Job ID = 4178415 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,444,950 reads read : 4,889,900 reads written : 4,889,900 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:24 2444950 reads; of these: 2444950 (100.00%) were paired; of these: 245850 (10.06%) aligned concordantly 0 times 1643270 (67.21%) aligned concordantly exactly 1 time 555830 (22.73%) aligned concordantly >1 times ---- 245850 pairs aligned concordantly 0 times; of these: 74634 (30.36%) aligned discordantly 1 time ---- 171216 pairs aligned 0 times concordantly or discordantly; of these: 342432 mates make up the pairs; of these: 228436 (66.71%) aligned 0 times 62397 (18.22%) aligned exactly 1 time 51599 (15.07%) aligned >1 times 95.33% overall alignment rate Time searching: 00:07:25 Overall time: 00:07:25 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] 486545 / 2270321 = 0.2143 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:29:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.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 @ Thu, 05 Dec 2019 12:29:08: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:29:08: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:29:20: 1000000 INFO @ Thu, 05 Dec 2019 12:29:32: 2000000 INFO @ Thu, 05 Dec 2019 12:29:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.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 @ Thu, 05 Dec 2019 12:29:37: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:29:37: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:29:44: 3000000 INFO @ Thu, 05 Dec 2019 12:29:47: 1000000 INFO @ Thu, 05 Dec 2019 12:29:53: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:29:53: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:29:53: #1 total tags in treatment: 1726389 INFO @ Thu, 05 Dec 2019 12:29:53: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:29:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:29:53: #1 tags after filtering in treatment: 1684897 INFO @ Thu, 05 Dec 2019 12:29:53: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 05 Dec 2019 12:29:53: #1 finished! INFO @ Thu, 05 Dec 2019 12:29:53: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:29:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:29:53: #2 number of paired peaks: 371 WARNING @ Thu, 05 Dec 2019 12:29:53: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Thu, 05 Dec 2019 12:29:53: start model_add_line... INFO @ Thu, 05 Dec 2019 12:29:53: start X-correlation... INFO @ Thu, 05 Dec 2019 12:29:53: end of X-cor INFO @ Thu, 05 Dec 2019 12:29:53: #2 finished! INFO @ Thu, 05 Dec 2019 12:29:53: #2 predicted fragment length is 159 bps INFO @ Thu, 05 Dec 2019 12:29:53: #2 alternative fragment length(s) may be 159 bps INFO @ Thu, 05 Dec 2019 12:29:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.05_model.r INFO @ Thu, 05 Dec 2019 12:29:53: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:29:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:29:57: 2000000 INFO @ Thu, 05 Dec 2019 12:29:58: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:30:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:30:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:30:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.05_summits.bed INFO @ Thu, 05 Dec 2019 12:30:01: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (591 records, 4 fields): 81 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:30:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.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 @ Thu, 05 Dec 2019 12:30:07: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:30:07: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:30:07: 3000000 INFO @ Thu, 05 Dec 2019 12:30:14: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:30:14: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:30:14: #1 total tags in treatment: 1726389 INFO @ Thu, 05 Dec 2019 12:30:14: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:30:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:30:14: #1 tags after filtering in treatment: 1684897 INFO @ Thu, 05 Dec 2019 12:30:14: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 05 Dec 2019 12:30:14: #1 finished! INFO @ Thu, 05 Dec 2019 12:30:14: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:30:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:30:14: #2 number of paired peaks: 371 WARNING @ Thu, 05 Dec 2019 12:30:14: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Thu, 05 Dec 2019 12:30:14: start model_add_line... INFO @ Thu, 05 Dec 2019 12:30:14: start X-correlation... INFO @ Thu, 05 Dec 2019 12:30:14: end of X-cor INFO @ Thu, 05 Dec 2019 12:30:14: #2 finished! INFO @ Thu, 05 Dec 2019 12:30:14: #2 predicted fragment length is 159 bps INFO @ Thu, 05 Dec 2019 12:30:14: #2 alternative fragment length(s) may be 159 bps INFO @ Thu, 05 Dec 2019 12:30:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.10_model.r INFO @ Thu, 05 Dec 2019 12:30:14: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:30:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:30:19: 1000000 INFO @ Thu, 05 Dec 2019 12:30:20: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:30:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:30:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:30:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.10_summits.bed INFO @ Thu, 05 Dec 2019 12:30:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (447 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:30:31: 2000000 INFO @ Thu, 05 Dec 2019 12:30:43: 3000000 INFO @ Thu, 05 Dec 2019 12:30:51: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:30:51: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:30:51: #1 total tags in treatment: 1726389 INFO @ Thu, 05 Dec 2019 12:30:51: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:30:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:30:51: #1 tags after filtering in treatment: 1684897 INFO @ Thu, 05 Dec 2019 12:30:51: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 05 Dec 2019 12:30:51: #1 finished! INFO @ Thu, 05 Dec 2019 12:30:51: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:30:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:30:51: #2 number of paired peaks: 371 WARNING @ Thu, 05 Dec 2019 12:30:51: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Thu, 05 Dec 2019 12:30:51: start model_add_line... INFO @ Thu, 05 Dec 2019 12:30:51: start X-correlation... INFO @ Thu, 05 Dec 2019 12:30:51: end of X-cor INFO @ Thu, 05 Dec 2019 12:30:51: #2 finished! INFO @ Thu, 05 Dec 2019 12:30:51: #2 predicted fragment length is 159 bps INFO @ Thu, 05 Dec 2019 12:30:51: #2 alternative fragment length(s) may be 159 bps INFO @ Thu, 05 Dec 2019 12:30:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.20_model.r INFO @ Thu, 05 Dec 2019 12:30:51: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:30:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:30:57: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:30:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:30:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:30:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2095155/SRX2095155.20_summits.bed INFO @ Thu, 05 Dec 2019 12:30:59: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (296 records, 4 fields): 85 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。