Job ID = 1292523 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,465,976 reads read : 13,465,976 reads written : 13,465,976 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: 00:03:16 13465976 reads; of these: 13465976 (100.00%) were unpaired; of these: 306623 (2.28%) aligned 0 times 10062460 (74.73%) aligned exactly 1 time 3096893 (23.00%) aligned >1 times 97.72% overall alignment rate Time searching: 00:03:16 Overall time: 00:03:16 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] 3312927 / 13159353 = 0.2518 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 19:22:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.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 19:22:27: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:22:27: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:22:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.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 19:22:27: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:22:27: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:22:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.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 19:22:27: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:22:27: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:22:37: 1000000 INFO @ Sun, 02 Jun 2019 19:22:37: 1000000 INFO @ Sun, 02 Jun 2019 19:22:37: 1000000 INFO @ Sun, 02 Jun 2019 19:22:46: 2000000 INFO @ Sun, 02 Jun 2019 19:22:47: 2000000 INFO @ Sun, 02 Jun 2019 19:22:47: 2000000 INFO @ Sun, 02 Jun 2019 19:22:56: 3000000 INFO @ Sun, 02 Jun 2019 19:22:57: 3000000 INFO @ Sun, 02 Jun 2019 19:22:57: 3000000 INFO @ Sun, 02 Jun 2019 19:23:06: 4000000 INFO @ Sun, 02 Jun 2019 19:23:07: 4000000 INFO @ Sun, 02 Jun 2019 19:23:07: 4000000 INFO @ Sun, 02 Jun 2019 19:23:16: 5000000 INFO @ Sun, 02 Jun 2019 19:23:17: 5000000 INFO @ Sun, 02 Jun 2019 19:23:17: 5000000 INFO @ Sun, 02 Jun 2019 19:23:26: 6000000 INFO @ Sun, 02 Jun 2019 19:23:27: 6000000 INFO @ Sun, 02 Jun 2019 19:23:28: 6000000 INFO @ Sun, 02 Jun 2019 19:23:36: 7000000 INFO @ Sun, 02 Jun 2019 19:23:37: 7000000 INFO @ Sun, 02 Jun 2019 19:23:38: 7000000 INFO @ Sun, 02 Jun 2019 19:23:46: 8000000 INFO @ Sun, 02 Jun 2019 19:23:46: 8000000 INFO @ Sun, 02 Jun 2019 19:23:48: 8000000 INFO @ Sun, 02 Jun 2019 19:23:56: 9000000 INFO @ Sun, 02 Jun 2019 19:23:56: 9000000 INFO @ Sun, 02 Jun 2019 19:23:59: 9000000 INFO @ Sun, 02 Jun 2019 19:24:05: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:24:05: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:24:05: #1 total tags in treatment: 9846426 INFO @ Sun, 02 Jun 2019 19:24:05: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:24:05: #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 19:24:05: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:24:05: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:24:05: #1 total tags in treatment: 9846426 INFO @ Sun, 02 Jun 2019 19:24:05: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:24:05: #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 19:24:05: #1 tags after filtering in treatment: 9846426 INFO @ Sun, 02 Jun 2019 19:24:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:24:05: #1 finished! INFO @ Sun, 02 Jun 2019 19:24:05: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:24:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:24:05: #1 tags after filtering in treatment: 9846426 INFO @ Sun, 02 Jun 2019 19:24:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:24:05: #1 finished! INFO @ Sun, 02 Jun 2019 19:24:05: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:24:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:24:06: #2 number of paired peaks: 767 WARNING @ Sun, 02 Jun 2019 19:24:06: Fewer paired peaks (767) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 767 pairs to build model! INFO @ Sun, 02 Jun 2019 19:24:06: start model_add_line... INFO @ Sun, 02 Jun 2019 19:24:06: #2 number of paired peaks: 767 WARNING @ Sun, 02 Jun 2019 19:24:06: Fewer paired peaks (767) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 767 pairs to build model! INFO @ Sun, 02 Jun 2019 19:24:06: start model_add_line... INFO @ Sun, 02 Jun 2019 19:24:06: start X-correlation... INFO @ Sun, 02 Jun 2019 19:24:06: end of X-cor INFO @ Sun, 02 Jun 2019 19:24:06: #2 finished! INFO @ Sun, 02 Jun 2019 19:24:06: #2 predicted fragment length is 42 bps INFO @ Sun, 02 Jun 2019 19:24:06: #2 alternative fragment length(s) may be 2,42 bps INFO @ Sun, 02 Jun 2019 19:24:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.05_model.r WARNING @ Sun, 02 Jun 2019 19:24:06: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:24:06: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Sun, 02 Jun 2019 19:24:06: #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 19:24:06: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:24:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:24:06: start X-correlation... INFO @ Sun, 02 Jun 2019 19:24:06: end of X-cor INFO @ Sun, 02 Jun 2019 19:24:06: #2 finished! INFO @ Sun, 02 Jun 2019 19:24:06: #2 predicted fragment length is 42 bps INFO @ Sun, 02 Jun 2019 19:24:06: #2 alternative fragment length(s) may be 2,42 bps INFO @ Sun, 02 Jun 2019 19:24:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.10_model.r WARNING @ Sun, 02 Jun 2019 19:24:06: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:24:06: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Sun, 02 Jun 2019 19:24:06: #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 19:24:06: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:24:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:24:07: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:24:07: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:24:07: #1 total tags in treatment: 9846426 INFO @ Sun, 02 Jun 2019 19:24:07: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:24:07: #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 19:24:07: #1 tags after filtering in treatment: 9846426 INFO @ Sun, 02 Jun 2019 19:24:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:24:07: #1 finished! INFO @ Sun, 02 Jun 2019 19:24:07: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:24:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:24:08: #2 number of paired peaks: 767 WARNING @ Sun, 02 Jun 2019 19:24:08: Fewer paired peaks (767) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 767 pairs to build model! INFO @ Sun, 02 Jun 2019 19:24:08: start model_add_line... INFO @ Sun, 02 Jun 2019 19:24:08: start X-correlation... INFO @ Sun, 02 Jun 2019 19:24:08: end of X-cor INFO @ Sun, 02 Jun 2019 19:24:08: #2 finished! INFO @ Sun, 02 Jun 2019 19:24:08: #2 predicted fragment length is 42 bps INFO @ Sun, 02 Jun 2019 19:24:08: #2 alternative fragment length(s) may be 2,42 bps INFO @ Sun, 02 Jun 2019 19:24:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.20_model.r WARNING @ Sun, 02 Jun 2019 19:24:08: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:24:08: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Sun, 02 Jun 2019 19:24:08: #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 19:24:08: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:24:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:24:35: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:24:35: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:24:37: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:24:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:24:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:24:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.05_summits.bed INFO @ Sun, 02 Jun 2019 19:24:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (993 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:24:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:24:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:24:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.10_summits.bed INFO @ Sun, 02 Jun 2019 19:24:49: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (476 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:24:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:24:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:24:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466537/SRX466537.20_summits.bed INFO @ Sun, 02 Jun 2019 19:24:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (151 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。