Job ID = 10924614 sra ファイルのダウンロード中... Completed: 426119K bytes transferred in 12 seconds (285870K 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 7149764 spots for /home/okishinya/chipatlas/results/dm3/SRX2396701/SRR5078071.sra Written 7149764 spots for /home/okishinya/chipatlas/results/dm3/SRX2396701/SRR5078071.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: 00:06:54 7149764 reads; of these: 7149764 (100.00%) were paired; of these: 1487996 (20.81%) aligned concordantly 0 times 5292562 (74.02%) aligned concordantly exactly 1 time 369206 (5.16%) aligned concordantly >1 times ---- 1487996 pairs aligned concordantly 0 times; of these: 240149 (16.14%) aligned discordantly 1 time ---- 1247847 pairs aligned 0 times concordantly or discordantly; of these: 2495694 mates make up the pairs; of these: 2229494 (89.33%) aligned 0 times 194835 (7.81%) aligned exactly 1 time 71365 (2.86%) aligned >1 times 84.41% overall alignment rate Time searching: 00:06:54 Overall time: 00:06:54 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] 182286 / 5887362 = 0.0310 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 10:36:56: # Command line: callpeak -t SRX2396701.bam -f BAM -g dm -n SRX2396701.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2396701.05 # format = BAM # ChIP-seq file = ['SRX2396701.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 10:36:56: # Command line: callpeak -t SRX2396701.bam -f BAM -g dm -n SRX2396701.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2396701.20 # format = BAM # ChIP-seq file = ['SRX2396701.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 10:36:56: # Command line: callpeak -t SRX2396701.bam -f BAM -g dm -n SRX2396701.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2396701.10 # format = BAM # ChIP-seq file = ['SRX2396701.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 10:36:56: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:36:56: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:36:56: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:36:56: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:36:56: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:36:56: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:37:03: 1000000 INFO @ Mon, 06 Aug 2018 10:37:03: 1000000 INFO @ Mon, 06 Aug 2018 10:37:03: 1000000 INFO @ Mon, 06 Aug 2018 10:37:09: 2000000 INFO @ Mon, 06 Aug 2018 10:37:10: 2000000 INFO @ Mon, 06 Aug 2018 10:37:10: 2000000 INFO @ Mon, 06 Aug 2018 10:37:16: 3000000 INFO @ Mon, 06 Aug 2018 10:37:17: 3000000 INFO @ Mon, 06 Aug 2018 10:37:17: 3000000 INFO @ Mon, 06 Aug 2018 10:37:23: 4000000 INFO @ Mon, 06 Aug 2018 10:37:23: 4000000 INFO @ Mon, 06 Aug 2018 10:37:24: 4000000 INFO @ Mon, 06 Aug 2018 10:37:29: 5000000 INFO @ Mon, 06 Aug 2018 10:37:30: 5000000 INFO @ Mon, 06 Aug 2018 10:37:30: 5000000 INFO @ Mon, 06 Aug 2018 10:37:36: 6000000 INFO @ Mon, 06 Aug 2018 10:37:37: 6000000 INFO @ Mon, 06 Aug 2018 10:37:37: 6000000 INFO @ Mon, 06 Aug 2018 10:37:42: 7000000 INFO @ Mon, 06 Aug 2018 10:37:44: 7000000 INFO @ Mon, 06 Aug 2018 10:37:44: 7000000 INFO @ Mon, 06 Aug 2018 10:37:49: 8000000 INFO @ Mon, 06 Aug 2018 10:37:51: 8000000 INFO @ Mon, 06 Aug 2018 10:37:51: 8000000 INFO @ Mon, 06 Aug 2018 10:37:56: 9000000 INFO @ Mon, 06 Aug 2018 10:37:58: 9000000 INFO @ Mon, 06 Aug 2018 10:37:58: 9000000 INFO @ Mon, 06 Aug 2018 10:38:02: 10000000 INFO @ Mon, 06 Aug 2018 10:38:05: 10000000 INFO @ Mon, 06 Aug 2018 10:38:05: 10000000 INFO @ Mon, 06 Aug 2018 10:38:09: 11000000 INFO @ Mon, 06 Aug 2018 10:38:12: 11000000 INFO @ Mon, 06 Aug 2018 10:38:12: 11000000 INFO @ Mon, 06 Aug 2018 10:38:13: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:38:13: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:38:13: #1 total tags in treatment: 5482530 INFO @ Mon, 06 Aug 2018 10:38:13: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:38:13: #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 10:38:14: #1 tags after filtering in treatment: 5269753 INFO @ Mon, 06 Aug 2018 10:38:14: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 06 Aug 2018 10:38:14: #1 finished! INFO @ Mon, 06 Aug 2018 10:38:14: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:38:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:38:14: #2 number of paired peaks: 2728 INFO @ Mon, 06 Aug 2018 10:38:14: start model_add_line... INFO @ Mon, 06 Aug 2018 10:38:14: start X-correlation... INFO @ Mon, 06 Aug 2018 10:38:14: end of X-cor INFO @ Mon, 06 Aug 2018 10:38:14: #2 finished! INFO @ Mon, 06 Aug 2018 10:38:14: #2 predicted fragment length is 294 bps INFO @ Mon, 06 Aug 2018 10:38:14: #2 alternative fragment length(s) may be 294 bps INFO @ Mon, 06 Aug 2018 10:38:14: #2.2 Generate R script for model : SRX2396701.10_model.r INFO @ Mon, 06 Aug 2018 10:38:14: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:38:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:38:16: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:38:16: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:38:16: #1 total tags in treatment: 5482530 INFO @ Mon, 06 Aug 2018 10:38:16: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:38:16: #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 10:38:16: #1 tags after filtering in treatment: 5269753 INFO @ Mon, 06 Aug 2018 10:38:16: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 06 Aug 2018 10:38:16: #1 finished! INFO @ Mon, 06 Aug 2018 10:38:16: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:38:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:38:17: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:38:17: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:38:17: #1 total tags in treatment: 5482530 INFO @ Mon, 06 Aug 2018 10:38:17: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:38:17: #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 10:38:17: #1 tags after filtering in treatment: 5269753 INFO @ Mon, 06 Aug 2018 10:38:17: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 06 Aug 2018 10:38:17: #1 finished! INFO @ Mon, 06 Aug 2018 10:38:17: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:38:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:38:17: #2 number of paired peaks: 2728 INFO @ Mon, 06 Aug 2018 10:38:17: start model_add_line... INFO @ Mon, 06 Aug 2018 10:38:17: start X-correlation... INFO @ Mon, 06 Aug 2018 10:38:17: end of X-cor INFO @ Mon, 06 Aug 2018 10:38:17: #2 finished! INFO @ Mon, 06 Aug 2018 10:38:17: #2 predicted fragment length is 294 bps INFO @ Mon, 06 Aug 2018 10:38:17: #2 alternative fragment length(s) may be 294 bps INFO @ Mon, 06 Aug 2018 10:38:17: #2.2 Generate R script for model : SRX2396701.20_model.r INFO @ Mon, 06 Aug 2018 10:38:17: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:38:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:38:17: #2 number of paired peaks: 2728 INFO @ Mon, 06 Aug 2018 10:38:17: start model_add_line... INFO @ Mon, 06 Aug 2018 10:38:17: start X-correlation... INFO @ Mon, 06 Aug 2018 10:38:17: end of X-cor INFO @ Mon, 06 Aug 2018 10:38:17: #2 finished! INFO @ Mon, 06 Aug 2018 10:38:17: #2 predicted fragment length is 294 bps INFO @ Mon, 06 Aug 2018 10:38:17: #2 alternative fragment length(s) may be 294 bps INFO @ Mon, 06 Aug 2018 10:38:17: #2.2 Generate R script for model : SRX2396701.05_model.r INFO @ Mon, 06 Aug 2018 10:38:17: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:38:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:38:29: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:38:31: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:38:31: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:38:37: #4 Write output xls file... SRX2396701.10_peaks.xls INFO @ Mon, 06 Aug 2018 10:38:37: #4 Write peak in narrowPeak format file... SRX2396701.10_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:38:37: #4 Write summits bed file... SRX2396701.10_summits.bed INFO @ Mon, 06 Aug 2018 10:38:37: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1929 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 06 Aug 2018 10:38:38: #4 Write output xls file... SRX2396701.20_peaks.xls INFO @ Mon, 06 Aug 2018 10:38:38: #4 Write peak in narrowPeak format file... SRX2396701.20_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:38:38: #4 Write summits bed file... SRX2396701.20_summits.bed INFO @ Mon, 06 Aug 2018 10:38:38: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (456 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 06 Aug 2018 10:38:38: #4 Write output xls file... SRX2396701.05_peaks.xls INFO @ Mon, 06 Aug 2018 10:38:38: #4 Write peak in narrowPeak format file... SRX2396701.05_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:38:39: #4 Write summits bed file... SRX2396701.05_summits.bed INFO @ Mon, 06 Aug 2018 10:38:39: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (4510 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。