Job ID = 1293847 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,858,993 reads read : 3,717,986 reads written : 1,858,993 reads 0-length : 1,858,993 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: 00:01:00 1858993 reads; of these: 1858993 (100.00%) were unpaired; of these: 489187 (26.31%) aligned 0 times 521212 (28.04%) aligned exactly 1 time 848594 (45.65%) aligned >1 times 73.69% overall alignment rate Time searching: 00:01:00 Overall time: 00:01:00 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] 443479 / 1369806 = 0.3238 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 02:46:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.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 02:46:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:46:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:46:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.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 02:46:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:46:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:46:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.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 02:46:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:46:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:46:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:46:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:46:08: #1 total tags in treatment: 926327 INFO @ Mon, 03 Jun 2019 02:46:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:46:08: #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 02:46:08: #1 tags after filtering in treatment: 926327 INFO @ Mon, 03 Jun 2019 02:46:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:46:08: #1 finished! INFO @ Mon, 03 Jun 2019 02:46:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:46:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:46:08: #2 number of paired peaks: 1111 INFO @ Mon, 03 Jun 2019 02:46:08: start model_add_line... INFO @ Mon, 03 Jun 2019 02:46:08: start X-correlation... INFO @ Mon, 03 Jun 2019 02:46:08: end of X-cor INFO @ Mon, 03 Jun 2019 02:46:08: #2 finished! INFO @ Mon, 03 Jun 2019 02:46:08: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 02:46:08: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 02:46:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.05_model.r WARNING @ Mon, 03 Jun 2019 02:46:08: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:46:08: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 02:46:08: #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 02:46:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:46:08: #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: 926327 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 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: 926327 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: 926327 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 tags after filtering in treatment: 926327 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: 1111 INFO @ Mon, 03 Jun 2019 02:46:09: start model_add_line... INFO @ Mon, 03 Jun 2019 02:46:09: #2 number of paired peaks: 1111 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: 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 48 bps INFO @ Mon, 03 Jun 2019 02:46:09: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 02:46:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.10_model.r 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 48 bps INFO @ Mon, 03 Jun 2019 02:46:09: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 02:46:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.20_model.r WARNING @ Mon, 03 Jun 2019 02:46:09: #2 Since the d (48) 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): 48 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... WARNING @ Mon, 03 Jun 2019 02:46:09: #2 Since the d (48) 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): 48 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 02:46:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:46:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:46:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:46:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:46:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:46:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.05_summits.bed INFO @ Mon, 03 Jun 2019 02:46:12: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (894 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 02:46:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:46:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:46:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.20_summits.bed INFO @ Mon, 03 Jun 2019 02:46:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:46:14: Done! INFO @ Mon, 03 Jun 2019 02:46:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:46:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299928/SRX1299928.10_summits.bed INFO @ Mon, 03 Jun 2019 02:46:14: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (367 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (663 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。