Job ID = 10924605 sra ファイルのダウンロード中... Completed: 419255K bytes transferred in 10 seconds (319978K 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 7155407 spots for /home/okishinya/chipatlas/results/dm3/SRX2396692/SRR5078062.sra Written 7155407 spots for /home/okishinya/chipatlas/results/dm3/SRX2396692/SRR5078062.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: 00:08:59 7155407 reads; of these: 7155407 (100.00%) were paired; of these: 2298615 (32.12%) aligned concordantly 0 times 4351424 (60.81%) aligned concordantly exactly 1 time 505368 (7.06%) aligned concordantly >1 times ---- 2298615 pairs aligned concordantly 0 times; of these: 145910 (6.35%) aligned discordantly 1 time ---- 2152705 pairs aligned 0 times concordantly or discordantly; of these: 4305410 mates make up the pairs; of these: 4051072 (94.09%) aligned 0 times 186891 (4.34%) aligned exactly 1 time 67447 (1.57%) aligned >1 times 71.69% overall alignment rate Time searching: 00:08:59 Overall time: 00:08:59 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] 800664 / 4999999 = 0.1601 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 10:38:01: # Command line: callpeak -t SRX2396692.bam -f BAM -g dm -n SRX2396692.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2396692.20 # format = BAM # ChIP-seq file = ['SRX2396692.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 10:38:01: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:38:01: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:38:01: # Command line: callpeak -t SRX2396692.bam -f BAM -g dm -n SRX2396692.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2396692.10 # format = BAM # ChIP-seq file = ['SRX2396692.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 10:38:01: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:38:01: # Command line: callpeak -t SRX2396692.bam -f BAM -g dm -n SRX2396692.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2396692.05 # format = BAM # ChIP-seq file = ['SRX2396692.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 10:38:01: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:38:01: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:38:01: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:38:08: 1000000 INFO @ Mon, 06 Aug 2018 10:38:09: 1000000 INFO @ Mon, 06 Aug 2018 10:38:09: 1000000 INFO @ Mon, 06 Aug 2018 10:38:14: 2000000 INFO @ Mon, 06 Aug 2018 10:38:16: 2000000 INFO @ Mon, 06 Aug 2018 10:38:16: 2000000 INFO @ Mon, 06 Aug 2018 10:38:20: 3000000 INFO @ Mon, 06 Aug 2018 10:38:22: 3000000 INFO @ Mon, 06 Aug 2018 10:38:22: 3000000 INFO @ Mon, 06 Aug 2018 10:38:26: 4000000 INFO @ Mon, 06 Aug 2018 10:38:28: 4000000 INFO @ Mon, 06 Aug 2018 10:38:29: 4000000 INFO @ Mon, 06 Aug 2018 10:38:31: 5000000 INFO @ Mon, 06 Aug 2018 10:38:35: 5000000 INFO @ Mon, 06 Aug 2018 10:38:35: 5000000 INFO @ Mon, 06 Aug 2018 10:38:37: 6000000 INFO @ Mon, 06 Aug 2018 10:38:41: 6000000 INFO @ Mon, 06 Aug 2018 10:38:41: 6000000 INFO @ Mon, 06 Aug 2018 10:38:43: 7000000 INFO @ Mon, 06 Aug 2018 10:38:47: 7000000 INFO @ Mon, 06 Aug 2018 10:38:48: 7000000 INFO @ Mon, 06 Aug 2018 10:38:49: 8000000 INFO @ Mon, 06 Aug 2018 10:38:53: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:38:53: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:38:53: #1 total tags in treatment: 4062275 INFO @ Mon, 06 Aug 2018 10:38:53: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:38:53: #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 10:38:53: #1 tags after filtering in treatment: 3990546 INFO @ Mon, 06 Aug 2018 10:38:53: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 06 Aug 2018 10:38:53: #1 finished! INFO @ Mon, 06 Aug 2018 10:38:53: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:38:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:38:53: #2 number of paired peaks: 583 WARNING @ Mon, 06 Aug 2018 10:38:53: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Mon, 06 Aug 2018 10:38:53: start model_add_line... INFO @ Mon, 06 Aug 2018 10:38:53: start X-correlation... INFO @ Mon, 06 Aug 2018 10:38:53: end of X-cor INFO @ Mon, 06 Aug 2018 10:38:53: #2 finished! INFO @ Mon, 06 Aug 2018 10:38:53: #2 predicted fragment length is 271 bps INFO @ Mon, 06 Aug 2018 10:38:53: #2 alternative fragment length(s) may be 271 bps INFO @ Mon, 06 Aug 2018 10:38:53: #2.2 Generate R script for model : SRX2396692.20_model.r INFO @ Mon, 06 Aug 2018 10:38:53: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:38:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:38:53: 8000000 INFO @ Mon, 06 Aug 2018 10:38:54: 8000000 INFO @ Mon, 06 Aug 2018 10:38:57: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:38:57: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:38:57: #1 total tags in treatment: 4062275 INFO @ Mon, 06 Aug 2018 10:38:57: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:38:57: #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 10:38:57: #1 tags after filtering in treatment: 3990546 INFO @ Mon, 06 Aug 2018 10:38:57: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 06 Aug 2018 10:38:57: #1 finished! INFO @ Mon, 06 Aug 2018 10:38:57: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:38:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:38:58: #2 number of paired peaks: 583 WARNING @ Mon, 06 Aug 2018 10:38:58: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Mon, 06 Aug 2018 10:38:58: start model_add_line... INFO @ Mon, 06 Aug 2018 10:38:58: start X-correlation... INFO @ Mon, 06 Aug 2018 10:38:58: end of X-cor INFO @ Mon, 06 Aug 2018 10:38:58: #2 finished! INFO @ Mon, 06 Aug 2018 10:38:58: #2 predicted fragment length is 271 bps INFO @ Mon, 06 Aug 2018 10:38:58: #2 alternative fragment length(s) may be 271 bps INFO @ Mon, 06 Aug 2018 10:38:58: #2.2 Generate R script for model : SRX2396692.10_model.r INFO @ Mon, 06 Aug 2018 10:38:58: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:38:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:38:58: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:38:58: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:38:58: #1 total tags in treatment: 4062275 INFO @ Mon, 06 Aug 2018 10:38:58: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:38:58: #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 10:38:58: #1 tags after filtering in treatment: 3990546 INFO @ Mon, 06 Aug 2018 10:38:58: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 06 Aug 2018 10:38:58: #1 finished! INFO @ Mon, 06 Aug 2018 10:38:58: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:38:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:38:59: #2 number of paired peaks: 583 WARNING @ Mon, 06 Aug 2018 10:38:59: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Mon, 06 Aug 2018 10:38:59: start model_add_line... INFO @ Mon, 06 Aug 2018 10:38:59: start X-correlation... INFO @ Mon, 06 Aug 2018 10:38:59: end of X-cor INFO @ Mon, 06 Aug 2018 10:38:59: #2 finished! INFO @ Mon, 06 Aug 2018 10:38:59: #2 predicted fragment length is 271 bps INFO @ Mon, 06 Aug 2018 10:38:59: #2 alternative fragment length(s) may be 271 bps INFO @ Mon, 06 Aug 2018 10:38:59: #2.2 Generate R script for model : SRX2396692.05_model.r INFO @ Mon, 06 Aug 2018 10:38:59: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:38:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:39:03: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:39:08: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:39:08: #4 Write output xls file... SRX2396692.20_peaks.xls INFO @ Mon, 06 Aug 2018 10:39:08: #4 Write peak in narrowPeak format file... SRX2396692.20_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:39:08: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:39:08: #4 Write summits bed file... SRX2396692.20_summits.bed INFO @ Mon, 06 Aug 2018 10:39:08: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (84 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 06 Aug 2018 10:39:13: #4 Write output xls file... SRX2396692.10_peaks.xls INFO @ Mon, 06 Aug 2018 10:39:13: #4 Write peak in narrowPeak format file... SRX2396692.10_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:39:13: #4 Write summits bed file... SRX2396692.10_summits.bed INFO @ Mon, 06 Aug 2018 10:39:13: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (448 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 06 Aug 2018 10:39:13: #4 Write output xls file... SRX2396692.05_peaks.xls INFO @ Mon, 06 Aug 2018 10:39:13: #4 Write peak in narrowPeak format file... SRX2396692.05_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:39:13: #4 Write summits bed file... SRX2396692.05_summits.bed INFO @ Mon, 06 Aug 2018 10:39:13: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1549 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。