Job ID = 1293373 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,109,256 reads read : 10,218,512 reads written : 10,218,512 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: 00:09:52 5109256 reads; of these: 5109256 (100.00%) were paired; of these: 1358290 (26.58%) aligned concordantly 0 times 2696768 (52.78%) aligned concordantly exactly 1 time 1054198 (20.63%) aligned concordantly >1 times ---- 1358290 pairs aligned concordantly 0 times; of these: 38830 (2.86%) aligned discordantly 1 time ---- 1319460 pairs aligned 0 times concordantly or discordantly; of these: 2638920 mates make up the pairs; of these: 2485251 (94.18%) aligned 0 times 94211 (3.57%) aligned exactly 1 time 59458 (2.25%) aligned >1 times 75.68% overall alignment rate Time searching: 00:09:52 Overall time: 00:09:52 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 761483 / 3786831 = 0.2011 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 @ Sun, 02 Jun 2019 23:24:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.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 @ Sun, 02 Jun 2019 23:24:16: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:24:16: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:24:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.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 @ Sun, 02 Jun 2019 23:24:16: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:24:16: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:24:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.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 @ Sun, 02 Jun 2019 23:24:16: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:24:16: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:24:26: 1000000 INFO @ Sun, 02 Jun 2019 23:24:26: 1000000 INFO @ Sun, 02 Jun 2019 23:24:27: 1000000 INFO @ Sun, 02 Jun 2019 23:24:36: 2000000 INFO @ Sun, 02 Jun 2019 23:24:36: 2000000 INFO @ Sun, 02 Jun 2019 23:24:38: 2000000 INFO @ Sun, 02 Jun 2019 23:24:45: 3000000 INFO @ Sun, 02 Jun 2019 23:24:45: 3000000 INFO @ Sun, 02 Jun 2019 23:24:48: 3000000 INFO @ Sun, 02 Jun 2019 23:24:55: 4000000 INFO @ Sun, 02 Jun 2019 23:24:55: 4000000 INFO @ Sun, 02 Jun 2019 23:24:59: 4000000 INFO @ Sun, 02 Jun 2019 23:25:04: 5000000 INFO @ Sun, 02 Jun 2019 23:25:04: 5000000 INFO @ Sun, 02 Jun 2019 23:25:09: 5000000 INFO @ Sun, 02 Jun 2019 23:25:13: 6000000 INFO @ Sun, 02 Jun 2019 23:25:13: 6000000 INFO @ Sun, 02 Jun 2019 23:25:15: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 23:25:15: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 23:25:15: #1 total tags in treatment: 2995219 INFO @ Sun, 02 Jun 2019 23:25:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:25:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:25:15: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 23:25:15: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 23:25:15: #1 total tags in treatment: 2995219 INFO @ Sun, 02 Jun 2019 23:25:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:25:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:25:15: #1 tags after filtering in treatment: 2893068 INFO @ Sun, 02 Jun 2019 23:25:15: #1 Redundant rate of treatment: 0.03 INFO @ Sun, 02 Jun 2019 23:25:15: #1 finished! INFO @ Sun, 02 Jun 2019 23:25:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:25:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:25:15: #1 tags after filtering in treatment: 2893068 INFO @ Sun, 02 Jun 2019 23:25:15: #1 Redundant rate of treatment: 0.03 INFO @ Sun, 02 Jun 2019 23:25:15: #1 finished! INFO @ Sun, 02 Jun 2019 23:25:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:25:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:25:16: #2 number of paired peaks: 188 WARNING @ Sun, 02 Jun 2019 23:25:16: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Sun, 02 Jun 2019 23:25:16: start model_add_line... INFO @ Sun, 02 Jun 2019 23:25:16: #2 number of paired peaks: 188 WARNING @ Sun, 02 Jun 2019 23:25:16: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Sun, 02 Jun 2019 23:25:16: start model_add_line... INFO @ Sun, 02 Jun 2019 23:25:16: start X-correlation... INFO @ Sun, 02 Jun 2019 23:25:16: start X-correlation... INFO @ Sun, 02 Jun 2019 23:25:16: end of X-cor INFO @ Sun, 02 Jun 2019 23:25:16: #2 finished! INFO @ Sun, 02 Jun 2019 23:25:16: #2 predicted fragment length is 105 bps INFO @ Sun, 02 Jun 2019 23:25:16: #2 alternative fragment length(s) may be 105 bps INFO @ Sun, 02 Jun 2019 23:25:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.10_model.r INFO @ Sun, 02 Jun 2019 23:25:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:25:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:25:16: end of X-cor INFO @ Sun, 02 Jun 2019 23:25:16: #2 finished! INFO @ Sun, 02 Jun 2019 23:25:16: #2 predicted fragment length is 105 bps INFO @ Sun, 02 Jun 2019 23:25:16: #2 alternative fragment length(s) may be 105 bps INFO @ Sun, 02 Jun 2019 23:25:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.20_model.r INFO @ Sun, 02 Jun 2019 23:25:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:25:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:25:19: 6000000 INFO @ Sun, 02 Jun 2019 23:25:21: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 23:25:21: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 23:25:21: #1 total tags in treatment: 2995219 INFO @ Sun, 02 Jun 2019 23:25:21: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:25:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:25:21: #1 tags after filtering in treatment: 2893068 INFO @ Sun, 02 Jun 2019 23:25:21: #1 Redundant rate of treatment: 0.03 INFO @ Sun, 02 Jun 2019 23:25:21: #1 finished! INFO @ Sun, 02 Jun 2019 23:25:21: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:25:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:25:22: #2 number of paired peaks: 188 WARNING @ Sun, 02 Jun 2019 23:25:22: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Sun, 02 Jun 2019 23:25:22: start model_add_line... INFO @ Sun, 02 Jun 2019 23:25:22: start X-correlation... INFO @ Sun, 02 Jun 2019 23:25:22: end of X-cor INFO @ Sun, 02 Jun 2019 23:25:22: #2 finished! INFO @ Sun, 02 Jun 2019 23:25:22: #2 predicted fragment length is 105 bps INFO @ Sun, 02 Jun 2019 23:25:22: #2 alternative fragment length(s) may be 105 bps INFO @ Sun, 02 Jun 2019 23:25:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.05_model.r INFO @ Sun, 02 Jun 2019 23:25:22: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:25:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:25:25: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:25:25: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:25:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:25:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:25:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.10_summits.bed INFO @ Sun, 02 Jun 2019 23:25:29: Done! INFO @ Sun, 02 Jun 2019 23:25:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:25:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:25:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.20_summits.bed INFO @ Sun, 02 Jun 2019 23:25:29: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (355 records, 4 fields): 2 millis pass1 - making usageList (6 chroms): 1 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (158 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:25:31: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:25:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:25:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:25:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818291/ERX1818291.05_summits.bed INFO @ Sun, 02 Jun 2019 23:25:35: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (599 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。