Job ID = 11192557 sra ファイルのダウンロード中... Completed: 999602K bytes transferred in 12 seconds (662229K 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 31224325 spots for /home/okishinya/chipatlas/results/rn6/SRX2226571/SRR4374821.sra Written 31224325 spots for /home/okishinya/chipatlas/results/rn6/SRX2226571/SRR4374821.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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:21:28 31224325 reads; of these: 31224325 (100.00%) were unpaired; of these: 5066950 (16.23%) aligned 0 times 20066597 (64.27%) aligned exactly 1 time 6090778 (19.51%) aligned >1 times 83.77% overall alignment rate Time searching: 00:21:30 Overall time: 00:21:30 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] 15829516 / 26157375 = 0.6052 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 09:14:49: # Command line: callpeak -t SRX2226571.bam -f BAM -g 2.15e9 -n SRX2226571.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2226571.10 # format = BAM # ChIP-seq file = ['SRX2226571.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 09:14:49: # Command line: callpeak -t SRX2226571.bam -f BAM -g 2.15e9 -n SRX2226571.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2226571.05 # format = BAM # ChIP-seq file = ['SRX2226571.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 09:14:49: # Command line: callpeak -t SRX2226571.bam -f BAM -g 2.15e9 -n SRX2226571.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2226571.20 # format = BAM # ChIP-seq file = ['SRX2226571.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 09:14:49: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:14:49: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:14:49: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:14:49: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:14:49: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:14:49: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:14:58: 1000000 INFO @ Sat, 15 Sep 2018 09:14:58: 1000000 INFO @ Sat, 15 Sep 2018 09:14:58: 1000000 INFO @ Sat, 15 Sep 2018 09:15:07: 2000000 INFO @ Sat, 15 Sep 2018 09:15:07: 2000000 INFO @ Sat, 15 Sep 2018 09:15:08: 2000000 INFO @ Sat, 15 Sep 2018 09:15:15: 3000000 INFO @ Sat, 15 Sep 2018 09:15:15: 3000000 INFO @ Sat, 15 Sep 2018 09:15:18: 3000000 INFO @ Sat, 15 Sep 2018 09:15:23: 4000000 INFO @ Sat, 15 Sep 2018 09:15:23: 4000000 INFO @ Sat, 15 Sep 2018 09:15:28: 4000000 INFO @ Sat, 15 Sep 2018 09:15:31: 5000000 INFO @ Sat, 15 Sep 2018 09:15:32: 5000000 INFO @ Sat, 15 Sep 2018 09:15:38: 5000000 INFO @ Sat, 15 Sep 2018 09:15:40: 6000000 INFO @ Sat, 15 Sep 2018 09:15:40: 6000000 INFO @ Sat, 15 Sep 2018 09:15:47: 6000000 INFO @ Sat, 15 Sep 2018 09:15:49: 7000000 INFO @ Sat, 15 Sep 2018 09:15:49: 7000000 INFO @ Sat, 15 Sep 2018 09:15:56: 7000000 INFO @ Sat, 15 Sep 2018 09:15:57: 8000000 INFO @ Sat, 15 Sep 2018 09:15:57: 8000000 INFO @ Sat, 15 Sep 2018 09:16:04: 8000000 INFO @ Sat, 15 Sep 2018 09:16:06: 9000000 INFO @ Sat, 15 Sep 2018 09:16:06: 9000000 INFO @ Sat, 15 Sep 2018 09:16:12: 9000000 INFO @ Sat, 15 Sep 2018 09:16:15: 10000000 INFO @ Sat, 15 Sep 2018 09:16:15: 10000000 INFO @ Sat, 15 Sep 2018 09:16:18: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:16:18: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:16:18: #1 total tags in treatment: 10327859 INFO @ Sat, 15 Sep 2018 09:16:18: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:16:18: #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 09:16:18: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:16:18: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:16:18: #1 total tags in treatment: 10327859 INFO @ Sat, 15 Sep 2018 09:16:18: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:16:18: #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 09:16:18: #1 tags after filtering in treatment: 10327680 INFO @ Sat, 15 Sep 2018 09:16:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:16:18: #1 finished! INFO @ Sat, 15 Sep 2018 09:16:18: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:16:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:16:18: #1 tags after filtering in treatment: 10327680 INFO @ Sat, 15 Sep 2018 09:16:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:16:18: #1 finished! INFO @ Sat, 15 Sep 2018 09:16:18: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:16:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:16:20: #2 number of paired peaks: 35337 INFO @ Sat, 15 Sep 2018 09:16:20: start model_add_line... INFO @ Sat, 15 Sep 2018 09:16:21: #2 number of paired peaks: 35337 INFO @ Sat, 15 Sep 2018 09:16:21: start model_add_line... INFO @ Sat, 15 Sep 2018 09:16:21: start X-correlation... INFO @ Sat, 15 Sep 2018 09:16:21: end of X-cor INFO @ Sat, 15 Sep 2018 09:16:21: #2 finished! INFO @ Sat, 15 Sep 2018 09:16:21: #2 predicted fragment length is 226 bps INFO @ Sat, 15 Sep 2018 09:16:21: #2 alternative fragment length(s) may be 226 bps INFO @ Sat, 15 Sep 2018 09:16:21: #2.2 Generate R script for model : SRX2226571.10_model.r INFO @ Sat, 15 Sep 2018 09:16:21: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:16:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:16:21: start X-correlation... INFO @ Sat, 15 Sep 2018 09:16:21: end of X-cor INFO @ Sat, 15 Sep 2018 09:16:21: #2 finished! INFO @ Sat, 15 Sep 2018 09:16:21: #2 predicted fragment length is 226 bps INFO @ Sat, 15 Sep 2018 09:16:21: #2 alternative fragment length(s) may be 226 bps INFO @ Sat, 15 Sep 2018 09:16:21: #2.2 Generate R script for model : SRX2226571.20_model.r INFO @ Sat, 15 Sep 2018 09:16:21: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:16:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:16:21: 10000000 INFO @ Sat, 15 Sep 2018 09:16:24: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:16:24: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:16:24: #1 total tags in treatment: 10327859 INFO @ Sat, 15 Sep 2018 09:16:24: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:16:24: #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 09:16:25: #1 tags after filtering in treatment: 10327680 INFO @ Sat, 15 Sep 2018 09:16:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:16:25: #1 finished! INFO @ Sat, 15 Sep 2018 09:16:25: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:16:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:16:27: #2 number of paired peaks: 35337 INFO @ Sat, 15 Sep 2018 09:16:27: start model_add_line... INFO @ Sat, 15 Sep 2018 09:16:27: start X-correlation... INFO @ Sat, 15 Sep 2018 09:16:27: end of X-cor INFO @ Sat, 15 Sep 2018 09:16:27: #2 finished! INFO @ Sat, 15 Sep 2018 09:16:27: #2 predicted fragment length is 226 bps INFO @ Sat, 15 Sep 2018 09:16:27: #2 alternative fragment length(s) may be 226 bps INFO @ Sat, 15 Sep 2018 09:16:27: #2.2 Generate R script for model : SRX2226571.05_model.r INFO @ Sat, 15 Sep 2018 09:16:27: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:16:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:16:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:16:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:16:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:17:05: #4 Write output xls file... SRX2226571.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:17:05: #4 Write output xls file... SRX2226571.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:17:05: #4 Write peak in narrowPeak format file... SRX2226571.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:17:05: #4 Write summits bed file... SRX2226571.20_summits.bed INFO @ Sat, 15 Sep 2018 09:17:05: #4 Write peak in narrowPeak format file... SRX2226571.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:17:05: Done! INFO @ Sat, 15 Sep 2018 09:17:05: #4 Write summits bed file... SRX2226571.10_summits.bed INFO @ Sat, 15 Sep 2018 09:17:05: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (669 records, 4 fields): 4 millis pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (1595 records, 4 fields): 6 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:17:14: #4 Write output xls file... SRX2226571.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:17:14: #4 Write peak in narrowPeak format file... SRX2226571.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:17:14: #4 Write summits bed file... SRX2226571.05_summits.bed INFO @ Sat, 15 Sep 2018 09:17:14: Done! pass1 - making usageList (53 chroms): 1 millis pass2 - checking and writing primary data (3984 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。