Job ID = 1293894 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 8,952,456 reads read : 17,904,912 reads written : 17,904,912 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: 00:09:41 8952456 reads; of these: 8952456 (100.00%) were paired; of these: 5453176 (60.91%) aligned concordantly 0 times 2655568 (29.66%) aligned concordantly exactly 1 time 843712 (9.42%) aligned concordantly >1 times ---- 5453176 pairs aligned concordantly 0 times; of these: 5416 (0.10%) aligned discordantly 1 time ---- 5447760 pairs aligned 0 times concordantly or discordantly; of these: 10895520 mates make up the pairs; of these: 10542123 (96.76%) aligned 0 times 260049 (2.39%) aligned exactly 1 time 93348 (0.86%) aligned >1 times 41.12% overall alignment rate Time searching: 00:09:41 Overall time: 00:09:41 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] 2752577 / 3499985 = 0.7865 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 03:12:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.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 03:12:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:12:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:12:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.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 03:12:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:12:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:12:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.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 03:12:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:12:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:12:47: 1000000 INFO @ Mon, 03 Jun 2019 03:12:49: 1000000 INFO @ Mon, 03 Jun 2019 03:12:50: 1000000 INFO @ Mon, 03 Jun 2019 03:12:54: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:12:54: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:12:54: #1 total tags in treatment: 748034 INFO @ Mon, 03 Jun 2019 03:12:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:12:54: #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 03:12:54: #1 tags after filtering in treatment: 697332 INFO @ Mon, 03 Jun 2019 03:12:54: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 03:12:54: #1 finished! INFO @ Mon, 03 Jun 2019 03:12:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:12:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:12:54: #2 number of paired peaks: 3154 INFO @ Mon, 03 Jun 2019 03:12:54: start model_add_line... INFO @ Mon, 03 Jun 2019 03:12:54: start X-correlation... INFO @ Mon, 03 Jun 2019 03:12:54: end of X-cor INFO @ Mon, 03 Jun 2019 03:12:54: #2 finished! INFO @ Mon, 03 Jun 2019 03:12:54: #2 predicted fragment length is 101 bps INFO @ Mon, 03 Jun 2019 03:12:54: #2 alternative fragment length(s) may be 101 bps INFO @ Mon, 03 Jun 2019 03:12:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.05_model.r INFO @ Mon, 03 Jun 2019 03:12:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:12:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:12:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:12:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:12:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:12:57: #1 total tags in treatment: 748034 INFO @ Mon, 03 Jun 2019 03:12:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:12:57: #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 03:12:57: #1 tags after filtering in treatment: 697332 INFO @ Mon, 03 Jun 2019 03:12:57: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 03:12:57: #1 finished! INFO @ Mon, 03 Jun 2019 03:12:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:12:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:12:57: #2 number of paired peaks: 3154 INFO @ Mon, 03 Jun 2019 03:12:57: start model_add_line... INFO @ Mon, 03 Jun 2019 03:12:57: start X-correlation... INFO @ Mon, 03 Jun 2019 03:12:57: end of X-cor INFO @ Mon, 03 Jun 2019 03:12:57: #2 finished! INFO @ Mon, 03 Jun 2019 03:12:57: #2 predicted fragment length is 101 bps INFO @ Mon, 03 Jun 2019 03:12:57: #2 alternative fragment length(s) may be 101 bps INFO @ Mon, 03 Jun 2019 03:12:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.20_model.r INFO @ Mon, 03 Jun 2019 03:12:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:12:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:12:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:12:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:12:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.05_summits.bed INFO @ Mon, 03 Jun 2019 03:12:57: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (905 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:12:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:12:59: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:12:59: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:12:59: #1 total tags in treatment: 748034 INFO @ Mon, 03 Jun 2019 03:12:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:12:59: #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 03:12:59: #1 tags after filtering in treatment: 697332 INFO @ Mon, 03 Jun 2019 03:12:59: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 03:12:59: #1 finished! INFO @ Mon, 03 Jun 2019 03:12:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:12:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:12:59: #2 number of paired peaks: 3154 INFO @ Mon, 03 Jun 2019 03:12:59: start model_add_line... INFO @ Mon, 03 Jun 2019 03:12:59: start X-correlation... INFO @ Mon, 03 Jun 2019 03:12:59: end of X-cor INFO @ Mon, 03 Jun 2019 03:12:59: #2 finished! INFO @ Mon, 03 Jun 2019 03:12:59: #2 predicted fragment length is 101 bps INFO @ Mon, 03 Jun 2019 03:12:59: #2 alternative fragment length(s) may be 101 bps INFO @ Mon, 03 Jun 2019 03:12:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.10_model.r INFO @ Mon, 03 Jun 2019 03:13:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:13:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:13:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:13:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:13:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.20_summits.bed INFO @ Mon, 03 Jun 2019 03:13:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (348 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:13:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:13:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:13:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:13:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX143463/SRX143463.10_summits.bed INFO @ Mon, 03 Jun 2019 03:13:03: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (543 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。