Job ID = 1294286 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,136,012 reads read : 6,136,012 reads written : 6,136,012 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: 00:00:53 6136012 reads; of these: 6136012 (100.00%) were unpaired; of these: 2813039 (45.84%) aligned 0 times 2726739 (44.44%) aligned exactly 1 time 596234 (9.72%) aligned >1 times 54.16% overall alignment rate Time searching: 00:00:53 Overall time: 00:00:53 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] 141630 / 3322973 = 0.0426 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 06:06:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.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 06:06:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:06:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:06:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.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 06:06:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:06:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:06:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.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 06:06:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:06:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:06:12: 1000000 INFO @ Mon, 03 Jun 2019 06:06:12: 1000000 INFO @ Mon, 03 Jun 2019 06:06:13: 1000000 INFO @ Mon, 03 Jun 2019 06:06:21: 2000000 INFO @ Mon, 03 Jun 2019 06:06:21: 2000000 INFO @ Mon, 03 Jun 2019 06:06:22: 2000000 INFO @ Mon, 03 Jun 2019 06:06:29: 3000000 INFO @ Mon, 03 Jun 2019 06:06:29: 3000000 INFO @ Mon, 03 Jun 2019 06:06:31: #1 tag size is determined as 35 bps INFO @ Mon, 03 Jun 2019 06:06:31: #1 tag size = 35 INFO @ Mon, 03 Jun 2019 06:06:31: #1 total tags in treatment: 3181343 INFO @ Mon, 03 Jun 2019 06:06:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:06:31: #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 06:06:31: #1 tag size is determined as 35 bps INFO @ Mon, 03 Jun 2019 06:06:31: #1 tag size = 35 INFO @ Mon, 03 Jun 2019 06:06:31: #1 total tags in treatment: 3181343 INFO @ Mon, 03 Jun 2019 06:06:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:06:31: #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 06:06:31: #1 tags after filtering in treatment: 3181343 INFO @ Mon, 03 Jun 2019 06:06:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:06:31: #1 finished! INFO @ Mon, 03 Jun 2019 06:06:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:06:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:06:31: #1 tags after filtering in treatment: 3181343 INFO @ Mon, 03 Jun 2019 06:06:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:06:31: #1 finished! INFO @ Mon, 03 Jun 2019 06:06:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:06:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:06:31: #2 number of paired peaks: 432 WARNING @ Mon, 03 Jun 2019 06:06:31: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Mon, 03 Jun 2019 06:06:31: start model_add_line... INFO @ Mon, 03 Jun 2019 06:06:31: #2 number of paired peaks: 432 WARNING @ Mon, 03 Jun 2019 06:06:31: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Mon, 03 Jun 2019 06:06:31: start model_add_line... INFO @ Mon, 03 Jun 2019 06:06:31: start X-correlation... INFO @ Mon, 03 Jun 2019 06:06:31: end of X-cor INFO @ Mon, 03 Jun 2019 06:06:31: #2 finished! INFO @ Mon, 03 Jun 2019 06:06:31: #2 predicted fragment length is 103 bps INFO @ Mon, 03 Jun 2019 06:06:31: #2 alternative fragment length(s) may be 103,564 bps INFO @ Mon, 03 Jun 2019 06:06:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.20_model.r INFO @ Mon, 03 Jun 2019 06:06:31: start X-correlation... INFO @ Mon, 03 Jun 2019 06:06:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:06:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:06:31: end of X-cor INFO @ Mon, 03 Jun 2019 06:06:31: #2 finished! INFO @ Mon, 03 Jun 2019 06:06:31: #2 predicted fragment length is 103 bps INFO @ Mon, 03 Jun 2019 06:06:31: #2 alternative fragment length(s) may be 103,564 bps INFO @ Mon, 03 Jun 2019 06:06:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.10_model.r INFO @ Mon, 03 Jun 2019 06:06:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:06:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:06:32: 3000000 INFO @ Mon, 03 Jun 2019 06:06:34: #1 tag size is determined as 35 bps INFO @ Mon, 03 Jun 2019 06:06:34: #1 tag size = 35 INFO @ Mon, 03 Jun 2019 06:06:34: #1 total tags in treatment: 3181343 INFO @ Mon, 03 Jun 2019 06:06:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:06:34: #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 06:06:34: #1 tags after filtering in treatment: 3181343 INFO @ Mon, 03 Jun 2019 06:06:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:06:34: #1 finished! INFO @ Mon, 03 Jun 2019 06:06:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:06:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:06:35: #2 number of paired peaks: 432 WARNING @ Mon, 03 Jun 2019 06:06:35: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Mon, 03 Jun 2019 06:06:35: start model_add_line... INFO @ Mon, 03 Jun 2019 06:06:35: start X-correlation... INFO @ Mon, 03 Jun 2019 06:06:35: end of X-cor INFO @ Mon, 03 Jun 2019 06:06:35: #2 finished! INFO @ Mon, 03 Jun 2019 06:06:35: #2 predicted fragment length is 103 bps INFO @ Mon, 03 Jun 2019 06:06:35: #2 alternative fragment length(s) may be 103,564 bps INFO @ Mon, 03 Jun 2019 06:06:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.05_model.r INFO @ Mon, 03 Jun 2019 06:06:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:06:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:06:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:06:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:06:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:06:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:06:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:06:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.20_summits.bed INFO @ Mon, 03 Jun 2019 06:06:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (55 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:06:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:06:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:06:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.10_summits.bed INFO @ Mon, 03 Jun 2019 06:06:46: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (315 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:06:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:06:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:06:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX231858/SRX231858.05_summits.bed INFO @ Mon, 03 Jun 2019 06:06:50: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1141 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。