Job ID = 10194878 sra ファイルのダウンロード中... Completed: 112229K bytes transferred in 5 seconds (181677K bits/sec), in 1 file. Completed: 112797K bytes transferred in 6 seconds (135788K bits/sec), in 1 file. Completed: 106374K bytes transferred in 6 seconds (135244K bits/sec), in 1 file. Completed: 104888K bytes transferred in 7 seconds (118259K bits/sec), in 1 file. Completed: 127154K bytes transferred in 5 seconds (180410K bits/sec), in 1 file. Completed: 128966K bytes transferred in 6 seconds (165823K 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 2359221 spots for /home/okishinya/chipatlas/results/rn6/SRX2202873/SRR4319785.sra Written 2359221 spots total Written 2387139 spots for /home/okishinya/chipatlas/results/rn6/SRX2202873/SRR4319784.sra Written 2387139 spots total Written 2508898 spots for /home/okishinya/chipatlas/results/rn6/SRX2202873/SRR4319782.sra Written 2508898 spots total Written 2512543 spots for /home/okishinya/chipatlas/results/rn6/SRX2202873/SRR4319783.sra Written 2512543 spots total Written 2778150 spots for /home/okishinya/chipatlas/results/rn6/SRX2202873/SRR4319786.sra Written 2778150 spots total Written 2806373 spots for /home/okishinya/chipatlas/results/rn6/SRX2202873/SRR4319787.sra Written 2806373 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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:19 15352324 reads; of these: 15352324 (100.00%) were unpaired; of these: 627352 (4.09%) aligned 0 times 11370388 (74.06%) aligned exactly 1 time 3354584 (21.85%) aligned >1 times 95.91% overall alignment rate Time searching: 00:11:21 Overall time: 00:11:21 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 8 files... [bam_rmdupse_core] 1200767 / 14724972 = 0.0815 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 17:46:05: # Command line: callpeak -t SRX2202873.bam -f BAM -g 2.15e9 -n SRX2202873.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202873.05 # format = BAM # ChIP-seq file = ['SRX2202873.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 17:46:05: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:46:05: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:46:05: # Command line: callpeak -t SRX2202873.bam -f BAM -g 2.15e9 -n SRX2202873.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202873.20 # format = BAM # ChIP-seq file = ['SRX2202873.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 17:46:05: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:46:05: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:46:05: # Command line: callpeak -t SRX2202873.bam -f BAM -g 2.15e9 -n SRX2202873.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202873.10 # format = BAM # ChIP-seq file = ['SRX2202873.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 17:46:05: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:46:05: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:46:12: 1000000 INFO @ Fri, 10 Nov 2017 17:46:13: 1000000 INFO @ Fri, 10 Nov 2017 17:46:13: 1000000 INFO @ Fri, 10 Nov 2017 17:46:20: 2000000 INFO @ Fri, 10 Nov 2017 17:46:21: 2000000 INFO @ Fri, 10 Nov 2017 17:46:21: 2000000 INFO @ Fri, 10 Nov 2017 17:46:27: 3000000 INFO @ Fri, 10 Nov 2017 17:46:28: 3000000 INFO @ Fri, 10 Nov 2017 17:46:30: 3000000 INFO @ Fri, 10 Nov 2017 17:46:35: 4000000 INFO @ Fri, 10 Nov 2017 17:46:36: 4000000 INFO @ Fri, 10 Nov 2017 17:46:38: 4000000 INFO @ Fri, 10 Nov 2017 17:46:43: 5000000 INFO @ Fri, 10 Nov 2017 17:46:43: 5000000 INFO @ Fri, 10 Nov 2017 17:46:47: 5000000 INFO @ Fri, 10 Nov 2017 17:46:51: 6000000 INFO @ Fri, 10 Nov 2017 17:46:51: 6000000 INFO @ Fri, 10 Nov 2017 17:46:55: 6000000 INFO @ Fri, 10 Nov 2017 17:46:58: 7000000 INFO @ Fri, 10 Nov 2017 17:46:58: 7000000 INFO @ Fri, 10 Nov 2017 17:47:03: 7000000 INFO @ Fri, 10 Nov 2017 17:47:06: 8000000 INFO @ Fri, 10 Nov 2017 17:47:06: 8000000 INFO @ Fri, 10 Nov 2017 17:47:11: 8000000 INFO @ Fri, 10 Nov 2017 17:47:14: 9000000 INFO @ Fri, 10 Nov 2017 17:47:14: 9000000 INFO @ Fri, 10 Nov 2017 17:47:20: 9000000 INFO @ Fri, 10 Nov 2017 17:47:21: 10000000 INFO @ Fri, 10 Nov 2017 17:47:21: 10000000 INFO @ Fri, 10 Nov 2017 17:47:28: 10000000 INFO @ Fri, 10 Nov 2017 17:47:29: 11000000 INFO @ Fri, 10 Nov 2017 17:47:29: 11000000 INFO @ Fri, 10 Nov 2017 17:47:35: 11000000 INFO @ Fri, 10 Nov 2017 17:47:36: 12000000 INFO @ Fri, 10 Nov 2017 17:47:37: 12000000 INFO @ Fri, 10 Nov 2017 17:47:43: 12000000 INFO @ Fri, 10 Nov 2017 17:47:44: 13000000 INFO @ Fri, 10 Nov 2017 17:47:45: 13000000 INFO @ Fri, 10 Nov 2017 17:47:48: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:47:48: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:47:48: #1 total tags in treatment: 13524205 INFO @ Fri, 10 Nov 2017 17:47:48: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:47:48: #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 17:47:48: #1 tags after filtering in treatment: 13524008 INFO @ Fri, 10 Nov 2017 17:47:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:47:48: #1 finished! INFO @ Fri, 10 Nov 2017 17:47:48: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:47:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:47:49: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:47:49: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:47:49: #1 total tags in treatment: 13524205 INFO @ Fri, 10 Nov 2017 17:47:49: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:47:49: #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 17:47:49: #1 tags after filtering in treatment: 13524008 INFO @ Fri, 10 Nov 2017 17:47:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:47:49: #1 finished! INFO @ Fri, 10 Nov 2017 17:47:49: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:47:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:47:51: 13000000 INFO @ Fri, 10 Nov 2017 17:47:51: #2 number of paired peaks: 44553 INFO @ Fri, 10 Nov 2017 17:47:51: start model_add_line... INFO @ Fri, 10 Nov 2017 17:47:52: start X-correlation... INFO @ Fri, 10 Nov 2017 17:47:52: end of X-cor INFO @ Fri, 10 Nov 2017 17:47:52: #2 finished! INFO @ Fri, 10 Nov 2017 17:47:52: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Nov 2017 17:47:52: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 10 Nov 2017 17:47:52: #2.2 Generate R script for model : SRX2202873.05_model.r INFO @ Fri, 10 Nov 2017 17:47:52: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:47:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:47:52: #2 number of paired peaks: 44553 INFO @ Fri, 10 Nov 2017 17:47:52: start model_add_line... INFO @ Fri, 10 Nov 2017 17:47:53: start X-correlation... INFO @ Fri, 10 Nov 2017 17:47:53: end of X-cor INFO @ Fri, 10 Nov 2017 17:47:53: #2 finished! INFO @ Fri, 10 Nov 2017 17:47:53: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Nov 2017 17:47:53: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 10 Nov 2017 17:47:53: #2.2 Generate R script for model : SRX2202873.10_model.r INFO @ Fri, 10 Nov 2017 17:47:53: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:47:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:47:55: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:47:55: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:47:55: #1 total tags in treatment: 13524205 INFO @ Fri, 10 Nov 2017 17:47:55: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:47:55: #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 17:47:55: #1 tags after filtering in treatment: 13524008 INFO @ Fri, 10 Nov 2017 17:47:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:47:55: #1 finished! INFO @ Fri, 10 Nov 2017 17:47:55: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:47:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:47:58: #2 number of paired peaks: 44553 INFO @ Fri, 10 Nov 2017 17:47:58: start model_add_line... INFO @ Fri, 10 Nov 2017 17:47:58: start X-correlation... INFO @ Fri, 10 Nov 2017 17:47:58: end of X-cor INFO @ Fri, 10 Nov 2017 17:47:58: #2 finished! INFO @ Fri, 10 Nov 2017 17:47:58: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Nov 2017 17:47:58: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 10 Nov 2017 17:47:58: #2.2 Generate R script for model : SRX2202873.20_model.r INFO @ Fri, 10 Nov 2017 17:47:58: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:47:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:48:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:48:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:48:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:48:45: #4 Write output xls file... SRX2202873.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:48:45: #4 Write peak in narrowPeak format file... SRX2202873.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:48:45: #4 Write summits bed file... SRX2202873.05_summits.bed INFO @ Fri, 10 Nov 2017 17:48:45: Done! pass1 - making usageList (66 chroms): 10 millis pass2 - checking and writing primary data (9572 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:48:49: #4 Write output xls file... SRX2202873.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:48:49: #4 Write peak in narrowPeak format file... SRX2202873.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:48:49: #4 Write summits bed file... SRX2202873.10_summits.bed INFO @ Fri, 10 Nov 2017 17:48:49: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (2587 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:48:53: #4 Write output xls file... SRX2202873.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:48:53: #4 Write peak in narrowPeak format file... SRX2202873.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:48:53: #4 Write summits bed file... SRX2202873.20_summits.bed INFO @ Fri, 10 Nov 2017 17:48:53: Done! pass1 - making usageList (25 chroms): 0 millis pass2 - checking and writing primary data (284 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。