Job ID = 1292897 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,534,775 reads read : 11,069,550 reads written : 5,534,775 reads 0-length : 5,534,775 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: 00:01:41 5534775 reads; of these: 5534775 (100.00%) were unpaired; of these: 157508 (2.85%) aligned 0 times 4255606 (76.89%) aligned exactly 1 time 1121661 (20.27%) aligned >1 times 97.15% overall alignment rate Time searching: 00:01:41 Overall time: 00:01:41 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] 531939 / 5377267 = 0.0989 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 21:04:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.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 21:04:22: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:04:22: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:04:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.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 21:04:22: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:04:22: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:04:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.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 21:04:22: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:04:22: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:04:30: 1000000 INFO @ Sun, 02 Jun 2019 21:04:30: 1000000 INFO @ Sun, 02 Jun 2019 21:04:32: 1000000 INFO @ Sun, 02 Jun 2019 21:04:39: 2000000 INFO @ Sun, 02 Jun 2019 21:04:39: 2000000 INFO @ Sun, 02 Jun 2019 21:04:41: 2000000 INFO @ Sun, 02 Jun 2019 21:04:47: 3000000 INFO @ Sun, 02 Jun 2019 21:04:47: 3000000 INFO @ Sun, 02 Jun 2019 21:04:51: 3000000 INFO @ Sun, 02 Jun 2019 21:04:55: 4000000 INFO @ Sun, 02 Jun 2019 21:04:55: 4000000 INFO @ Sun, 02 Jun 2019 21:05:00: 4000000 INFO @ Sun, 02 Jun 2019 21:05:02: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:05:02: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:05:02: #1 total tags in treatment: 4845328 INFO @ Sun, 02 Jun 2019 21:05:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:05:02: #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 21:05:02: #1 tags after filtering in treatment: 4845328 INFO @ Sun, 02 Jun 2019 21:05:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:05:02: #1 finished! INFO @ Sun, 02 Jun 2019 21:05:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:05:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:05:02: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:05:02: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:05:02: #1 total tags in treatment: 4845328 INFO @ Sun, 02 Jun 2019 21:05:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:05:02: #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 21:05:02: #1 tags after filtering in treatment: 4845328 INFO @ Sun, 02 Jun 2019 21:05:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:05:02: #1 finished! INFO @ Sun, 02 Jun 2019 21:05:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:05:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:05:02: #2 number of paired peaks: 522 WARNING @ Sun, 02 Jun 2019 21:05:02: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Sun, 02 Jun 2019 21:05:02: start model_add_line... INFO @ Sun, 02 Jun 2019 21:05:02: start X-correlation... INFO @ Sun, 02 Jun 2019 21:05:02: end of X-cor INFO @ Sun, 02 Jun 2019 21:05:02: #2 finished! INFO @ Sun, 02 Jun 2019 21:05:02: #2 predicted fragment length is 57 bps INFO @ Sun, 02 Jun 2019 21:05:02: #2 alternative fragment length(s) may be 57 bps INFO @ Sun, 02 Jun 2019 21:05:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.10_model.r WARNING @ Sun, 02 Jun 2019 21:05:02: #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 21:05:02: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sun, 02 Jun 2019 21:05:02: #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 21:05:02: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:05:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:05:03: #2 number of paired peaks: 522 WARNING @ Sun, 02 Jun 2019 21:05:03: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Sun, 02 Jun 2019 21:05:03: start model_add_line... INFO @ Sun, 02 Jun 2019 21:05:03: start X-correlation... INFO @ Sun, 02 Jun 2019 21:05:03: end of X-cor INFO @ Sun, 02 Jun 2019 21:05:03: #2 finished! INFO @ Sun, 02 Jun 2019 21:05:03: #2 predicted fragment length is 57 bps INFO @ Sun, 02 Jun 2019 21:05:03: #2 alternative fragment length(s) may be 57 bps INFO @ Sun, 02 Jun 2019 21:05:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.20_model.r WARNING @ Sun, 02 Jun 2019 21:05:03: #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 21:05:03: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sun, 02 Jun 2019 21:05:03: #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 21:05:03: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:05:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:05:08: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:05:08: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:05:08: #1 total tags in treatment: 4845328 INFO @ Sun, 02 Jun 2019 21:05:08: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:05:08: #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 21:05:08: #1 tags after filtering in treatment: 4845328 INFO @ Sun, 02 Jun 2019 21:05:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:05:08: #1 finished! INFO @ Sun, 02 Jun 2019 21:05:08: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:05:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:05:08: #2 number of paired peaks: 522 WARNING @ Sun, 02 Jun 2019 21:05:08: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Sun, 02 Jun 2019 21:05:08: start model_add_line... INFO @ Sun, 02 Jun 2019 21:05:08: start X-correlation... INFO @ Sun, 02 Jun 2019 21:05:08: end of X-cor INFO @ Sun, 02 Jun 2019 21:05:08: #2 finished! INFO @ Sun, 02 Jun 2019 21:05:08: #2 predicted fragment length is 57 bps INFO @ Sun, 02 Jun 2019 21:05:08: #2 alternative fragment length(s) may be 57 bps INFO @ Sun, 02 Jun 2019 21:05:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.05_model.r WARNING @ Sun, 02 Jun 2019 21:05:08: #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 21:05:08: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sun, 02 Jun 2019 21:05:08: #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 21:05:08: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:05:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:05:19: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:05:19: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:05:24: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:05:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:05:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:05:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.10_summits.bed INFO @ Sun, 02 Jun 2019 21:05:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (304 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:05:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:05:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:05:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.20_summits.bed INFO @ Sun, 02 Jun 2019 21:05:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (145 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:05:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:05:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:05:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020698/SRX5020698.05_summits.bed INFO @ Sun, 02 Jun 2019 21:05:32: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (599 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。