Job ID = 10194744 sra ファイルのダウンロード中... Completed: 369577K bytes transferred in 6 seconds (436719K 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 13956260 spots for /home/okishinya/chipatlas/results/rn6/SRX1068233/SRR2073192.sra Written 13956260 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: 00:00:02 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:10:35 13956260 reads; of these: 13956260 (100.00%) were unpaired; of these: 410072 (2.94%) aligned 0 times 12109993 (86.77%) aligned exactly 1 time 1436195 (10.29%) aligned >1 times 97.06% overall alignment rate Time searching: 00:10:40 Overall time: 00:10:40 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 8 files... [bam_rmdupse_core] 2553504 / 13546188 = 0.1885 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 23:45:38: # Command line: callpeak -t SRX1068233.bam -f BAM -g 2.15e9 -n SRX1068233.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1068233.20 # format = BAM # ChIP-seq file = ['SRX1068233.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 23:45:38: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:45:38: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:45:38: # Command line: callpeak -t SRX1068233.bam -f BAM -g 2.15e9 -n SRX1068233.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1068233.05 # format = BAM # ChIP-seq file = ['SRX1068233.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 23:45:38: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:45:38: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:45:38: # Command line: callpeak -t SRX1068233.bam -f BAM -g 2.15e9 -n SRX1068233.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1068233.10 # format = BAM # ChIP-seq file = ['SRX1068233.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 23:45:38: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:45:38: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:45:47: 1000000 INFO @ Fri, 10 Nov 2017 23:45:47: 1000000 INFO @ Fri, 10 Nov 2017 23:45:49: 1000000 INFO @ Fri, 10 Nov 2017 23:45:53: 2000000 INFO @ Fri, 10 Nov 2017 23:45:56: 2000000 INFO @ Fri, 10 Nov 2017 23:45:56: 2000000 INFO @ Fri, 10 Nov 2017 23:46:01: 3000000 INFO @ Fri, 10 Nov 2017 23:46:05: 3000000 INFO @ Fri, 10 Nov 2017 23:46:05: 3000000 INFO @ Fri, 10 Nov 2017 23:46:10: 4000000 INFO @ Fri, 10 Nov 2017 23:46:14: 4000000 INFO @ Fri, 10 Nov 2017 23:46:16: 4000000 INFO @ Fri, 10 Nov 2017 23:46:18: 5000000 INFO @ Fri, 10 Nov 2017 23:46:23: 5000000 INFO @ Fri, 10 Nov 2017 23:46:26: 5000000 INFO @ Fri, 10 Nov 2017 23:46:27: 6000000 INFO @ Fri, 10 Nov 2017 23:46:33: 6000000 INFO @ Fri, 10 Nov 2017 23:46:34: 6000000 INFO @ Fri, 10 Nov 2017 23:46:35: 7000000 INFO @ Fri, 10 Nov 2017 23:46:41: 7000000 INFO @ Fri, 10 Nov 2017 23:46:43: 7000000 INFO @ Fri, 10 Nov 2017 23:46:43: 8000000 INFO @ Fri, 10 Nov 2017 23:46:51: 9000000 INFO @ Fri, 10 Nov 2017 23:46:52: 8000000 INFO @ Fri, 10 Nov 2017 23:46:52: 8000000 INFO @ Fri, 10 Nov 2017 23:46:58: 10000000 INFO @ Fri, 10 Nov 2017 23:47:00: 9000000 INFO @ Fri, 10 Nov 2017 23:47:01: 9000000 INFO @ Fri, 10 Nov 2017 23:47:07: #1 tag size is determined as 64 bps INFO @ Fri, 10 Nov 2017 23:47:07: #1 tag size = 64 INFO @ Fri, 10 Nov 2017 23:47:07: #1 total tags in treatment: 10992684 INFO @ Fri, 10 Nov 2017 23:47:07: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:47:07: #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 23:47:07: #1 tags after filtering in treatment: 10992352 INFO @ Fri, 10 Nov 2017 23:47:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:47:07: #1 finished! INFO @ Fri, 10 Nov 2017 23:47:07: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:47:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:47:08: 10000000 INFO @ Fri, 10 Nov 2017 23:47:09: 10000000 INFO @ Fri, 10 Nov 2017 23:47:10: #2 number of paired peaks: 28905 INFO @ Fri, 10 Nov 2017 23:47:10: start model_add_line... INFO @ Fri, 10 Nov 2017 23:47:11: start X-correlation... INFO @ Fri, 10 Nov 2017 23:47:11: end of X-cor INFO @ Fri, 10 Nov 2017 23:47:11: #2 finished! INFO @ Fri, 10 Nov 2017 23:47:11: #2 predicted fragment length is 229 bps INFO @ Fri, 10 Nov 2017 23:47:11: #2 alternative fragment length(s) may be 229 bps INFO @ Fri, 10 Nov 2017 23:47:11: #2.2 Generate R script for model : SRX1068233.05_model.r INFO @ Fri, 10 Nov 2017 23:47:11: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:47:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:47:17: #1 tag size is determined as 64 bps INFO @ Fri, 10 Nov 2017 23:47:17: #1 tag size = 64 INFO @ Fri, 10 Nov 2017 23:47:17: #1 total tags in treatment: 10992684 INFO @ Fri, 10 Nov 2017 23:47:17: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:47:17: #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 23:47:17: #1 tags after filtering in treatment: 10992352 INFO @ Fri, 10 Nov 2017 23:47:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:47:17: #1 finished! INFO @ Fri, 10 Nov 2017 23:47:17: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:47:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:47:17: #1 tag size is determined as 64 bps INFO @ Fri, 10 Nov 2017 23:47:17: #1 tag size = 64 INFO @ Fri, 10 Nov 2017 23:47:17: #1 total tags in treatment: 10992684 INFO @ Fri, 10 Nov 2017 23:47:17: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:47:17: #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 23:47:18: #1 tags after filtering in treatment: 10992352 INFO @ Fri, 10 Nov 2017 23:47:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:47:18: #1 finished! INFO @ Fri, 10 Nov 2017 23:47:18: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:47:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:47:19: #2 number of paired peaks: 28905 INFO @ Fri, 10 Nov 2017 23:47:19: start model_add_line... INFO @ Fri, 10 Nov 2017 23:47:20: start X-correlation... INFO @ Fri, 10 Nov 2017 23:47:20: end of X-cor INFO @ Fri, 10 Nov 2017 23:47:20: #2 finished! INFO @ Fri, 10 Nov 2017 23:47:20: #2 predicted fragment length is 229 bps INFO @ Fri, 10 Nov 2017 23:47:20: #2 alternative fragment length(s) may be 229 bps INFO @ Fri, 10 Nov 2017 23:47:20: #2.2 Generate R script for model : SRX1068233.20_model.r INFO @ Fri, 10 Nov 2017 23:47:20: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:47:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:47:20: #2 number of paired peaks: 28905 INFO @ Fri, 10 Nov 2017 23:47:20: start model_add_line... INFO @ Fri, 10 Nov 2017 23:47:20: start X-correlation... INFO @ Fri, 10 Nov 2017 23:47:20: end of X-cor INFO @ Fri, 10 Nov 2017 23:47:20: #2 finished! INFO @ Fri, 10 Nov 2017 23:47:20: #2 predicted fragment length is 229 bps INFO @ Fri, 10 Nov 2017 23:47:20: #2 alternative fragment length(s) may be 229 bps INFO @ Fri, 10 Nov 2017 23:47:20: #2.2 Generate R script for model : SRX1068233.10_model.r INFO @ Fri, 10 Nov 2017 23:47:20: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:47:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:47:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:47:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:47:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:48:11: #4 Write output xls file... SRX1068233.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:48:11: #4 Write peak in narrowPeak format file... SRX1068233.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:48:11: #4 Write summits bed file... SRX1068233.05_summits.bed INFO @ Fri, 10 Nov 2017 23:48:11: Done! pass1 - making usageList (112 chroms): 8 millis pass2 - checking and writing primary data (24856 records, 4 fields): 69 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:48:18: #4 Write output xls file... SRX1068233.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:48:18: #4 Write peak in narrowPeak format file... SRX1068233.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:48:18: #4 Write summits bed file... SRX1068233.10_summits.bed INFO @ Fri, 10 Nov 2017 23:48:18: Done! pass1 - making usageList (99 chroms): 4 millis pass2 - checking and writing primary data (21722 records, 4 fields): 55 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:48:20: #4 Write output xls file... SRX1068233.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:48:20: #4 Write peak in narrowPeak format file... SRX1068233.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:48:20: #4 Write summits bed file... SRX1068233.20_summits.bed INFO @ Fri, 10 Nov 2017 23:48:20: Done! pass1 - making usageList (87 chroms): 4 millis pass2 - checking and writing primary data (17792 records, 4 fields): 25 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。