Job ID = 9730440 sra ファイルのダウンロード中... Completed: 495341K bytes transferred in 9 seconds (412918K bits/sec), in 1 file, 2 directories. 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... Written 7257641 spots for /home/okishinya/chipatlas/results/dm3/SRX2559027/SRR5253492.sra Written 7257641 spots total 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: 00:45:08 7257641 reads; of these: 7257641 (100.00%) were paired; of these: 429375 (5.92%) aligned concordantly 0 times 1409633 (19.42%) aligned concordantly exactly 1 time 5418633 (74.66%) aligned concordantly >1 times ---- 429375 pairs aligned concordantly 0 times; of these: 24686 (5.75%) aligned discordantly 1 time ---- 404689 pairs aligned 0 times concordantly or discordantly; of these: 809378 mates make up the pairs; of these: 429094 (53.02%) aligned 0 times 64134 (7.92%) aligned exactly 1 time 316150 (39.06%) aligned >1 times 97.04% overall alignment rate Time searching: 00:45:08 Overall time: 00:45:08 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] 368560 / 6835769 = 0.0539 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 @ Sun, 03 Sep 2017 01:44:02: # Command line: callpeak -t SRX2559027.bam -f BAM -g dm -n SRX2559027.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2559027.20 # format = BAM # ChIP-seq file = ['SRX2559027.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 @ Sun, 03 Sep 2017 01:44:02: # Command line: callpeak -t SRX2559027.bam -f BAM -g dm -n SRX2559027.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2559027.05 # format = BAM # ChIP-seq file = ['SRX2559027.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 @ Sun, 03 Sep 2017 01:44:02: # Command line: callpeak -t SRX2559027.bam -f BAM -g dm -n SRX2559027.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2559027.10 # format = BAM # ChIP-seq file = ['SRX2559027.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 @ Sun, 03 Sep 2017 01:44:02: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:44:02: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:44:02: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:44:02: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:44:02: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:44:02: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:44:08: 1000000 INFO @ Sun, 03 Sep 2017 01:44:08: 1000000 INFO @ Sun, 03 Sep 2017 01:44:08: 1000000 INFO @ Sun, 03 Sep 2017 01:44:14: 2000000 INFO @ Sun, 03 Sep 2017 01:44:14: 2000000 INFO @ Sun, 03 Sep 2017 01:44:14: 2000000 INFO @ Sun, 03 Sep 2017 01:44:20: 3000000 INFO @ Sun, 03 Sep 2017 01:44:20: 3000000 INFO @ Sun, 03 Sep 2017 01:44:20: 3000000 INFO @ Sun, 03 Sep 2017 01:44:26: 4000000 INFO @ Sun, 03 Sep 2017 01:44:26: 4000000 INFO @ Sun, 03 Sep 2017 01:44:26: 4000000 INFO @ Sun, 03 Sep 2017 01:44:31: 5000000 INFO @ Sun, 03 Sep 2017 01:44:32: 5000000 INFO @ Sun, 03 Sep 2017 01:44:32: 5000000 INFO @ Sun, 03 Sep 2017 01:44:37: 6000000 INFO @ Sun, 03 Sep 2017 01:44:38: 6000000 INFO @ Sun, 03 Sep 2017 01:44:38: 6000000 INFO @ Sun, 03 Sep 2017 01:44:44: 7000000 INFO @ Sun, 03 Sep 2017 01:44:44: 7000000 INFO @ Sun, 03 Sep 2017 01:44:44: 7000000 INFO @ Sun, 03 Sep 2017 01:44:49: 8000000 INFO @ Sun, 03 Sep 2017 01:44:50: 8000000 INFO @ Sun, 03 Sep 2017 01:44:50: 8000000 INFO @ Sun, 03 Sep 2017 01:44:55: 9000000 INFO @ Sun, 03 Sep 2017 01:44:56: 9000000 INFO @ Sun, 03 Sep 2017 01:44:56: 9000000 INFO @ Sun, 03 Sep 2017 01:45:01: 10000000 INFO @ Sun, 03 Sep 2017 01:45:03: 10000000 INFO @ Sun, 03 Sep 2017 01:45:03: 10000000 INFO @ Sun, 03 Sep 2017 01:45:07: 11000000 INFO @ Sun, 03 Sep 2017 01:45:09: 11000000 INFO @ Sun, 03 Sep 2017 01:45:09: 11000000 INFO @ Sun, 03 Sep 2017 01:45:14: 12000000 INFO @ Sun, 03 Sep 2017 01:45:15: 12000000 INFO @ Sun, 03 Sep 2017 01:45:15: 12000000 INFO @ Sun, 03 Sep 2017 01:45:19: 13000000 INFO @ Sun, 03 Sep 2017 01:45:21: 13000000 INFO @ Sun, 03 Sep 2017 01:45:21: 13000000 INFO @ Sun, 03 Sep 2017 01:45:22: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:45:22: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:45:22: #1 total tags in treatment: 6459886 INFO @ Sun, 03 Sep 2017 01:45:22: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:45:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:45:22: #1 tags after filtering in treatment: 5172412 INFO @ Sun, 03 Sep 2017 01:45:22: #1 Redundant rate of treatment: 0.20 INFO @ Sun, 03 Sep 2017 01:45:22: #1 finished! INFO @ Sun, 03 Sep 2017 01:45:22: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:45:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:45:22: #2 number of paired peaks: 5171 INFO @ Sun, 03 Sep 2017 01:45:22: start model_add_line... INFO @ Sun, 03 Sep 2017 01:45:22: start X-correlation... INFO @ Sun, 03 Sep 2017 01:45:23: end of X-cor INFO @ Sun, 03 Sep 2017 01:45:23: #2 finished! INFO @ Sun, 03 Sep 2017 01:45:23: #2 predicted fragment length is 155 bps INFO @ Sun, 03 Sep 2017 01:45:23: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 03 Sep 2017 01:45:23: #2.2 Generate R script for model : SRX2559027.20_model.r INFO @ Sun, 03 Sep 2017 01:45:23: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:45:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:45:23: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:45:23: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:45:23: #1 total tags in treatment: 6459886 INFO @ Sun, 03 Sep 2017 01:45:23: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:45:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:45:23: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:45:23: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:45:23: #1 total tags in treatment: 6459886 INFO @ Sun, 03 Sep 2017 01:45:23: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:45:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:45:23: #1 tags after filtering in treatment: 5172412 INFO @ Sun, 03 Sep 2017 01:45:23: #1 Redundant rate of treatment: 0.20 INFO @ Sun, 03 Sep 2017 01:45:23: #1 finished! INFO @ Sun, 03 Sep 2017 01:45:23: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:45:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:45:23: #1 tags after filtering in treatment: 5172412 INFO @ Sun, 03 Sep 2017 01:45:23: #1 Redundant rate of treatment: 0.20 INFO @ Sun, 03 Sep 2017 01:45:23: #1 finished! INFO @ Sun, 03 Sep 2017 01:45:23: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:45:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:45:24: #2 number of paired peaks: 5171 INFO @ Sun, 03 Sep 2017 01:45:24: start model_add_line... INFO @ Sun, 03 Sep 2017 01:45:24: start X-correlation... INFO @ Sun, 03 Sep 2017 01:45:24: end of X-cor INFO @ Sun, 03 Sep 2017 01:45:24: #2 finished! INFO @ Sun, 03 Sep 2017 01:45:24: #2 predicted fragment length is 155 bps INFO @ Sun, 03 Sep 2017 01:45:24: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 03 Sep 2017 01:45:24: #2.2 Generate R script for model : SRX2559027.05_model.r INFO @ Sun, 03 Sep 2017 01:45:24: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:45:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:45:24: #2 number of paired peaks: 5171 INFO @ Sun, 03 Sep 2017 01:45:24: start model_add_line... INFO @ Sun, 03 Sep 2017 01:45:24: start X-correlation... INFO @ Sun, 03 Sep 2017 01:45:24: end of X-cor INFO @ Sun, 03 Sep 2017 01:45:24: #2 finished! INFO @ Sun, 03 Sep 2017 01:45:24: #2 predicted fragment length is 155 bps INFO @ Sun, 03 Sep 2017 01:45:24: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 03 Sep 2017 01:45:24: #2.2 Generate R script for model : SRX2559027.10_model.r INFO @ Sun, 03 Sep 2017 01:45:24: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:45:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:45:38: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:45:39: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:45:39: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:45:46: #4 Write output xls file... SRX2559027.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:45:46: #4 Write peak in narrowPeak format file... SRX2559027.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:45:46: #4 Write summits bed file... SRX2559027.20_summits.bed INFO @ Sun, 03 Sep 2017 01:45:46: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1569 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:45:47: #4 Write output xls file... SRX2559027.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:45:47: #4 Write peak in narrowPeak format file... SRX2559027.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:45:47: #4 Write summits bed file... SRX2559027.10_summits.bed INFO @ Sun, 03 Sep 2017 01:45:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4319 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:45:47: #4 Write output xls file... SRX2559027.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:45:48: #4 Write peak in narrowPeak format file... SRX2559027.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:45:48: #4 Write summits bed file... SRX2559027.05_summits.bed INFO @ Sun, 03 Sep 2017 01:45:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (8775 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。