Job ID = 1293226 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,495,804 reads read : 1,495,804 reads written : 1,495,804 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: 00:00:32 1495804 reads; of these: 1495804 (100.00%) were unpaired; of these: 37597 (2.51%) aligned 0 times 1236151 (82.64%) aligned exactly 1 time 222056 (14.85%) aligned >1 times 97.49% overall alignment rate Time searching: 00:00:32 Overall time: 00:00:32 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] 28637 / 1458207 = 0.0196 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 22:24:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.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 22:24:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:24:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:24:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.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 22:24:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:24:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:24:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.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 22:24:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:24:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:24:39: 1000000 INFO @ Sun, 02 Jun 2019 22:24:40: 1000000 INFO @ Sun, 02 Jun 2019 22:24:40: 1000000 INFO @ Sun, 02 Jun 2019 22:24:43: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:24:43: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:24:43: #1 total tags in treatment: 1429570 INFO @ Sun, 02 Jun 2019 22:24:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:24:43: #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 22:24:43: #1 tags after filtering in treatment: 1429570 INFO @ Sun, 02 Jun 2019 22:24:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:24:43: #1 finished! INFO @ Sun, 02 Jun 2019 22:24:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:24:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:24:43: #2 number of paired peaks: 363 WARNING @ Sun, 02 Jun 2019 22:24:43: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Sun, 02 Jun 2019 22:24:43: start model_add_line... INFO @ Sun, 02 Jun 2019 22:24:43: start X-correlation... INFO @ Sun, 02 Jun 2019 22:24:43: end of X-cor INFO @ Sun, 02 Jun 2019 22:24:43: #2 finished! INFO @ Sun, 02 Jun 2019 22:24:43: #2 predicted fragment length is 57 bps INFO @ Sun, 02 Jun 2019 22:24:43: #2 alternative fragment length(s) may be 57,128 bps INFO @ Sun, 02 Jun 2019 22:24:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.10_model.r WARNING @ Sun, 02 Jun 2019 22:24:43: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:24:43: #2 You may need to consider one of the other alternative d(s): 57,128 WARNING @ Sun, 02 Jun 2019 22:24:43: #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 22:24:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:24:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:24:44: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:24:44: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:24:44: #1 total tags in treatment: 1429570 INFO @ Sun, 02 Jun 2019 22:24:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:24:44: #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 22:24:44: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:24:44: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:24:44: #1 total tags in treatment: 1429570 INFO @ Sun, 02 Jun 2019 22:24:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:24:44: #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 22:24:44: #1 tags after filtering in treatment: 1429570 INFO @ Sun, 02 Jun 2019 22:24:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:24:44: #1 finished! INFO @ Sun, 02 Jun 2019 22:24:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:24:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:24:44: #1 tags after filtering in treatment: 1429570 INFO @ Sun, 02 Jun 2019 22:24:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:24:44: #1 finished! INFO @ Sun, 02 Jun 2019 22:24:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:24:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:24:45: #2 number of paired peaks: 363 WARNING @ Sun, 02 Jun 2019 22:24:45: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Sun, 02 Jun 2019 22:24:45: start model_add_line... INFO @ Sun, 02 Jun 2019 22:24:45: start X-correlation... INFO @ Sun, 02 Jun 2019 22:24:45: #2 number of paired peaks: 363 WARNING @ Sun, 02 Jun 2019 22:24:45: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Sun, 02 Jun 2019 22:24:45: start model_add_line... INFO @ Sun, 02 Jun 2019 22:24:45: end of X-cor INFO @ Sun, 02 Jun 2019 22:24:45: #2 finished! INFO @ Sun, 02 Jun 2019 22:24:45: #2 predicted fragment length is 57 bps INFO @ Sun, 02 Jun 2019 22:24:45: #2 alternative fragment length(s) may be 57,128 bps INFO @ Sun, 02 Jun 2019 22:24:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.05_model.r INFO @ Sun, 02 Jun 2019 22:24:45: start X-correlation... WARNING @ Sun, 02 Jun 2019 22:24:45: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:24:45: #2 You may need to consider one of the other alternative d(s): 57,128 WARNING @ Sun, 02 Jun 2019 22:24:45: #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 22:24:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:24:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:24:45: end of X-cor INFO @ Sun, 02 Jun 2019 22:24:45: #2 finished! INFO @ Sun, 02 Jun 2019 22:24:45: #2 predicted fragment length is 57 bps INFO @ Sun, 02 Jun 2019 22:24:45: #2 alternative fragment length(s) may be 57,128 bps INFO @ Sun, 02 Jun 2019 22:24:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.20_model.r WARNING @ Sun, 02 Jun 2019 22:24:45: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:24:45: #2 You may need to consider one of the other alternative d(s): 57,128 WARNING @ Sun, 02 Jun 2019 22:24:45: #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 22:24:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:24:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:24:47: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:24:49: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:24:49: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:24:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:24:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:24:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.10_summits.bed INFO @ Sun, 02 Jun 2019 22:24:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (94 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:24:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:24:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:24:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.20_summits.bed INFO @ Sun, 02 Jun 2019 22:24:51: Done! INFO @ Sun, 02 Jun 2019 22:24:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:24:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:24:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX554715/SRX554715.05_summits.bed INFO @ Sun, 02 Jun 2019 22:24:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (31 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (224 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。