Job ID = 10194775 sra ファイルのダウンロード中... Completed: 520703K bytes transferred in 6 seconds (620389K 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 22732857 spots for /home/okishinya/chipatlas/results/rn6/SRX1774908/SRR3544937.sra Written 22732857 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: 00:00:00 Multiseed full-index search: 00:16:17 22732857 reads; of these: 22732857 (100.00%) were unpaired; of these: 720431 (3.17%) aligned 0 times 17532904 (77.13%) aligned exactly 1 time 4479522 (19.71%) aligned >1 times 96.83% overall alignment rate Time searching: 00:16:21 Overall time: 00:16:21 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] 5497267 / 22012426 = 0.2497 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 17:09:44: # Command line: callpeak -t SRX1774908.bam -f BAM -g 2.15e9 -n SRX1774908.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1774908.05 # format = BAM # ChIP-seq file = ['SRX1774908.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 17:09:44: # Command line: callpeak -t SRX1774908.bam -f BAM -g 2.15e9 -n SRX1774908.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1774908.10 # format = BAM # ChIP-seq file = ['SRX1774908.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 17:09:44: # Command line: callpeak -t SRX1774908.bam -f BAM -g 2.15e9 -n SRX1774908.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1774908.20 # format = BAM # ChIP-seq file = ['SRX1774908.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 17:09:44: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:09:44: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:09:44: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:09:44: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:09:44: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:09:44: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:09:52: 1000000 INFO @ Fri, 10 Nov 2017 17:09:52: 1000000 INFO @ Fri, 10 Nov 2017 17:09:52: 1000000 INFO @ Fri, 10 Nov 2017 17:10:00: 2000000 INFO @ Fri, 10 Nov 2017 17:10:00: 2000000 INFO @ Fri, 10 Nov 2017 17:10:00: 2000000 INFO @ Fri, 10 Nov 2017 17:10:08: 3000000 INFO @ Fri, 10 Nov 2017 17:10:08: 3000000 INFO @ Fri, 10 Nov 2017 17:10:08: 3000000 INFO @ Fri, 10 Nov 2017 17:10:16: 4000000 INFO @ Fri, 10 Nov 2017 17:10:16: 4000000 INFO @ Fri, 10 Nov 2017 17:10:17: 4000000 INFO @ Fri, 10 Nov 2017 17:10:24: 5000000 INFO @ Fri, 10 Nov 2017 17:10:24: 5000000 INFO @ Fri, 10 Nov 2017 17:10:25: 5000000 INFO @ Fri, 10 Nov 2017 17:10:32: 6000000 INFO @ Fri, 10 Nov 2017 17:10:32: 6000000 INFO @ Fri, 10 Nov 2017 17:10:33: 6000000 INFO @ Fri, 10 Nov 2017 17:10:39: 7000000 INFO @ Fri, 10 Nov 2017 17:10:39: 7000000 INFO @ Fri, 10 Nov 2017 17:10:41: 7000000 INFO @ Fri, 10 Nov 2017 17:10:48: 8000000 INFO @ Fri, 10 Nov 2017 17:10:48: 8000000 INFO @ Fri, 10 Nov 2017 17:10:49: 8000000 INFO @ Fri, 10 Nov 2017 17:10:56: 9000000 INFO @ Fri, 10 Nov 2017 17:10:56: 9000000 INFO @ Fri, 10 Nov 2017 17:10:57: 9000000 INFO @ Fri, 10 Nov 2017 17:11:04: 10000000 INFO @ Fri, 10 Nov 2017 17:11:04: 10000000 INFO @ Fri, 10 Nov 2017 17:11:06: 10000000 INFO @ Fri, 10 Nov 2017 17:11:11: 11000000 INFO @ Fri, 10 Nov 2017 17:11:11: 11000000 INFO @ Fri, 10 Nov 2017 17:11:14: 11000000 INFO @ Fri, 10 Nov 2017 17:11:19: 12000000 INFO @ Fri, 10 Nov 2017 17:11:19: 12000000 INFO @ Fri, 10 Nov 2017 17:11:22: 12000000 INFO @ Fri, 10 Nov 2017 17:11:27: 13000000 INFO @ Fri, 10 Nov 2017 17:11:27: 13000000 INFO @ Fri, 10 Nov 2017 17:11:30: 13000000 INFO @ Fri, 10 Nov 2017 17:11:35: 14000000 INFO @ Fri, 10 Nov 2017 17:11:35: 14000000 INFO @ Fri, 10 Nov 2017 17:11:38: 14000000 INFO @ Fri, 10 Nov 2017 17:11:43: 15000000 INFO @ Fri, 10 Nov 2017 17:11:43: 15000000 INFO @ Fri, 10 Nov 2017 17:11:47: 15000000 INFO @ Fri, 10 Nov 2017 17:11:51: 16000000 INFO @ Fri, 10 Nov 2017 17:11:51: 16000000 INFO @ Fri, 10 Nov 2017 17:11:55: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:11:55: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:11:55: #1 total tags in treatment: 16515159 INFO @ Fri, 10 Nov 2017 17:11:55: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:11:55: #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 17:11:55: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:11:55: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:11:55: #1 total tags in treatment: 16515159 INFO @ Fri, 10 Nov 2017 17:11:55: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:11:55: #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 17:11:55: 16000000 INFO @ Fri, 10 Nov 2017 17:11:55: #1 tags after filtering in treatment: 16514963 INFO @ Fri, 10 Nov 2017 17:11:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:11:55: #1 finished! INFO @ Fri, 10 Nov 2017 17:11:55: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:11:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:11:55: #1 tags after filtering in treatment: 16514963 INFO @ Fri, 10 Nov 2017 17:11:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:11:55: #1 finished! INFO @ Fri, 10 Nov 2017 17:11:55: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:11:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:11:58: #2 number of paired peaks: 47203 INFO @ Fri, 10 Nov 2017 17:11:58: start model_add_line... INFO @ Fri, 10 Nov 2017 17:11:58: #2 number of paired peaks: 47203 INFO @ Fri, 10 Nov 2017 17:11:58: start model_add_line... INFO @ Fri, 10 Nov 2017 17:11:59: start X-correlation... INFO @ Fri, 10 Nov 2017 17:11:59: end of X-cor INFO @ Fri, 10 Nov 2017 17:11:59: #2 finished! INFO @ Fri, 10 Nov 2017 17:11:59: #2 predicted fragment length is 175 bps INFO @ Fri, 10 Nov 2017 17:11:59: #2 alternative fragment length(s) may be 175 bps INFO @ Fri, 10 Nov 2017 17:11:59: #2.2 Generate R script for model : SRX1774908.20_model.r INFO @ Fri, 10 Nov 2017 17:11:59: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:11:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:11:59: start X-correlation... INFO @ Fri, 10 Nov 2017 17:11:59: end of X-cor INFO @ Fri, 10 Nov 2017 17:11:59: #2 finished! INFO @ Fri, 10 Nov 2017 17:11:59: #2 predicted fragment length is 175 bps INFO @ Fri, 10 Nov 2017 17:11:59: #2 alternative fragment length(s) may be 175 bps INFO @ Fri, 10 Nov 2017 17:11:59: #2.2 Generate R script for model : SRX1774908.10_model.r INFO @ Fri, 10 Nov 2017 17:11:59: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:11:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:11:59: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:11:59: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:11:59: #1 total tags in treatment: 16515159 INFO @ Fri, 10 Nov 2017 17:11:59: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:11:59: #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 17:12:00: #1 tags after filtering in treatment: 16514963 INFO @ Fri, 10 Nov 2017 17:12:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:12:00: #1 finished! INFO @ Fri, 10 Nov 2017 17:12:00: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:12:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:12:03: #2 number of paired peaks: 47203 INFO @ Fri, 10 Nov 2017 17:12:03: start model_add_line... INFO @ Fri, 10 Nov 2017 17:12:03: start X-correlation... INFO @ Fri, 10 Nov 2017 17:12:03: end of X-cor INFO @ Fri, 10 Nov 2017 17:12:03: #2 finished! INFO @ Fri, 10 Nov 2017 17:12:03: #2 predicted fragment length is 175 bps INFO @ Fri, 10 Nov 2017 17:12:03: #2 alternative fragment length(s) may be 175 bps INFO @ Fri, 10 Nov 2017 17:12:03: #2.2 Generate R script for model : SRX1774908.05_model.r INFO @ Fri, 10 Nov 2017 17:12:03: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:12:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:12:38: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:12:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:12:49: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:13:03: #4 Write output xls file... SRX1774908.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:13:03: #4 Write peak in narrowPeak format file... SRX1774908.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:13:03: #4 Write summits bed file... SRX1774908.10_summits.bed INFO @ Fri, 10 Nov 2017 17:13:03: Done! pass1 - making usageList (67 chroms): 3 millis pass2 - checking and writing primary data (15506 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:13:07: #4 Write output xls file... SRX1774908.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:13:07: #4 Write peak in narrowPeak format file... SRX1774908.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:13:07: #4 Write summits bed file... SRX1774908.20_summits.bed INFO @ Fri, 10 Nov 2017 17:13:07: Done! pass1 - making usageList (40 chroms): 2 millis pass2 - checking and writing primary data (6723 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:13:14: #4 Write output xls file... SRX1774908.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:13:14: #4 Write peak in narrowPeak format file... SRX1774908.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:13:14: #4 Write summits bed file... SRX1774908.05_summits.bed INFO @ Fri, 10 Nov 2017 17:13:14: Done! pass1 - making usageList (97 chroms): 5 millis pass2 - checking and writing primary data (27166 records, 4 fields): 35 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。