Job ID = 10194920 sra ファイルのダウンロード中... Completed: 95633K bytes transferred in 6 seconds (119471K bits/sec), in 1 file. Completed: 93494K bytes transferred in 5 seconds (133419K bits/sec), in 1 file. Completed: 158825K bytes transferred in 9 seconds (143105K bits/sec), in 1 file. Completed: 155876K bytes transferred in 7 seconds (170999K bits/sec), in 1 file. Completed: 155736K bytes transferred in 13 seconds (96379K bits/sec), in 1 file. Completed: 153684K bytes transferred in 11 seconds (107570K 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 2245321 spots for /home/okishinya/chipatlas/results/rn6/SRX2202915/SRR4320034.sra Written 2245321 spots total Written 2185849 spots for /home/okishinya/chipatlas/results/rn6/SRX2202915/SRR4320035.sra Written 2185849 spots total Written 3348415 spots for /home/okishinya/chipatlas/results/rn6/SRX2202915/SRR4320039.sra Written 3348415 spots total Written 3386947 spots for /home/okishinya/chipatlas/results/rn6/SRX2202915/SRR4320038.sra Written 3386947 spots total Written 3452657 spots for /home/okishinya/chipatlas/results/rn6/SRX2202915/SRR4320036.sra Written 3452657 spots total Written 3366627 spots for /home/okishinya/chipatlas/results/rn6/SRX2202915/SRR4320037.sra Written 3366627 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 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: 00:34:53 17985816 reads; of these: 17985816 (100.00%) were unpaired; of these: 517686 (2.88%) aligned 0 times 12132458 (67.46%) aligned exactly 1 time 5335672 (29.67%) aligned >1 times 97.12% overall alignment rate Time searching: 00:34:57 Overall time: 00:34:57 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] 1401677 / 17468130 = 0.0802 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 23:46:18: # Command line: callpeak -t SRX2202915.bam -f BAM -g 2.15e9 -n SRX2202915.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202915.10 # format = BAM # ChIP-seq file = ['SRX2202915.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 23:46:18: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:46:18: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:46:18: # Command line: callpeak -t SRX2202915.bam -f BAM -g 2.15e9 -n SRX2202915.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202915.05 # format = BAM # ChIP-seq file = ['SRX2202915.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 23:46:18: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:46:18: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:46:18: # Command line: callpeak -t SRX2202915.bam -f BAM -g 2.15e9 -n SRX2202915.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202915.20 # format = BAM # ChIP-seq file = ['SRX2202915.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 23:46:18: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:46:18: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:46:30: 1000000 INFO @ Fri, 10 Nov 2017 23:46:30: 1000000 INFO @ Fri, 10 Nov 2017 23:46:36: 1000000 INFO @ Fri, 10 Nov 2017 23:46:43: 2000000 INFO @ Fri, 10 Nov 2017 23:46:43: 2000000 INFO @ Fri, 10 Nov 2017 23:46:54: 2000000 INFO @ Fri, 10 Nov 2017 23:46:56: 3000000 INFO @ Fri, 10 Nov 2017 23:46:56: 3000000 INFO @ Fri, 10 Nov 2017 23:47:09: 4000000 INFO @ Fri, 10 Nov 2017 23:47:09: 4000000 INFO @ Fri, 10 Nov 2017 23:47:11: 3000000 INFO @ Fri, 10 Nov 2017 23:47:22: 5000000 INFO @ Fri, 10 Nov 2017 23:47:23: 5000000 INFO @ Fri, 10 Nov 2017 23:47:28: 4000000 INFO @ Fri, 10 Nov 2017 23:47:33: 6000000 INFO @ Fri, 10 Nov 2017 23:47:42: 6000000 INFO @ Fri, 10 Nov 2017 23:47:43: 7000000 INFO @ Fri, 10 Nov 2017 23:47:47: 5000000 INFO @ Fri, 10 Nov 2017 23:47:52: 8000000 INFO @ Fri, 10 Nov 2017 23:48:02: 7000000 INFO @ Fri, 10 Nov 2017 23:48:02: 9000000 INFO @ Fri, 10 Nov 2017 23:48:07: 6000000 INFO @ Fri, 10 Nov 2017 23:48:15: 10000000 INFO @ Fri, 10 Nov 2017 23:48:21: 8000000 INFO @ Fri, 10 Nov 2017 23:48:27: 7000000 INFO @ Fri, 10 Nov 2017 23:48:29: 11000000 INFO @ Fri, 10 Nov 2017 23:48:42: 9000000 INFO @ Fri, 10 Nov 2017 23:48:44: 12000000 INFO @ Fri, 10 Nov 2017 23:48:47: 8000000 INFO @ Fri, 10 Nov 2017 23:48:58: 13000000 INFO @ Fri, 10 Nov 2017 23:49:02: 10000000 INFO @ Fri, 10 Nov 2017 23:49:08: 9000000 INFO @ Fri, 10 Nov 2017 23:49:16: 14000000 INFO @ Fri, 10 Nov 2017 23:49:22: 11000000 INFO @ Fri, 10 Nov 2017 23:49:26: 10000000 INFO @ Fri, 10 Nov 2017 23:49:37: 15000000 INFO @ Fri, 10 Nov 2017 23:49:40: 12000000 INFO @ Fri, 10 Nov 2017 23:49:44: 11000000 INFO @ Fri, 10 Nov 2017 23:49:59: 13000000 INFO @ Fri, 10 Nov 2017 23:49:59: 16000000 INFO @ Fri, 10 Nov 2017 23:50:00: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:50:00: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:50:00: #1 total tags in treatment: 16066453 INFO @ Fri, 10 Nov 2017 23:50:00: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:50:00: #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 23:50:01: #1 tags after filtering in treatment: 16066324 INFO @ Fri, 10 Nov 2017 23:50:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:50:01: #1 finished! INFO @ Fri, 10 Nov 2017 23:50:01: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:50:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:50:02: 12000000 INFO @ Fri, 10 Nov 2017 23:50:05: #2 number of paired peaks: 26633 INFO @ Fri, 10 Nov 2017 23:50:05: start model_add_line... INFO @ Fri, 10 Nov 2017 23:50:05: start X-correlation... INFO @ Fri, 10 Nov 2017 23:50:05: end of X-cor INFO @ Fri, 10 Nov 2017 23:50:05: #2 finished! INFO @ Fri, 10 Nov 2017 23:50:05: #2 predicted fragment length is 116 bps INFO @ Fri, 10 Nov 2017 23:50:05: #2 alternative fragment length(s) may be 116 bps INFO @ Fri, 10 Nov 2017 23:50:05: #2.2 Generate R script for model : SRX2202915.05_model.r INFO @ Fri, 10 Nov 2017 23:50:05: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:50:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:50:17: 14000000 INFO @ Fri, 10 Nov 2017 23:50:19: 13000000 INFO @ Fri, 10 Nov 2017 23:50:36: 15000000 INFO @ Fri, 10 Nov 2017 23:50:38: 14000000 INFO @ Fri, 10 Nov 2017 23:50:54: 16000000 INFO @ Fri, 10 Nov 2017 23:50:55: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:50:55: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:50:55: #1 total tags in treatment: 16066453 INFO @ Fri, 10 Nov 2017 23:50:55: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:50:55: #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 23:50:56: 15000000 INFO @ Fri, 10 Nov 2017 23:50:56: #1 tags after filtering in treatment: 16066324 INFO @ Fri, 10 Nov 2017 23:50:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:50:56: #1 finished! INFO @ Fri, 10 Nov 2017 23:50:56: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:50:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:50:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:50:59: #2 number of paired peaks: 26633 INFO @ Fri, 10 Nov 2017 23:50:59: start model_add_line... INFO @ Fri, 10 Nov 2017 23:50:59: start X-correlation... INFO @ Fri, 10 Nov 2017 23:50:59: end of X-cor INFO @ Fri, 10 Nov 2017 23:50:59: #2 finished! INFO @ Fri, 10 Nov 2017 23:50:59: #2 predicted fragment length is 116 bps INFO @ Fri, 10 Nov 2017 23:50:59: #2 alternative fragment length(s) may be 116 bps INFO @ Fri, 10 Nov 2017 23:50:59: #2.2 Generate R script for model : SRX2202915.20_model.r INFO @ Fri, 10 Nov 2017 23:50:59: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:50:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:51:16: 16000000 INFO @ Fri, 10 Nov 2017 23:51:17: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:51:17: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:51:17: #1 total tags in treatment: 16066453 INFO @ Fri, 10 Nov 2017 23:51:17: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:51:17: #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 23:51:18: #1 tags after filtering in treatment: 16066324 INFO @ Fri, 10 Nov 2017 23:51:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:51:18: #1 finished! INFO @ Fri, 10 Nov 2017 23:51:18: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:51:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:51:21: #2 number of paired peaks: 26633 INFO @ Fri, 10 Nov 2017 23:51:21: start model_add_line... INFO @ Fri, 10 Nov 2017 23:51:21: start X-correlation... INFO @ Fri, 10 Nov 2017 23:51:21: end of X-cor INFO @ Fri, 10 Nov 2017 23:51:21: #2 finished! INFO @ Fri, 10 Nov 2017 23:51:21: #2 predicted fragment length is 116 bps INFO @ Fri, 10 Nov 2017 23:51:21: #2 alternative fragment length(s) may be 116 bps INFO @ Fri, 10 Nov 2017 23:51:21: #2.2 Generate R script for model : SRX2202915.10_model.r INFO @ Fri, 10 Nov 2017 23:51:21: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:51:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:51:30: #4 Write output xls file... SRX2202915.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:51:30: #4 Write peak in narrowPeak format file... SRX2202915.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:51:31: #4 Write summits bed file... SRX2202915.05_summits.bed INFO @ Fri, 10 Nov 2017 23:51:31: Done! pass1 - making usageList (61 chroms): 4 millis pass2 - checking and writing primary data (8313 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:51:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:52:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:52:20: #4 Write output xls file... SRX2202915.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:52:20: #4 Write peak in narrowPeak format file... SRX2202915.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:52:20: #4 Write summits bed file... SRX2202915.20_summits.bed INFO @ Fri, 10 Nov 2017 23:52:20: Done! pass1 - making usageList (35 chroms): 2 millis pass2 - checking and writing primary data (442 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:52:47: #4 Write output xls file... SRX2202915.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:52:47: #4 Write peak in narrowPeak format file... SRX2202915.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:52:47: #4 Write summits bed file... SRX2202915.10_summits.bed INFO @ Fri, 10 Nov 2017 23:52:47: Done! pass1 - making usageList (45 chroms): 2 millis pass2 - checking and writing primary data (1777 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。