Job ID = 1293851 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,585,104 reads read : 3,170,208 reads written : 1,585,104 reads 0-length : 1,585,104 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: 00:00:51 1585104 reads; of these: 1585104 (100.00%) were unpaired; of these: 413425 (26.08%) aligned 0 times 501712 (31.65%) aligned exactly 1 time 669967 (42.27%) aligned >1 times 73.92% overall alignment rate Time searching: 00:00:51 Overall time: 00:00:51 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] 273036 / 1171679 = 0.2330 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 02:46:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.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 02:46:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:46:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:46:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.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 02:46:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:46:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:46:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.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 02:46:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:46:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:46:36: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:46:36: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:46:36: #1 total tags in treatment: 898643 INFO @ Mon, 03 Jun 2019 02:46:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:46:36: #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 02:46:36: #1 tags after filtering in treatment: 898643 INFO @ Mon, 03 Jun 2019 02:46:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:46:36: #1 finished! INFO @ Mon, 03 Jun 2019 02:46:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:46:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:46:36: #2 number of paired peaks: 1083 INFO @ Mon, 03 Jun 2019 02:46:36: start model_add_line... INFO @ Mon, 03 Jun 2019 02:46:36: start X-correlation... INFO @ Mon, 03 Jun 2019 02:46:36: end of X-cor INFO @ Mon, 03 Jun 2019 02:46:36: #2 finished! INFO @ Mon, 03 Jun 2019 02:46:36: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 02:46:36: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 02:46:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.10_model.r WARNING @ Mon, 03 Jun 2019 02:46:36: #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 02:46:36: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 02:46:36: #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 02:46:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:46:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:46:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:46:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:46:37: #1 total tags in treatment: 898643 INFO @ Mon, 03 Jun 2019 02:46:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:46:37: #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 02:46:37: #1 tags after filtering in treatment: 898643 INFO @ Mon, 03 Jun 2019 02:46:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:46:37: #1 finished! INFO @ Mon, 03 Jun 2019 02:46:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:46:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:46:37: #2 number of paired peaks: 1083 INFO @ Mon, 03 Jun 2019 02:46:37: start model_add_line... INFO @ Mon, 03 Jun 2019 02:46:38: start X-correlation... INFO @ Mon, 03 Jun 2019 02:46:38: end of X-cor INFO @ Mon, 03 Jun 2019 02:46:38: #2 finished! INFO @ Mon, 03 Jun 2019 02:46:38: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 02:46:38: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 02:46:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.20_model.r WARNING @ Mon, 03 Jun 2019 02:46:38: #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 02:46:38: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 02:46:38: #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 02:46:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:46:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:46:38: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:46:38: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:46:38: #1 total tags in treatment: 898643 INFO @ Mon, 03 Jun 2019 02:46:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:46:38: #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 02:46:38: #1 tags after filtering in treatment: 898643 INFO @ Mon, 03 Jun 2019 02:46:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:46:38: #1 finished! INFO @ Mon, 03 Jun 2019 02:46:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:46:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:46:38: #2 number of paired peaks: 1083 INFO @ Mon, 03 Jun 2019 02:46:38: start model_add_line... INFO @ Mon, 03 Jun 2019 02:46:38: start X-correlation... INFO @ Mon, 03 Jun 2019 02:46:38: end of X-cor INFO @ Mon, 03 Jun 2019 02:46:38: #2 finished! INFO @ Mon, 03 Jun 2019 02:46:38: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 02:46:38: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 02:46:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.05_model.r WARNING @ Mon, 03 Jun 2019 02:46:38: #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 02:46:38: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 02:46:38: #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 02:46:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:46:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:46:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:46:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:46:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:46:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:46:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.10_summits.bed INFO @ Mon, 03 Jun 2019 02:46:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:46:41: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (648 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:46:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:46:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:46:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.20_summits.bed INFO @ Mon, 03 Jun 2019 02:46:42: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (375 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:46:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:46:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:46:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299930/SRX1299930.05_summits.bed INFO @ Mon, 03 Jun 2019 02:46:42: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (918 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。