Job ID = 1292116 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,557,793 reads read : 6,557,793 reads written : 6,557,793 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: 00:01:13 6557793 reads; of these: 6557793 (100.00%) were unpaired; of these: 77911 (1.19%) aligned 0 times 5401753 (82.37%) aligned exactly 1 time 1078129 (16.44%) aligned >1 times 98.81% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 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] 650399 / 6479882 = 0.1004 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 17:31:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.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 17:31:14: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:31:14: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:31:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.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 17:31:14: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:31:14: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:31:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.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 17:31:14: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:31:14: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:31:21: 1000000 INFO @ Sun, 02 Jun 2019 17:31:21: 1000000 INFO @ Sun, 02 Jun 2019 17:31:21: 1000000 INFO @ Sun, 02 Jun 2019 17:31:29: 2000000 INFO @ Sun, 02 Jun 2019 17:31:29: 2000000 INFO @ Sun, 02 Jun 2019 17:31:29: 2000000 INFO @ Sun, 02 Jun 2019 17:31:36: 3000000 INFO @ Sun, 02 Jun 2019 17:31:36: 3000000 INFO @ Sun, 02 Jun 2019 17:31:36: 3000000 INFO @ Sun, 02 Jun 2019 17:31:43: 4000000 INFO @ Sun, 02 Jun 2019 17:31:43: 4000000 INFO @ Sun, 02 Jun 2019 17:31:44: 4000000 INFO @ Sun, 02 Jun 2019 17:31:51: 5000000 INFO @ Sun, 02 Jun 2019 17:31:51: 5000000 INFO @ Sun, 02 Jun 2019 17:31:51: 5000000 INFO @ Sun, 02 Jun 2019 17:31:57: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 17:31:57: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 17:31:57: #1 total tags in treatment: 5829483 INFO @ Sun, 02 Jun 2019 17:31:57: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:31:57: #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 17:31:57: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 17:31:57: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 17:31:57: #1 total tags in treatment: 5829483 INFO @ Sun, 02 Jun 2019 17:31:57: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:31:57: #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 17:31:57: #1 tags after filtering in treatment: 5829483 INFO @ Sun, 02 Jun 2019 17:31:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:31:57: #1 finished! INFO @ Sun, 02 Jun 2019 17:31:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:31:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:31:57: #1 tags after filtering in treatment: 5829483 INFO @ Sun, 02 Jun 2019 17:31:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:31:57: #1 finished! INFO @ Sun, 02 Jun 2019 17:31:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:31:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:31:57: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 17:31:57: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 17:31:57: #1 total tags in treatment: 5829483 INFO @ Sun, 02 Jun 2019 17:31:57: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:31:57: #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 17:31:57: #1 tags after filtering in treatment: 5829483 INFO @ Sun, 02 Jun 2019 17:31:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:31:57: #1 finished! INFO @ Sun, 02 Jun 2019 17:31:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:31:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:31:57: #2 number of paired peaks: 382 WARNING @ Sun, 02 Jun 2019 17:31:57: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Sun, 02 Jun 2019 17:31:57: start model_add_line... INFO @ Sun, 02 Jun 2019 17:31:57: #2 number of paired peaks: 382 WARNING @ Sun, 02 Jun 2019 17:31:57: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Sun, 02 Jun 2019 17:31:57: start model_add_line... INFO @ Sun, 02 Jun 2019 17:31:58: start X-correlation... INFO @ Sun, 02 Jun 2019 17:31:58: start X-correlation... INFO @ Sun, 02 Jun 2019 17:31:58: end of X-cor INFO @ Sun, 02 Jun 2019 17:31:58: #2 finished! INFO @ Sun, 02 Jun 2019 17:31:58: #2 predicted fragment length is 31 bps INFO @ Sun, 02 Jun 2019 17:31:58: #2 alternative fragment length(s) may be 3,31,463,565 bps INFO @ Sun, 02 Jun 2019 17:31:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.05_model.r INFO @ Sun, 02 Jun 2019 17:31:58: end of X-cor INFO @ Sun, 02 Jun 2019 17:31:58: #2 finished! INFO @ Sun, 02 Jun 2019 17:31:58: #2 predicted fragment length is 31 bps INFO @ Sun, 02 Jun 2019 17:31:58: #2 alternative fragment length(s) may be 3,31,463,565 bps INFO @ Sun, 02 Jun 2019 17:31:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.20_model.r WARNING @ Sun, 02 Jun 2019 17:31:58: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:31:58: #2 You may need to consider one of the other alternative d(s): 3,31,463,565 WARNING @ Sun, 02 Jun 2019 17:31:58: #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 17:31:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:31:58: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 02 Jun 2019 17:31:58: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:31:58: #2 You may need to consider one of the other alternative d(s): 3,31,463,565 WARNING @ Sun, 02 Jun 2019 17:31:58: #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 17:31:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:31:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:31:58: #2 number of paired peaks: 382 WARNING @ Sun, 02 Jun 2019 17:31:58: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Sun, 02 Jun 2019 17:31:58: start model_add_line... INFO @ Sun, 02 Jun 2019 17:31:58: start X-correlation... INFO @ Sun, 02 Jun 2019 17:31:58: end of X-cor INFO @ Sun, 02 Jun 2019 17:31:58: #2 finished! INFO @ Sun, 02 Jun 2019 17:31:58: #2 predicted fragment length is 31 bps INFO @ Sun, 02 Jun 2019 17:31:58: #2 alternative fragment length(s) may be 3,31,463,565 bps INFO @ Sun, 02 Jun 2019 17:31:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.10_model.r WARNING @ Sun, 02 Jun 2019 17:31:58: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:31:58: #2 You may need to consider one of the other alternative d(s): 3,31,463,565 WARNING @ Sun, 02 Jun 2019 17:31:58: #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 17:31:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:31:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:32:14: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:32:14: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:32:15: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:32:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:32:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:32:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.05_summits.bed INFO @ Sun, 02 Jun 2019 17:32:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (511 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:32:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:32:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:32:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.20_summits.bed INFO @ Sun, 02 Jun 2019 17:32:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (61 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:32:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:32:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:32:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331153/SRX331153.10_summits.bed INFO @ Sun, 02 Jun 2019 17:32:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (251 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。