Job ID = 11192560 sra ファイルのダウンロード中... Completed: 864534K bytes transferred in 11 seconds (628611K 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... Read 27469967 spots for /home/okishinya/chipatlas/results/rn6/SRX2226574/SRR4374824.sra Written 27469967 spots for /home/okishinya/chipatlas/results/rn6/SRX2226574/SRR4374824.sra 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: 00:16:37 27469967 reads; of these: 27469967 (100.00%) were unpaired; of these: 6138672 (22.35%) aligned 0 times 16760124 (61.01%) aligned exactly 1 time 4571171 (16.64%) aligned >1 times 77.65% overall alignment rate Time searching: 00:16:41 Overall time: 00:16:41 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] 11710588 / 21331295 = 0.5490 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 @ Sat, 15 Sep 2018 09:11:13: # Command line: callpeak -t SRX2226574.bam -f BAM -g 2.15e9 -n SRX2226574.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2226574.05 # format = BAM # ChIP-seq file = ['SRX2226574.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 @ Sat, 15 Sep 2018 09:11:13: # Command line: callpeak -t SRX2226574.bam -f BAM -g 2.15e9 -n SRX2226574.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2226574.20 # format = BAM # ChIP-seq file = ['SRX2226574.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 @ Sat, 15 Sep 2018 09:11:13: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:11:13: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:11:13: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:11:13: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:11:13: # Command line: callpeak -t SRX2226574.bam -f BAM -g 2.15e9 -n SRX2226574.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2226574.10 # format = BAM # ChIP-seq file = ['SRX2226574.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 @ Sat, 15 Sep 2018 09:11:13: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:11:13: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:11:22: 1000000 INFO @ Sat, 15 Sep 2018 09:11:22: 1000000 INFO @ Sat, 15 Sep 2018 09:11:22: 1000000 INFO @ Sat, 15 Sep 2018 09:11:30: 2000000 INFO @ Sat, 15 Sep 2018 09:11:30: 2000000 INFO @ Sat, 15 Sep 2018 09:11:32: 2000000 INFO @ Sat, 15 Sep 2018 09:11:38: 3000000 INFO @ Sat, 15 Sep 2018 09:11:38: 3000000 INFO @ Sat, 15 Sep 2018 09:11:41: 3000000 INFO @ Sat, 15 Sep 2018 09:11:47: 4000000 INFO @ Sat, 15 Sep 2018 09:11:47: 4000000 INFO @ Sat, 15 Sep 2018 09:11:51: 4000000 INFO @ Sat, 15 Sep 2018 09:11:55: 5000000 INFO @ Sat, 15 Sep 2018 09:11:55: 5000000 INFO @ Sat, 15 Sep 2018 09:12:00: 5000000 INFO @ Sat, 15 Sep 2018 09:12:03: 6000000 INFO @ Sat, 15 Sep 2018 09:12:04: 6000000 INFO @ Sat, 15 Sep 2018 09:12:10: 6000000 INFO @ Sat, 15 Sep 2018 09:12:12: 7000000 INFO @ Sat, 15 Sep 2018 09:12:12: 7000000 INFO @ Sat, 15 Sep 2018 09:12:19: 7000000 INFO @ Sat, 15 Sep 2018 09:12:20: 8000000 INFO @ Sat, 15 Sep 2018 09:12:20: 8000000 INFO @ Sat, 15 Sep 2018 09:12:29: 8000000 INFO @ Sat, 15 Sep 2018 09:12:29: 9000000 INFO @ Sat, 15 Sep 2018 09:12:29: 9000000 INFO @ Sat, 15 Sep 2018 09:12:34: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:12:34: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:12:34: #1 total tags in treatment: 9620707 INFO @ Sat, 15 Sep 2018 09:12:34: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:12:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:12:34: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:12:34: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:12:34: #1 total tags in treatment: 9620707 INFO @ Sat, 15 Sep 2018 09:12:34: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:12:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:12:35: #1 tags after filtering in treatment: 9620509 INFO @ Sat, 15 Sep 2018 09:12:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:12:35: #1 finished! INFO @ Sat, 15 Sep 2018 09:12:35: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:12:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:12:35: #1 tags after filtering in treatment: 9620509 INFO @ Sat, 15 Sep 2018 09:12:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:12:35: #1 finished! INFO @ Sat, 15 Sep 2018 09:12:35: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:12:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:12:37: #2 number of paired peaks: 37254 INFO @ Sat, 15 Sep 2018 09:12:37: start model_add_line... INFO @ Sat, 15 Sep 2018 09:12:37: #2 number of paired peaks: 37254 INFO @ Sat, 15 Sep 2018 09:12:37: start model_add_line... INFO @ Sat, 15 Sep 2018 09:12:37: start X-correlation... INFO @ Sat, 15 Sep 2018 09:12:37: end of X-cor INFO @ Sat, 15 Sep 2018 09:12:37: #2 finished! INFO @ Sat, 15 Sep 2018 09:12:37: #2 predicted fragment length is 238 bps INFO @ Sat, 15 Sep 2018 09:12:37: #2 alternative fragment length(s) may be 238 bps INFO @ Sat, 15 Sep 2018 09:12:37: #2.2 Generate R script for model : SRX2226574.20_model.r INFO @ Sat, 15 Sep 2018 09:12:37: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:12:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:12:37: start X-correlation... INFO @ Sat, 15 Sep 2018 09:12:37: end of X-cor INFO @ Sat, 15 Sep 2018 09:12:37: #2 finished! INFO @ Sat, 15 Sep 2018 09:12:37: #2 predicted fragment length is 238 bps INFO @ Sat, 15 Sep 2018 09:12:37: #2 alternative fragment length(s) may be 238 bps INFO @ Sat, 15 Sep 2018 09:12:37: #2.2 Generate R script for model : SRX2226574.10_model.r INFO @ Sat, 15 Sep 2018 09:12:37: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:12:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:12:38: 9000000 INFO @ Sat, 15 Sep 2018 09:12:44: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:12:44: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:12:44: #1 total tags in treatment: 9620707 INFO @ Sat, 15 Sep 2018 09:12:44: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:12:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:12:45: #1 tags after filtering in treatment: 9620509 INFO @ Sat, 15 Sep 2018 09:12:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:12:45: #1 finished! INFO @ Sat, 15 Sep 2018 09:12:45: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:12:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:12:47: #2 number of paired peaks: 37254 INFO @ Sat, 15 Sep 2018 09:12:47: start model_add_line... INFO @ Sat, 15 Sep 2018 09:12:47: start X-correlation... INFO @ Sat, 15 Sep 2018 09:12:47: end of X-cor INFO @ Sat, 15 Sep 2018 09:12:47: #2 finished! INFO @ Sat, 15 Sep 2018 09:12:47: #2 predicted fragment length is 238 bps INFO @ Sat, 15 Sep 2018 09:12:47: #2 alternative fragment length(s) may be 238 bps INFO @ Sat, 15 Sep 2018 09:12:47: #2.2 Generate R script for model : SRX2226574.05_model.r INFO @ Sat, 15 Sep 2018 09:12:47: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:12:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:13:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:13:04: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:13:14: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:13:18: #4 Write output xls file... SRX2226574.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:13:18: #4 Write peak in narrowPeak format file... SRX2226574.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:13:18: #4 Write summits bed file... SRX2226574.20_summits.bed INFO @ Sat, 15 Sep 2018 09:13:18: Done! INFO @ Sat, 15 Sep 2018 09:13:19: #4 Write output xls file... SRX2226574.10_peaks.xls pass1 - making usageList (43 chroms): 13 millis INFO @ Sat, 15 Sep 2018 09:13:19: #4 Write peak in narrowPeak format file... SRX2226574.10_peaks.narrowPeak pass2 - checking and writing primary data (2999 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:13:19: #4 Write summits bed file... SRX2226574.10_summits.bed INFO @ Sat, 15 Sep 2018 09:13:19: Done! pass1 - making usageList (66 chroms): 2 millis pass2 - checking and writing primary data (6170 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:13:31: #4 Write output xls file... SRX2226574.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:13:31: #4 Write peak in narrowPeak format file... SRX2226574.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:13:32: #4 Write summits bed file... SRX2226574.05_summits.bed INFO @ Sat, 15 Sep 2018 09:13:32: Done! pass1 - making usageList (86 chroms): 2 millis pass2 - checking and writing primary data (9469 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。