Job ID = 10194777 sra ファイルのダウンロード中... Completed: 473534K bytes transferred in 8 seconds (475716K 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: SINGLE fastq に変換中... Written 20693677 spots for /home/okishinya/chipatlas/results/rn6/SRX1774910/SRR3544940.sra Written 20693677 spots total 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: 00:00:01 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:14:26 20693677 reads; of these: 20693677 (100.00%) were unpaired; of these: 705193 (3.41%) aligned 0 times 15901804 (76.84%) aligned exactly 1 time 4086680 (19.75%) aligned >1 times 96.59% overall alignment rate Time searching: 00:14:32 Overall time: 00:14:32 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4592197 / 19988484 = 0.2297 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 @ Fri, 10 Nov 2017 17:10:20: # Command line: callpeak -t SRX1774910.bam -f BAM -g 2.15e9 -n SRX1774910.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1774910.05 # format = BAM # ChIP-seq file = ['SRX1774910.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 10 Nov 2017 17:10:20: # Command line: callpeak -t SRX1774910.bam -f BAM -g 2.15e9 -n SRX1774910.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1774910.20 # format = BAM # ChIP-seq file = ['SRX1774910.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 10 Nov 2017 17:10:20: # Command line: callpeak -t SRX1774910.bam -f BAM -g 2.15e9 -n SRX1774910.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1774910.10 # format = BAM # ChIP-seq file = ['SRX1774910.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 10 Nov 2017 17:10:20: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:10:20: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:10:20: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:10:20: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:10:20: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:10:20: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:10:27: 1000000 INFO @ Fri, 10 Nov 2017 17:10:27: 1000000 INFO @ Fri, 10 Nov 2017 17:10:27: 1000000 INFO @ Fri, 10 Nov 2017 17:10:33: 2000000 INFO @ Fri, 10 Nov 2017 17:10:33: 2000000 INFO @ Fri, 10 Nov 2017 17:10:34: 2000000 INFO @ Fri, 10 Nov 2017 17:10:40: 3000000 INFO @ Fri, 10 Nov 2017 17:10:40: 3000000 INFO @ Fri, 10 Nov 2017 17:10:41: 3000000 INFO @ Fri, 10 Nov 2017 17:10:48: 4000000 INFO @ Fri, 10 Nov 2017 17:10:48: 4000000 INFO @ Fri, 10 Nov 2017 17:10:48: 4000000 INFO @ Fri, 10 Nov 2017 17:10:55: 5000000 INFO @ Fri, 10 Nov 2017 17:10:56: 5000000 INFO @ Fri, 10 Nov 2017 17:10:56: 5000000 INFO @ Fri, 10 Nov 2017 17:11:03: 6000000 INFO @ Fri, 10 Nov 2017 17:11:03: 6000000 INFO @ Fri, 10 Nov 2017 17:11:03: 6000000 INFO @ Fri, 10 Nov 2017 17:11:10: 7000000 INFO @ Fri, 10 Nov 2017 17:11:11: 7000000 INFO @ Fri, 10 Nov 2017 17:11:11: 7000000 INFO @ Fri, 10 Nov 2017 17:11:18: 8000000 INFO @ Fri, 10 Nov 2017 17:11:19: 8000000 INFO @ Fri, 10 Nov 2017 17:11:19: 8000000 INFO @ Fri, 10 Nov 2017 17:11:25: 9000000 INFO @ Fri, 10 Nov 2017 17:11:27: 9000000 INFO @ Fri, 10 Nov 2017 17:11:28: 9000000 INFO @ Fri, 10 Nov 2017 17:11:34: 10000000 INFO @ Fri, 10 Nov 2017 17:11:35: 10000000 INFO @ Fri, 10 Nov 2017 17:11:37: 10000000 INFO @ Fri, 10 Nov 2017 17:11:42: 11000000 INFO @ Fri, 10 Nov 2017 17:11:43: 11000000 INFO @ Fri, 10 Nov 2017 17:11:46: 11000000 INFO @ Fri, 10 Nov 2017 17:11:50: 12000000 INFO @ Fri, 10 Nov 2017 17:11:51: 12000000 INFO @ Fri, 10 Nov 2017 17:11:55: 12000000 INFO @ Fri, 10 Nov 2017 17:11:58: 13000000 INFO @ Fri, 10 Nov 2017 17:11:59: 13000000 INFO @ Fri, 10 Nov 2017 17:12:03: 13000000 INFO @ Fri, 10 Nov 2017 17:12:05: 14000000 INFO @ Fri, 10 Nov 2017 17:12:07: 14000000 INFO @ Fri, 10 Nov 2017 17:12:12: 14000000 INFO @ Fri, 10 Nov 2017 17:12:13: 15000000 INFO @ Fri, 10 Nov 2017 17:12:15: 15000000 INFO @ Fri, 10 Nov 2017 17:12:16: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:12:16: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:12:16: #1 total tags in treatment: 15396287 INFO @ Fri, 10 Nov 2017 17:12:16: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:12:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 17:12:17: #1 tags after filtering in treatment: 15396100 INFO @ Fri, 10 Nov 2017 17:12:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:12:17: #1 finished! INFO @ Fri, 10 Nov 2017 17:12:17: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:12:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:12:18: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:12:18: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:12:18: #1 total tags in treatment: 15396287 INFO @ Fri, 10 Nov 2017 17:12:18: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:12:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 17:12:19: #1 tags after filtering in treatment: 15396100 INFO @ Fri, 10 Nov 2017 17:12:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:12:19: #1 finished! INFO @ Fri, 10 Nov 2017 17:12:19: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:12:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:12:19: 15000000 INFO @ Fri, 10 Nov 2017 17:12:20: #2 number of paired peaks: 47677 INFO @ Fri, 10 Nov 2017 17:12:20: start model_add_line... INFO @ Fri, 10 Nov 2017 17:12:20: start X-correlation... INFO @ Fri, 10 Nov 2017 17:12:20: end of X-cor INFO @ Fri, 10 Nov 2017 17:12:20: #2 finished! INFO @ Fri, 10 Nov 2017 17:12:20: #2 predicted fragment length is 172 bps INFO @ Fri, 10 Nov 2017 17:12:20: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 10 Nov 2017 17:12:20: #2.2 Generate R script for model : SRX1774910.20_model.r INFO @ Fri, 10 Nov 2017 17:12:20: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:12:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:12:21: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:12:21: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:12:21: #1 total tags in treatment: 15396287 INFO @ Fri, 10 Nov 2017 17:12:21: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:12:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 17:12:22: #2 number of paired peaks: 47677 INFO @ Fri, 10 Nov 2017 17:12:22: start model_add_line... INFO @ Fri, 10 Nov 2017 17:12:22: #1 tags after filtering in treatment: 15396100 INFO @ Fri, 10 Nov 2017 17:12:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:12:22: #1 finished! INFO @ Fri, 10 Nov 2017 17:12:22: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:12:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:12:22: start X-correlation... INFO @ Fri, 10 Nov 2017 17:12:22: end of X-cor INFO @ Fri, 10 Nov 2017 17:12:22: #2 finished! INFO @ Fri, 10 Nov 2017 17:12:22: #2 predicted fragment length is 172 bps INFO @ Fri, 10 Nov 2017 17:12:22: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 10 Nov 2017 17:12:22: #2.2 Generate R script for model : SRX1774910.05_model.r INFO @ Fri, 10 Nov 2017 17:12:22: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:12:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:12:25: #2 number of paired peaks: 47677 INFO @ Fri, 10 Nov 2017 17:12:25: start model_add_line... INFO @ Fri, 10 Nov 2017 17:12:25: start X-correlation... INFO @ Fri, 10 Nov 2017 17:12:25: end of X-cor INFO @ Fri, 10 Nov 2017 17:12:25: #2 finished! INFO @ Fri, 10 Nov 2017 17:12:25: #2 predicted fragment length is 172 bps INFO @ Fri, 10 Nov 2017 17:12:25: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 10 Nov 2017 17:12:25: #2.2 Generate R script for model : SRX1774910.10_model.r INFO @ Fri, 10 Nov 2017 17:12:25: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:12:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:12:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:12:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:13:02: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:13:19: #4 Write output xls file... SRX1774910.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:13:19: #4 Write peak in narrowPeak format file... SRX1774910.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:13:19: #4 Write summits bed file... SRX1774910.20_summits.bed INFO @ Fri, 10 Nov 2017 17:13:19: Done! pass1 - making usageList (47 chroms): 2 millis pass2 - checking and writing primary data (6254 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:13:24: #4 Write output xls file... SRX1774910.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:13:25: #4 Write peak in narrowPeak format file... SRX1774910.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:13:25: #4 Write summits bed file... SRX1774910.05_summits.bed INFO @ Fri, 10 Nov 2017 17:13:25: Done! pass1 - making usageList (97 chroms): 5 millis pass2 - checking and writing primary data (25776 records, 4 fields): 65 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:13:26: #4 Write output xls file... SRX1774910.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:13:26: #4 Write peak in narrowPeak format file... SRX1774910.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:13:26: #4 Write summits bed file... SRX1774910.10_summits.bed INFO @ Fri, 10 Nov 2017 17:13:26: Done! pass1 - making usageList (66 chroms): 3 millis pass2 - checking and writing primary data (14492 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。