Job ID = 10194716 sra ファイルのダウンロード中... Completed: 423526K bytes transferred in 8 seconds (430036K 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 12125758 spots for /home/okishinya/chipatlas/results/rn6/SRX039669/SRR096824.sra Written 12125758 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:14:21 12125758 reads; of these: 12125758 (100.00%) were unpaired; of these: 3557078 (29.33%) aligned 0 times 6816026 (56.21%) aligned exactly 1 time 1752654 (14.45%) aligned >1 times 70.67% overall alignment rate Time searching: 00:14:25 Overall time: 00:14:25 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_rmdupse_core] 3462574 / 8568680 = 0.4041 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 19:01:53: # Command line: callpeak -t SRX039669.bam -f BAM -g 2.15e9 -n SRX039669.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX039669.05 # format = BAM # ChIP-seq file = ['SRX039669.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 19:01:53: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:01:53: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:01:53: # Command line: callpeak -t SRX039669.bam -f BAM -g 2.15e9 -n SRX039669.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX039669.20 # format = BAM # ChIP-seq file = ['SRX039669.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 19:01:53: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:01:53: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:01:53: # Command line: callpeak -t SRX039669.bam -f BAM -g 2.15e9 -n SRX039669.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX039669.10 # format = BAM # ChIP-seq file = ['SRX039669.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 19:01:53: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:01:53: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:02:06: 1000000 INFO @ Fri, 10 Nov 2017 19:02:09: 1000000 INFO @ Fri, 10 Nov 2017 19:02:12: 1000000 INFO @ Fri, 10 Nov 2017 19:02:17: 2000000 INFO @ Fri, 10 Nov 2017 19:02:28: 3000000 INFO @ Fri, 10 Nov 2017 19:02:28: 2000000 INFO @ Fri, 10 Nov 2017 19:02:30: 2000000 INFO @ Fri, 10 Nov 2017 19:02:39: 4000000 INFO @ Fri, 10 Nov 2017 19:02:48: 3000000 INFO @ Fri, 10 Nov 2017 19:02:49: 3000000 INFO @ Fri, 10 Nov 2017 19:02:50: 5000000 INFO @ Fri, 10 Nov 2017 19:02:51: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 19:02:51: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 19:02:51: #1 total tags in treatment: 5106106 INFO @ Fri, 10 Nov 2017 19:02:51: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:02:51: #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 19:02:52: #1 tags after filtering in treatment: 5105881 INFO @ Fri, 10 Nov 2017 19:02:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:02:52: #1 finished! INFO @ Fri, 10 Nov 2017 19:02:52: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:02:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:02:56: #2 number of paired peaks: 82310 INFO @ Fri, 10 Nov 2017 19:02:56: start model_add_line... INFO @ Fri, 10 Nov 2017 19:02:56: start X-correlation... INFO @ Fri, 10 Nov 2017 19:02:56: end of X-cor INFO @ Fri, 10 Nov 2017 19:02:56: #2 finished! INFO @ Fri, 10 Nov 2017 19:02:56: #2 predicted fragment length is 175 bps INFO @ Fri, 10 Nov 2017 19:02:56: #2 alternative fragment length(s) may be 175 bps INFO @ Fri, 10 Nov 2017 19:02:56: #2.2 Generate R script for model : SRX039669.05_model.r INFO @ Fri, 10 Nov 2017 19:02:56: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:02:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:03:09: 4000000 INFO @ Fri, 10 Nov 2017 19:03:09: 4000000 INFO @ Fri, 10 Nov 2017 19:03:13: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:03:24: #4 Write output xls file... SRX039669.05_peaks.xls INFO @ Fri, 10 Nov 2017 19:03:25: #4 Write peak in narrowPeak format file... SRX039669.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:03:25: #4 Write summits bed file... SRX039669.05_summits.bed INFO @ Fri, 10 Nov 2017 19:03:25: Done! pass1 - making usageList (96 chroms): 4 millis pass2 - checking and writing primary data (8678 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 19:03:26: 5000000 INFO @ Fri, 10 Nov 2017 19:03:27: 5000000 INFO @ Fri, 10 Nov 2017 19:03:27: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 19:03:27: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 19:03:27: #1 total tags in treatment: 5106106 INFO @ Fri, 10 Nov 2017 19:03:27: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:03:27: #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 19:03:28: #1 tags after filtering in treatment: 5105881 INFO @ Fri, 10 Nov 2017 19:03:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:03:28: #1 finished! INFO @ Fri, 10 Nov 2017 19:03:28: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:03:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:03:28: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 19:03:28: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 19:03:28: #1 total tags in treatment: 5106106 INFO @ Fri, 10 Nov 2017 19:03:28: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:03:28: #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 19:03:29: #1 tags after filtering in treatment: 5105881 INFO @ Fri, 10 Nov 2017 19:03:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:03:29: #1 finished! INFO @ Fri, 10 Nov 2017 19:03:29: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:03:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:03:32: #2 number of paired peaks: 82310 INFO @ Fri, 10 Nov 2017 19:03:32: start model_add_line... INFO @ Fri, 10 Nov 2017 19:03:32: start X-correlation... INFO @ Fri, 10 Nov 2017 19:03:32: end of X-cor INFO @ Fri, 10 Nov 2017 19:03:32: #2 finished! INFO @ Fri, 10 Nov 2017 19:03:32: #2 predicted fragment length is 175 bps INFO @ Fri, 10 Nov 2017 19:03:32: #2 alternative fragment length(s) may be 175 bps INFO @ Fri, 10 Nov 2017 19:03:32: #2.2 Generate R script for model : SRX039669.20_model.r INFO @ Fri, 10 Nov 2017 19:03:32: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:03:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:03:33: #2 number of paired peaks: 82310 INFO @ Fri, 10 Nov 2017 19:03:33: start model_add_line... INFO @ Fri, 10 Nov 2017 19:03:33: start X-correlation... INFO @ Fri, 10 Nov 2017 19:03:33: end of X-cor INFO @ Fri, 10 Nov 2017 19:03:33: #2 finished! INFO @ Fri, 10 Nov 2017 19:03:33: #2 predicted fragment length is 175 bps INFO @ Fri, 10 Nov 2017 19:03:33: #2 alternative fragment length(s) may be 175 bps INFO @ Fri, 10 Nov 2017 19:03:33: #2.2 Generate R script for model : SRX039669.10_model.r INFO @ Fri, 10 Nov 2017 19:03:33: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:03:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:03:49: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:03:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:03:59: #4 Write output xls file... SRX039669.20_peaks.xls INFO @ Fri, 10 Nov 2017 19:03:59: #4 Write peak in narrowPeak format file... SRX039669.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:03:59: #4 Write summits bed file... SRX039669.20_summits.bed INFO @ Fri, 10 Nov 2017 19:03:59: Done! pass1 - making usageList (34 chroms): 2 millis pass2 - checking and writing primary data (1159 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 19:04:00: #4 Write output xls file... SRX039669.10_peaks.xls INFO @ Fri, 10 Nov 2017 19:04:00: #4 Write peak in narrowPeak format file... SRX039669.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:04:00: #4 Write summits bed file... SRX039669.10_summits.bed INFO @ Fri, 10 Nov 2017 19:04:00: Done! pass1 - making usageList (65 chroms): 2 millis pass2 - checking and writing primary data (3338 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。