Job ID = 1295515 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,669,643 reads read : 11,669,643 reads written : 11,669,643 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: 00:01:08 11669643 reads; of these: 11669643 (100.00%) were unpaired; of these: 11306376 (96.89%) aligned 0 times 288398 (2.47%) aligned exactly 1 time 74869 (0.64%) aligned >1 times 3.11% overall alignment rate Time searching: 00:01:09 Overall time: 00:01:09 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] 80513 / 363267 = 0.2216 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 14:07:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.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 14:07:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:07:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:07:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.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 14:07:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:07:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:07:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.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 14:07:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:07:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:08:00: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 14:08:00: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 14:08:00: #1 total tags in treatment: 282754 INFO @ Mon, 03 Jun 2019 14:08:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:08:00: #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 14:08:00: #1 tags after filtering in treatment: 282754 INFO @ Mon, 03 Jun 2019 14:08:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:08:00: #1 finished! INFO @ Mon, 03 Jun 2019 14:08:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:08:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:08:00: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 14:08:00: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 14:08:00: #1 total tags in treatment: 282754 INFO @ Mon, 03 Jun 2019 14:08:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:08:00: #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 14:08:00: #1 tags after filtering in treatment: 282754 INFO @ Mon, 03 Jun 2019 14:08:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:08:00: #1 finished! INFO @ Mon, 03 Jun 2019 14:08:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:08:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:08:00: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 14:08:00: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 14:08:00: #1 total tags in treatment: 282754 INFO @ Mon, 03 Jun 2019 14:08:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:08:00: #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 14:08:00: #1 tags after filtering in treatment: 282754 INFO @ Mon, 03 Jun 2019 14:08:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:08:00: #1 finished! INFO @ Mon, 03 Jun 2019 14:08:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:08:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:08:00: #2 number of paired peaks: 3925 INFO @ Mon, 03 Jun 2019 14:08:00: start model_add_line... INFO @ Mon, 03 Jun 2019 14:08:00: start X-correlation... INFO @ Mon, 03 Jun 2019 14:08:00: #2 number of paired peaks: 3925 INFO @ Mon, 03 Jun 2019 14:08:00: start model_add_line... INFO @ Mon, 03 Jun 2019 14:08:00: start X-correlation... INFO @ Mon, 03 Jun 2019 14:08:00: end of X-cor INFO @ Mon, 03 Jun 2019 14:08:00: #2 finished! INFO @ Mon, 03 Jun 2019 14:08:00: #2 predicted fragment length is 35 bps INFO @ Mon, 03 Jun 2019 14:08:00: #2 alternative fragment length(s) may be 35,527,581 bps INFO @ Mon, 03 Jun 2019 14:08:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.05_model.r WARNING @ Mon, 03 Jun 2019 14:08:00: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:08:00: #2 You may need to consider one of the other alternative d(s): 35,527,581 WARNING @ Mon, 03 Jun 2019 14:08:00: #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 14:08:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:08:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:08:00: end of X-cor INFO @ Mon, 03 Jun 2019 14:08:00: #2 finished! INFO @ Mon, 03 Jun 2019 14:08:00: #2 predicted fragment length is 35 bps INFO @ Mon, 03 Jun 2019 14:08:00: #2 alternative fragment length(s) may be 35,527,581 bps INFO @ Mon, 03 Jun 2019 14:08:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.10_model.r WARNING @ Mon, 03 Jun 2019 14:08:00: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:08:00: #2 You may need to consider one of the other alternative d(s): 35,527,581 WARNING @ Mon, 03 Jun 2019 14:08:00: #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 14:08:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:08:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:08:01: #2 number of paired peaks: 3925 INFO @ Mon, 03 Jun 2019 14:08:01: start model_add_line... INFO @ Mon, 03 Jun 2019 14:08:01: start X-correlation... INFO @ Mon, 03 Jun 2019 14:08:01: end of X-cor INFO @ Mon, 03 Jun 2019 14:08:01: #2 finished! INFO @ Mon, 03 Jun 2019 14:08:01: #2 predicted fragment length is 35 bps INFO @ Mon, 03 Jun 2019 14:08:01: #2 alternative fragment length(s) may be 35,527,581 bps INFO @ Mon, 03 Jun 2019 14:08:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.20_model.r WARNING @ Mon, 03 Jun 2019 14:08:01: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:08:01: #2 You may need to consider one of the other alternative d(s): 35,527,581 WARNING @ Mon, 03 Jun 2019 14:08:01: #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 14:08:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:08:01: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 14:08:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:08:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:08:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:08:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:08:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:08:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:08:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.10_summits.bed INFO @ Mon, 03 Jun 2019 14:08:02: Done! INFO @ Mon, 03 Jun 2019 14:08:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:08:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.05_summits.bed INFO @ Mon, 03 Jun 2019 14:08:02: Done! INFO @ Mon, 03 Jun 2019 14:08:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:08:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:08:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX348470/SRX348470.20_summits.bed INFO @ Mon, 03 Jun 2019 14:08:02: Done! pass1 - making usageList (14 chroms): 1 millis pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (152 records, 4 fields): 3 millis pass2 - checking and writing primary data (623 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。 pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (39 records, 4 fields): 1 millis CompletedMACS2peakCalling