Job ID = 1295831 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,410,998 reads read : 8,410,998 reads written : 8,410,998 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: 00:03:40 8410998 reads; of these: 8410998 (100.00%) were unpaired; of these: 212862 (2.53%) aligned 0 times 6028033 (71.67%) aligned exactly 1 time 2170103 (25.80%) aligned >1 times 97.47% overall alignment rate Time searching: 00:03:40 Overall time: 00:03:40 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 433644 / 8198136 = 0.0529 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 @ Mon, 03 Jun 2019 15:50:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 15:50:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:50:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:50:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 15:50:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:50:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:50:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 15:50:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:50:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:50:22: 1000000 INFO @ Mon, 03 Jun 2019 15:50:22: 1000000 INFO @ Mon, 03 Jun 2019 15:50:23: 1000000 INFO @ Mon, 03 Jun 2019 15:50:29: 2000000 INFO @ Mon, 03 Jun 2019 15:50:29: 2000000 INFO @ Mon, 03 Jun 2019 15:50:33: 2000000 INFO @ Mon, 03 Jun 2019 15:50:36: 3000000 INFO @ Mon, 03 Jun 2019 15:50:37: 3000000 INFO @ Mon, 03 Jun 2019 15:50:42: 3000000 INFO @ Mon, 03 Jun 2019 15:50:44: 4000000 INFO @ Mon, 03 Jun 2019 15:50:44: 4000000 INFO @ Mon, 03 Jun 2019 15:50:50: 4000000 INFO @ Mon, 03 Jun 2019 15:50:51: 5000000 INFO @ Mon, 03 Jun 2019 15:50:51: 5000000 INFO @ Mon, 03 Jun 2019 15:50:58: 6000000 INFO @ Mon, 03 Jun 2019 15:50:58: 5000000 INFO @ Mon, 03 Jun 2019 15:50:59: 6000000 INFO @ Mon, 03 Jun 2019 15:51:05: 7000000 INFO @ Mon, 03 Jun 2019 15:51:06: 7000000 INFO @ Mon, 03 Jun 2019 15:51:06: 6000000 INFO @ Mon, 03 Jun 2019 15:51:11: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:51:11: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:51:11: #1 total tags in treatment: 7764492 INFO @ Mon, 03 Jun 2019 15:51:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:51:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:51:11: #1 tags after filtering in treatment: 7764492 INFO @ Mon, 03 Jun 2019 15:51:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:51:11: #1 finished! INFO @ Mon, 03 Jun 2019 15:51:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:51:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:51:12: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:51:12: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:51:12: #1 total tags in treatment: 7764492 INFO @ Mon, 03 Jun 2019 15:51:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:51:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:51:12: #1 tags after filtering in treatment: 7764492 INFO @ Mon, 03 Jun 2019 15:51:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:51:12: #1 finished! INFO @ Mon, 03 Jun 2019 15:51:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:51:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:51:12: #2 number of paired peaks: 196 WARNING @ Mon, 03 Jun 2019 15:51:12: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Mon, 03 Jun 2019 15:51:12: start model_add_line... INFO @ Mon, 03 Jun 2019 15:51:12: start X-correlation... INFO @ Mon, 03 Jun 2019 15:51:12: end of X-cor INFO @ Mon, 03 Jun 2019 15:51:12: #2 finished! INFO @ Mon, 03 Jun 2019 15:51:12: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 15:51:12: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 15:51:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.20_model.r WARNING @ Mon, 03 Jun 2019 15:51:12: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:51:12: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 15:51:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 15:51:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:51:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:51:13: #2 number of paired peaks: 196 WARNING @ Mon, 03 Jun 2019 15:51:13: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Mon, 03 Jun 2019 15:51:13: start model_add_line... INFO @ Mon, 03 Jun 2019 15:51:13: start X-correlation... INFO @ Mon, 03 Jun 2019 15:51:13: end of X-cor INFO @ Mon, 03 Jun 2019 15:51:13: #2 finished! INFO @ Mon, 03 Jun 2019 15:51:13: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 15:51:13: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 15:51:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.10_model.r WARNING @ Mon, 03 Jun 2019 15:51:13: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:51:13: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 15:51:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 15:51:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:51:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:51:15: 7000000 INFO @ Mon, 03 Jun 2019 15:51:21: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:51:21: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:51:21: #1 total tags in treatment: 7764492 INFO @ Mon, 03 Jun 2019 15:51:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:51:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:51:21: #1 tags after filtering in treatment: 7764492 INFO @ Mon, 03 Jun 2019 15:51:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:51:21: #1 finished! INFO @ Mon, 03 Jun 2019 15:51:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:51:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:51:22: #2 number of paired peaks: 196 WARNING @ Mon, 03 Jun 2019 15:51:22: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Mon, 03 Jun 2019 15:51:22: start model_add_line... INFO @ Mon, 03 Jun 2019 15:51:22: start X-correlation... INFO @ Mon, 03 Jun 2019 15:51:22: end of X-cor INFO @ Mon, 03 Jun 2019 15:51:22: #2 finished! INFO @ Mon, 03 Jun 2019 15:51:22: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 15:51:22: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 15:51:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.05_model.r WARNING @ Mon, 03 Jun 2019 15:51:22: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:51:22: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 15:51:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 15:51:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:51:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:51:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:51:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:51:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:51:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:51:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:51:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.20_summits.bed INFO @ Mon, 03 Jun 2019 15:51:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (621 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:51:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:51:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:51:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.10_summits.bed INFO @ Mon, 03 Jun 2019 15:51:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (989 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:51:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:51:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:51:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX457601/SRX457601.05_summits.bed INFO @ Mon, 03 Jun 2019 15:51:55: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1274 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。