Job ID = 1301218 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,368,792 reads read : 12,368,792 reads written : 12,368,792 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: 00:01:52 12368792 reads; of these: 12368792 (100.00%) were unpaired; of these: 7898844 (63.86%) aligned 0 times 3879897 (31.37%) aligned exactly 1 time 590051 (4.77%) aligned >1 times 36.14% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 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] 2033112 / 4469948 = 0.4548 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 19:51:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.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 19:51:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:51:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:51:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.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 19:51:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:51:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:51:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.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 19:51:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:51:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:51:28: 1000000 INFO @ Mon, 03 Jun 2019 19:51:31: 1000000 INFO @ Mon, 03 Jun 2019 19:51:31: 1000000 INFO @ Mon, 03 Jun 2019 19:51:36: 2000000 INFO @ Mon, 03 Jun 2019 19:51:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:51:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:51:39: #1 total tags in treatment: 2436836 INFO @ Mon, 03 Jun 2019 19:51:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:51:39: #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 19:51:39: #1 tags after filtering in treatment: 2436836 INFO @ Mon, 03 Jun 2019 19:51:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:51:39: #1 finished! INFO @ Mon, 03 Jun 2019 19:51:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:51:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:51:40: #2 number of paired peaks: 288 WARNING @ Mon, 03 Jun 2019 19:51:40: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Mon, 03 Jun 2019 19:51:40: start model_add_line... INFO @ Mon, 03 Jun 2019 19:51:40: start X-correlation... INFO @ Mon, 03 Jun 2019 19:51:40: end of X-cor INFO @ Mon, 03 Jun 2019 19:51:40: #2 finished! INFO @ Mon, 03 Jun 2019 19:51:40: #2 predicted fragment length is 141 bps INFO @ Mon, 03 Jun 2019 19:51:40: #2 alternative fragment length(s) may be 141,155 bps INFO @ Mon, 03 Jun 2019 19:51:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.10_model.r INFO @ Mon, 03 Jun 2019 19:51:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:51:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:51:42: 2000000 INFO @ Mon, 03 Jun 2019 19:51:42: 2000000 INFO @ Mon, 03 Jun 2019 19:51:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:51:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:51:46: #1 total tags in treatment: 2436836 INFO @ Mon, 03 Jun 2019 19:51:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:51:46: #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 19:51:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:51:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:51:46: #1 total tags in treatment: 2436836 INFO @ Mon, 03 Jun 2019 19:51:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:51:46: #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 19:51:46: #1 tags after filtering in treatment: 2436836 INFO @ Mon, 03 Jun 2019 19:51:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:51:46: #1 finished! INFO @ Mon, 03 Jun 2019 19:51:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:51:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:51:46: #1 tags after filtering in treatment: 2436836 INFO @ Mon, 03 Jun 2019 19:51:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:51:46: #1 finished! INFO @ Mon, 03 Jun 2019 19:51:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:51:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:51:47: #2 number of paired peaks: 288 WARNING @ Mon, 03 Jun 2019 19:51:47: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Mon, 03 Jun 2019 19:51:47: start model_add_line... INFO @ Mon, 03 Jun 2019 19:51:47: start X-correlation... INFO @ Mon, 03 Jun 2019 19:51:47: #2 number of paired peaks: 288 WARNING @ Mon, 03 Jun 2019 19:51:47: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Mon, 03 Jun 2019 19:51:47: start model_add_line... INFO @ Mon, 03 Jun 2019 19:51:47: end of X-cor INFO @ Mon, 03 Jun 2019 19:51:47: #2 finished! INFO @ Mon, 03 Jun 2019 19:51:47: #2 predicted fragment length is 141 bps INFO @ Mon, 03 Jun 2019 19:51:47: #2 alternative fragment length(s) may be 141,155 bps INFO @ Mon, 03 Jun 2019 19:51:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.20_model.r INFO @ Mon, 03 Jun 2019 19:51:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:51:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:51:47: start X-correlation... INFO @ Mon, 03 Jun 2019 19:51:47: end of X-cor INFO @ Mon, 03 Jun 2019 19:51:47: #2 finished! INFO @ Mon, 03 Jun 2019 19:51:47: #2 predicted fragment length is 141 bps INFO @ Mon, 03 Jun 2019 19:51:47: #2 alternative fragment length(s) may be 141,155 bps INFO @ Mon, 03 Jun 2019 19:51:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.05_model.r INFO @ Mon, 03 Jun 2019 19:51:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:51:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:51:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:51:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:51:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:51:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.10_summits.bed INFO @ Mon, 03 Jun 2019 19:51:51: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (91 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:51:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:51:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:51:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:51:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:51:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.20_summits.bed INFO @ Mon, 03 Jun 2019 19:51:58: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (19 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:51:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:51:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:51:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485205/SRX485205.05_summits.bed INFO @ Mon, 03 Jun 2019 19:51:58: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (288 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。