 19:12:44: 5000000 INFO @ Sun, 02 Jun 2019 19:12:44: 5000000 INFO @ Sun, 02 Jun 2019 19:12:50: 5000000 INFO @ Sun, 02 Jun 2019 19:12:52: 6000000 INFO @ Sun, 02 Jun 2019 19:12:52: 6000000 INFO @ Sun, 02 Jun 2019 19:12:59: 6000000 INFO @ Sun, 02 Jun 2019 19:13:00: 7000000 INFO @ Sun, 02 Jun 2019 19:13:00: 7000000 INFO @ Sun, 02 Jun 2019 19:13:07: 8000000 INFO @ Sun, 02 Jun 2019 19:13:07: 8000000 INFO @ Sun, 02 Jun 2019 19:13:08: 7000000 INFO @ Sun, 02 Jun 2019 19:13:15: 9000000 INFO @ Sun, 02 Jun 2019 19:13:15: 9000000 INFO @ Sun, 02 Jun 2019 19:13:15: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:13:15: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:13:15: #1 total tags in treatment: 9041267 INFO @ Sun, 02 Jun 2019 19:13:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:13:15: #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 19:13:15: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:13:15: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:13:15: #1 total tags in treatment: 9041267 INFO @ Sun, 02 Jun 2019 19:13:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:13:15: #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 19:13:16: #1 tags after filtering in treatment: 9041267 INFO @ Sun, 02 Jun 2019 19:13:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:13:16: #1 finished! INFO @ Sun, 02 Jun 2019 19:13:16: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:13:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:13:16: #1 tags after filtering in treatment: 9041267 INFO @ Sun, 02 Jun 2019 19:13:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:13:16: #1 finished! INFO @ Sun, 02 Jun 2019 19:13:16: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:13:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:13:16: #2 number of paired peaks: 861 WARNING @ Sun, 02 Jun 2019 19:13:16: Fewer paired peaks (861) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 861 pairs to build model! INFO @ Sun, 02 Jun 2019 19:13:16: start model_add_line... INFO @ Sun, 02 Jun 2019 19:13:17: #2 number of paired peaks: 861 WARNING @ Sun, 02 Jun 2019 19:13:17: Fewer paired peaks (861) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 861 pairs to build model! INFO @ Sun, 02 Jun 2019 19:13:17: start model_add_line... INFO @ Sun, 02 Jun 2019 19:13:17: start X-correlation... INFO @ Sun, 02 Jun 2019 19:13:17: end of X-cor INFO @ Sun, 02 Jun 2019 19:13:17: #2 finished! INFO @ Sun, 02 Jun 2019 19:13:17: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 19:13:17: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 02 Jun 2019 19:13:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.20_model.r WARNING @ Sun, 02 Jun 2019 19:13:17: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:13:17: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 02 Jun 2019 19:13:17: #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 19:13:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:13:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:13:17: start X-correlation... INFO @ Sun, 02 Jun 2019 19:13:17: end of X-cor INFO @ Sun, 02 Jun 2019 19:13:17: #2 finished! INFO @ Sun, 02 Jun 2019 19:13:17: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 19:13:17: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 02 Jun 2019 19:13:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.05_model.r WARNING @ Sun, 02 Jun 2019 19:13:17: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:13:17: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 02 Jun 2019 19:13:17: #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 19:13:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:13:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:13:17: 8000000 INFO @ Sun, 02 Jun 2019 19:13:25: 9000000 INFO @ Sun, 02 Jun 2019 19:13:26: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:13:26: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:13:26: #1 total tags in treatment: 9041267 INFO @ Sun, 02 Jun 2019 19:13:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:13:26: #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 19:13:26: #1 tags after filtering in treatment: 9041267 INFO @ Sun, 02 Jun 2019 19:13:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:13:26: #1 finished! INFO @ Sun, 02 Jun 2019 19:13:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:13:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:13:27: #2 number of paired peaks: 861 WARNING @ Sun, 02 Jun 2019 19:13:27: Fewer paired peaks (861) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 861 pairs to build model! INFO @ Sun, 02 Jun 2019 19:13:27: start model_add_line... INFO @ Sun, 02 Jun 2019 19:13:27: start X-correlation... INFO @ Sun, 02 Jun 2019 19:13:27: end of X-cor INFO @ Sun, 02 Jun 2019 19:13:27: #2 finished! INFO @ Sun, 02 Jun 2019 19:13:27: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 19:13:27: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 02 Jun 2019 19:13:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.10_model.r WARNING @ Sun, 02 Jun 2019 19:13:27: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:13:27: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 02 Jun 2019 19:13:27: #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 19:13:27: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:13:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:13:42: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:13:42: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:13:52: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:13:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:13:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:13:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.05_summits.bed INFO @ Sun, 02 Jun 2019 19:13:54: Done! INFO @ Sun, 02 Jun 2019 19:13:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:13:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:13:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.20_summits.bed INFO @ Sun, 02 Jun 2019 19:13:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (878 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (232 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:14:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:14:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:14:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466466/SRX466466.10_summits.bed INFO @ Sun, 02 Jun 2019 19:14:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (516 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。