Job ID = 1293850 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,639,581 reads read : 3,279,162 reads written : 1,639,581 reads 0-length : 1,639,581 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:34 1639581 reads; of these: 1639581 (100.00%) were unpaired; of these: 959746 (58.54%) aligned 0 times 273874 (16.70%) aligned exactly 1 time 405961 (24.76%) aligned >1 times 41.46% overall alignment rate Time searching: 00:00:35 Overall time: 00:00:35 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] 174903 / 679835 = 0.2573 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 02:46:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.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 02:46:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:46:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:46:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.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 02:46:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:46:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:46:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.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 02:46:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:46:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:46:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:46:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:46:09: #1 total tags in treatment: 504932 INFO @ Mon, 03 Jun 2019 02:46:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:46:09: #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 02:46:09: #1 tags after filtering in treatment: 504932 INFO @ Mon, 03 Jun 2019 02:46:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:46:09: #1 finished! INFO @ Mon, 03 Jun 2019 02:46:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:46:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:46:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:46:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:46:09: #1 total tags in treatment: 504932 INFO @ Mon, 03 Jun 2019 02:46:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:46:09: #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 02:46:09: #1 tags after filtering in treatment: 504932 INFO @ Mon, 03 Jun 2019 02:46:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:46:09: #1 finished! INFO @ Mon, 03 Jun 2019 02:46:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:46:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:46:09: #2 number of paired peaks: 1637 INFO @ Mon, 03 Jun 2019 02:46:09: start model_add_line... INFO @ Mon, 03 Jun 2019 02:46:09: start X-correlation... INFO @ Mon, 03 Jun 2019 02:46:09: end of X-cor INFO @ Mon, 03 Jun 2019 02:46:09: #2 finished! INFO @ Mon, 03 Jun 2019 02:46:09: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 02:46:09: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 02:46:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.10_model.r WARNING @ Mon, 03 Jun 2019 02:46:09: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:46:09: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 02:46:09: #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 02:46:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:46:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:46:09: #2 number of paired peaks: 1637 INFO @ Mon, 03 Jun 2019 02:46:09: start model_add_line... INFO @ Mon, 03 Jun 2019 02:46:09: start X-correlation... INFO @ Mon, 03 Jun 2019 02:46:09: end of X-cor INFO @ Mon, 03 Jun 2019 02:46:09: #2 finished! INFO @ Mon, 03 Jun 2019 02:46:09: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 02:46:09: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 02:46:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.20_model.r WARNING @ Mon, 03 Jun 2019 02:46:09: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:46:09: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 02:46:09: #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 02:46:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:46:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:46:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:46:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:46:09: #1 total tags in treatment: 504932 INFO @ Mon, 03 Jun 2019 02:46:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:46:09: #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 02:46:09: #1 tags after filtering in treatment: 504932 INFO @ Mon, 03 Jun 2019 02:46:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:46:09: #1 finished! INFO @ Mon, 03 Jun 2019 02:46:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:46:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:46:09: #2 number of paired peaks: 1637 INFO @ Mon, 03 Jun 2019 02:46:09: start model_add_line... INFO @ Mon, 03 Jun 2019 02:46:09: start X-correlation... INFO @ Mon, 03 Jun 2019 02:46:09: end of X-cor INFO @ Mon, 03 Jun 2019 02:46:09: #2 finished! INFO @ Mon, 03 Jun 2019 02:46:09: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 02:46:09: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 02:46:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.05_model.r WARNING @ Mon, 03 Jun 2019 02:46:09: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:46:09: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 02:46:09: #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 02:46:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:46:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:46:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:46:11: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 02:46:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:46:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:46:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:46:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.10_summits.bed INFO @ Mon, 03 Jun 2019 02:46:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (652 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:46:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:46:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:46:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.20_summits.bed INFO @ Mon, 03 Jun 2019 02:46:11: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (310 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:46:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:46:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:46:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299929/SRX1299929.05_summits.bed INFO @ Mon, 03 Jun 2019 02:46:12: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1078 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。