Job ID = 10924608 sra ファイルのダウンロード中... Completed: 478431K bytes transferred in 11 seconds (332923K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Read 8016333 spots for /home/okishinya/chipatlas/results/dm3/SRX2396695/SRR5078065.sra Written 8016333 spots for /home/okishinya/chipatlas/results/dm3/SRX2396695/SRR5078065.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:08:44 8016333 reads; of these: 8016333 (100.00%) were paired; of these: 1080753 (13.48%) aligned concordantly 0 times 6491561 (80.98%) aligned concordantly exactly 1 time 444019 (5.54%) aligned concordantly >1 times ---- 1080753 pairs aligned concordantly 0 times; of these: 198067 (18.33%) aligned discordantly 1 time ---- 882686 pairs aligned 0 times concordantly or discordantly; of these: 1765372 mates make up the pairs; of these: 1545502 (87.55%) aligned 0 times 160763 (9.11%) aligned exactly 1 time 59107 (3.35%) aligned >1 times 90.36% overall alignment rate Time searching: 00:08:44 Overall time: 00:08:44 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_sort_core] merging from 8 files... [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] 81070 / 7131488 = 0.0114 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, 06 Aug 2018 10:39:22: # Command line: callpeak -t SRX2396695.bam -f BAM -g dm -n SRX2396695.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2396695.20 # format = BAM # ChIP-seq file = ['SRX2396695.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, 06 Aug 2018 10:39:22: # Command line: callpeak -t SRX2396695.bam -f BAM -g dm -n SRX2396695.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2396695.05 # format = BAM # ChIP-seq file = ['SRX2396695.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, 06 Aug 2018 10:39:22: # Command line: callpeak -t SRX2396695.bam -f BAM -g dm -n SRX2396695.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2396695.10 # format = BAM # ChIP-seq file = ['SRX2396695.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, 06 Aug 2018 10:39:22: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:39:22: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:39:22: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:39:22: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:39:22: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:39:22: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:39:28: 1000000 INFO @ Mon, 06 Aug 2018 10:39:28: 1000000 INFO @ Mon, 06 Aug 2018 10:39:28: 1000000 INFO @ Mon, 06 Aug 2018 10:39:34: 2000000 INFO @ Mon, 06 Aug 2018 10:39:34: 2000000 INFO @ Mon, 06 Aug 2018 10:39:34: 2000000 INFO @ Mon, 06 Aug 2018 10:39:40: 3000000 INFO @ Mon, 06 Aug 2018 10:39:41: 3000000 INFO @ Mon, 06 Aug 2018 10:39:41: 3000000 INFO @ Mon, 06 Aug 2018 10:39:46: 4000000 INFO @ Mon, 06 Aug 2018 10:39:47: 4000000 INFO @ Mon, 06 Aug 2018 10:39:47: 4000000 INFO @ Mon, 06 Aug 2018 10:39:52: 5000000 INFO @ Mon, 06 Aug 2018 10:39:53: 5000000 INFO @ Mon, 06 Aug 2018 10:39:53: 5000000 INFO @ Mon, 06 Aug 2018 10:39:59: 6000000 INFO @ Mon, 06 Aug 2018 10:39:59: 6000000 INFO @ Mon, 06 Aug 2018 10:39:59: 6000000 INFO @ Mon, 06 Aug 2018 10:40:05: 7000000 INFO @ Mon, 06 Aug 2018 10:40:05: 7000000 INFO @ Mon, 06 Aug 2018 10:40:05: 7000000 INFO @ Mon, 06 Aug 2018 10:40:11: 8000000 INFO @ Mon, 06 Aug 2018 10:40:11: 8000000 INFO @ Mon, 06 Aug 2018 10:40:12: 8000000 INFO @ Mon, 06 Aug 2018 10:40:17: 9000000 INFO @ Mon, 06 Aug 2018 10:40:17: 9000000 INFO @ Mon, 06 Aug 2018 10:40:18: 9000000 INFO @ Mon, 06 Aug 2018 10:40:23: 10000000 INFO @ Mon, 06 Aug 2018 10:40:23: 10000000 INFO @ Mon, 06 Aug 2018 10:40:24: 10000000 INFO @ Mon, 06 Aug 2018 10:40:29: 11000000 INFO @ Mon, 06 Aug 2018 10:40:30: 11000000 INFO @ Mon, 06 Aug 2018 10:40:30: 11000000 INFO @ Mon, 06 Aug 2018 10:40:35: 12000000 INFO @ Mon, 06 Aug 2018 10:40:36: 12000000 INFO @ Mon, 06 Aug 2018 10:40:36: 12000000 INFO @ Mon, 06 Aug 2018 10:40:41: 13000000 INFO @ Mon, 06 Aug 2018 10:40:42: 13000000 INFO @ Mon, 06 Aug 2018 10:40:42: 13000000 INFO @ Mon, 06 Aug 2018 10:40:47: 14000000 INFO @ Mon, 06 Aug 2018 10:40:48: 14000000 INFO @ Mon, 06 Aug 2018 10:40:49: 14000000 INFO @ Mon, 06 Aug 2018 10:40:49: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:40:49: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:40:49: #1 total tags in treatment: 6855681 INFO @ Mon, 06 Aug 2018 10:40:49: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:40:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:40:49: #1 tags after filtering in treatment: 6511112 INFO @ Mon, 06 Aug 2018 10:40:49: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 06 Aug 2018 10:40:49: #1 finished! INFO @ Mon, 06 Aug 2018 10:40:49: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:40:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:40:50: #2 number of paired peaks: 4163 INFO @ Mon, 06 Aug 2018 10:40:50: start model_add_line... INFO @ Mon, 06 Aug 2018 10:40:50: start X-correlation... INFO @ Mon, 06 Aug 2018 10:40:50: end of X-cor INFO @ Mon, 06 Aug 2018 10:40:50: #2 finished! INFO @ Mon, 06 Aug 2018 10:40:50: #2 predicted fragment length is 197 bps INFO @ Mon, 06 Aug 2018 10:40:50: #2 alternative fragment length(s) may be 197 bps INFO @ Mon, 06 Aug 2018 10:40:50: #2.2 Generate R script for model : SRX2396695.05_model.r INFO @ Mon, 06 Aug 2018 10:40:50: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:40:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:40:50: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:40:50: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:40:50: #1 total tags in treatment: 6855681 INFO @ Mon, 06 Aug 2018 10:40:50: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:40:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:40:50: #1 tags after filtering in treatment: 6511112 INFO @ Mon, 06 Aug 2018 10:40:50: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 06 Aug 2018 10:40:50: #1 finished! INFO @ Mon, 06 Aug 2018 10:40:50: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:40:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:40:51: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:40:51: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:40:51: #1 total tags in treatment: 6855681 INFO @ Mon, 06 Aug 2018 10:40:51: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:40:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:40:51: #1 tags after filtering in treatment: 6511112 INFO @ Mon, 06 Aug 2018 10:40:51: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 06 Aug 2018 10:40:51: #1 finished! INFO @ Mon, 06 Aug 2018 10:40:51: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:40:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:40:51: #2 number of paired peaks: 4163 INFO @ Mon, 06 Aug 2018 10:40:51: start model_add_line... INFO @ Mon, 06 Aug 2018 10:40:51: start X-correlation... INFO @ Mon, 06 Aug 2018 10:40:51: end of X-cor INFO @ Mon, 06 Aug 2018 10:40:51: #2 finished! INFO @ Mon, 06 Aug 2018 10:40:51: #2 predicted fragment length is 197 bps INFO @ Mon, 06 Aug 2018 10:40:51: #2 alternative fragment length(s) may be 197 bps INFO @ Mon, 06 Aug 2018 10:40:51: #2.2 Generate R script for model : SRX2396695.10_model.r INFO @ Mon, 06 Aug 2018 10:40:51: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:40:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:40:51: #2 number of paired peaks: 4163 INFO @ Mon, 06 Aug 2018 10:40:51: start model_add_line... INFO @ Mon, 06 Aug 2018 10:40:52: start X-correlation... INFO @ Mon, 06 Aug 2018 10:40:52: end of X-cor INFO @ Mon, 06 Aug 2018 10:40:52: #2 finished! INFO @ Mon, 06 Aug 2018 10:40:52: #2 predicted fragment length is 197 bps INFO @ Mon, 06 Aug 2018 10:40:52: #2 alternative fragment length(s) may be 197 bps INFO @ Mon, 06 Aug 2018 10:40:52: #2.2 Generate R script for model : SRX2396695.20_model.r INFO @ Mon, 06 Aug 2018 10:40:52: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:40:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:41:08: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:41:08: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:41:08: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:41:17: #4 Write output xls file... SRX2396695.10_peaks.xls INFO @ Mon, 06 Aug 2018 10:41:17: #4 Write peak in narrowPeak format file... SRX2396695.10_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:41:17: #4 Write summits bed file... SRX2396695.10_summits.bed INFO @ Mon, 06 Aug 2018 10:41:17: Done! INFO @ Mon, 06 Aug 2018 10:41:17: #4 Write output xls file... SRX2396695.05_peaks.xls INFO @ Mon, 06 Aug 2018 10:41:17: #4 Write peak in narrowPeak format file... SRX2396695.05_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:41:17: #4 Write summits bed file... SRX2396695.05_summits.bed INFO @ Mon, 06 Aug 2018 10:41:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5842 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 06 Aug 2018 10:41:18: #4 Write output xls file... SRX2396695.20_peaks.xls INFO @ Mon, 06 Aug 2018 10:41:18: #4 Write peak in narrowPeak format file... SRX2396695.20_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:41:18: #4 Write summits bed file... SRX2396695.20_summits.bed INFO @ Mon, 06 Aug 2018 10:41:18: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (3103 records, 4 fields): 13 millis CompletedMACS2peakCalling pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1080 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。