Job ID = 4178419 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,528,722 reads read : 5,057,444 reads written : 5,057,444 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:07:40 2528722 reads; of these: 2528722 (100.00%) were paired; of these: 285210 (11.28%) aligned concordantly 0 times 1656924 (65.52%) aligned concordantly exactly 1 time 586588 (23.20%) aligned concordantly >1 times ---- 285210 pairs aligned concordantly 0 times; of these: 124928 (43.80%) aligned discordantly 1 time ---- 160282 pairs aligned 0 times concordantly or discordantly; of these: 320564 mates make up the pairs; of these: 165153 (51.52%) aligned 0 times 72258 (22.54%) aligned exactly 1 time 83153 (25.94%) aligned >1 times 96.73% overall alignment rate Time searching: 00:07:41 Overall time: 00:07:41 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] 459942 / 2364208 = 0.1945 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:29:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.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 12:29:28: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:29:28: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:29:34: 1000000 INFO @ Thu, 05 Dec 2019 12:29:41: 2000000 INFO @ Thu, 05 Dec 2019 12:29:47: 3000000 INFO @ Thu, 05 Dec 2019 12:29:54: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:29:54: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:29:54: #1 total tags in treatment: 1803686 INFO @ Thu, 05 Dec 2019 12:29:54: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:29:54: #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 12:29:54: #1 tags after filtering in treatment: 1760592 INFO @ Thu, 05 Dec 2019 12:29:54: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 05 Dec 2019 12:29:54: #1 finished! INFO @ Thu, 05 Dec 2019 12:29:54: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:29:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:29:54: #2 number of paired peaks: 383 WARNING @ Thu, 05 Dec 2019 12:29:54: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Thu, 05 Dec 2019 12:29:54: start model_add_line... INFO @ Thu, 05 Dec 2019 12:29:54: start X-correlation... INFO @ Thu, 05 Dec 2019 12:29:54: end of X-cor INFO @ Thu, 05 Dec 2019 12:29:54: #2 finished! INFO @ Thu, 05 Dec 2019 12:29:54: #2 predicted fragment length is 153 bps INFO @ Thu, 05 Dec 2019 12:29:54: #2 alternative fragment length(s) may be 153 bps INFO @ Thu, 05 Dec 2019 12:29:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.05_model.r INFO @ Thu, 05 Dec 2019 12:29:54: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:29:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:29:57: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:29:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.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 12:29:57: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:29:57: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:29:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:29:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:29:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.05_summits.bed INFO @ Thu, 05 Dec 2019 12:29:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (609 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:30:04: 1000000 INFO @ Thu, 05 Dec 2019 12:30:11: 2000000 INFO @ Thu, 05 Dec 2019 12:30:18: 3000000 INFO @ Thu, 05 Dec 2019 12:30:24: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:30:24: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:30:24: #1 total tags in treatment: 1803686 INFO @ Thu, 05 Dec 2019 12:30:24: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:30:24: #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 12:30:24: #1 tags after filtering in treatment: 1760592 INFO @ Thu, 05 Dec 2019 12:30:24: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 05 Dec 2019 12:30:24: #1 finished! INFO @ Thu, 05 Dec 2019 12:30:24: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:30:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:30:24: #2 number of paired peaks: 383 WARNING @ Thu, 05 Dec 2019 12:30:24: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Thu, 05 Dec 2019 12:30:24: start model_add_line... INFO @ Thu, 05 Dec 2019 12:30:24: start X-correlation... INFO @ Thu, 05 Dec 2019 12:30:24: end of X-cor INFO @ Thu, 05 Dec 2019 12:30:24: #2 finished! INFO @ Thu, 05 Dec 2019 12:30:24: #2 predicted fragment length is 153 bps INFO @ Thu, 05 Dec 2019 12:30:24: #2 alternative fragment length(s) may be 153 bps INFO @ Thu, 05 Dec 2019 12:30:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.10_model.r INFO @ Thu, 05 Dec 2019 12:30:24: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:30:24: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:30:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.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 12:30:27: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:30:27: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:30:28: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:30:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:30:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:30:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.10_summits.bed INFO @ Thu, 05 Dec 2019 12:30:30: Done! INFO @ Thu, 05 Dec 2019 12:30:34: 1000000 INFO @ Thu, 05 Dec 2019 12:30:40: 2000000 INFO @ Thu, 05 Dec 2019 12:30:46: 3000000 INFO @ Thu, 05 Dec 2019 12:30:52: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:30:52: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:30:52: #1 total tags in treatment: 1803686 INFO @ Thu, 05 Dec 2019 12:30:52: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:30:52: #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 12:30:53: #1 tags after filtering in treatment: 1760592 INFO @ Thu, 05 Dec 2019 12:30:53: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 05 Dec 2019 12:30:53: #1 finished! INFO @ Thu, 05 Dec 2019 12:30:53: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:30:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:30:53: #2 number of paired peaks: 383 WARNING @ Thu, 05 Dec 2019 12:30:53: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Thu, 05 Dec 2019 12:30:53: start model_add_line... INFO @ Thu, 05 Dec 2019 12:30:53: start X-correlation... INFO @ Thu, 05 Dec 2019 12:30:53: end of X-cor INFO @ Thu, 05 Dec 2019 12:30:53: #2 finished! INFO @ Thu, 05 Dec 2019 12:30:53: #2 predicted fragment length is 153 bps INFO @ Thu, 05 Dec 2019 12:30:53: #2 alternative fragment length(s) may be 153 bps INFO @ Thu, 05 Dec 2019 12:30:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.20_model.r INFO @ Thu, 05 Dec 2019 12:30:53: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:30:53: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (458 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:30:56: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:30:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:30:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:30:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2095157/SRX2095157.20_summits.bed INFO @ Thu, 05 Dec 2019 12:30:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (306 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。