Job ID = 11192564 sra ファイルのダウンロード中... Completed: 809722K bytes transferred in 12 seconds (534057K 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 25805540 spots for /home/okishinya/chipatlas/results/rn6/SRX2226578/SRR4374828.sra Written 25805540 spots for /home/okishinya/chipatlas/results/rn6/SRX2226578/SRR4374828.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: 00:00:00 Multiseed full-index search: 00:13:55 25805540 reads; of these: 25805540 (100.00%) were unpaired; of these: 5747045 (22.27%) aligned 0 times 15666747 (60.71%) aligned exactly 1 time 4391748 (17.02%) aligned >1 times 77.73% overall alignment rate Time searching: 00:13:58 Overall time: 00:13:58 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] 9334670 / 20058495 = 0.4654 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 09:13:38: # Command line: callpeak -t SRX2226578.bam -f BAM -g 2.15e9 -n SRX2226578.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2226578.20 # format = BAM # ChIP-seq file = ['SRX2226578.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 09:13:38: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:13:38: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:13:38: # Command line: callpeak -t SRX2226578.bam -f BAM -g 2.15e9 -n SRX2226578.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2226578.05 # format = BAM # ChIP-seq file = ['SRX2226578.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 09:13:38: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:13:38: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:13:38: # Command line: callpeak -t SRX2226578.bam -f BAM -g 2.15e9 -n SRX2226578.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2226578.10 # format = BAM # ChIP-seq file = ['SRX2226578.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 09:13:38: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:13:38: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:13:45: 1000000 INFO @ Sat, 15 Sep 2018 09:13:45: 1000000 INFO @ Sat, 15 Sep 2018 09:13:45: 1000000 INFO @ Sat, 15 Sep 2018 09:13:51: 2000000 INFO @ Sat, 15 Sep 2018 09:13:51: 2000000 INFO @ Sat, 15 Sep 2018 09:13:51: 2000000 INFO @ Sat, 15 Sep 2018 09:13:57: 3000000 INFO @ Sat, 15 Sep 2018 09:13:57: 3000000 INFO @ Sat, 15 Sep 2018 09:13:57: 3000000 INFO @ Sat, 15 Sep 2018 09:14:03: 4000000 INFO @ Sat, 15 Sep 2018 09:14:04: 4000000 INFO @ Sat, 15 Sep 2018 09:14:04: 4000000 INFO @ Sat, 15 Sep 2018 09:14:09: 5000000 INFO @ Sat, 15 Sep 2018 09:14:10: 5000000 INFO @ Sat, 15 Sep 2018 09:14:10: 5000000 INFO @ Sat, 15 Sep 2018 09:14:16: 6000000 INFO @ Sat, 15 Sep 2018 09:14:16: 6000000 INFO @ Sat, 15 Sep 2018 09:14:16: 6000000 INFO @ Sat, 15 Sep 2018 09:14:22: 7000000 INFO @ Sat, 15 Sep 2018 09:14:22: 7000000 INFO @ Sat, 15 Sep 2018 09:14:23: 7000000 INFO @ Sat, 15 Sep 2018 09:14:28: 8000000 INFO @ Sat, 15 Sep 2018 09:14:29: 8000000 INFO @ Sat, 15 Sep 2018 09:14:29: 8000000 INFO @ Sat, 15 Sep 2018 09:14:35: 9000000 INFO @ Sat, 15 Sep 2018 09:14:35: 9000000 INFO @ Sat, 15 Sep 2018 09:14:36: 9000000 INFO @ Sat, 15 Sep 2018 09:14:41: 10000000 INFO @ Sat, 15 Sep 2018 09:14:41: 10000000 INFO @ Sat, 15 Sep 2018 09:14:42: 10000000 INFO @ Sat, 15 Sep 2018 09:14:46: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:14:46: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:14:46: #1 total tags in treatment: 10723825 INFO @ Sat, 15 Sep 2018 09:14:46: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:14:46: #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 09:14:46: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:14:46: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:14:46: #1 total tags in treatment: 10723825 INFO @ Sat, 15 Sep 2018 09:14:46: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:14:46: #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 09:14:46: #1 tags after filtering in treatment: 10723656 INFO @ Sat, 15 Sep 2018 09:14:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:14:46: #1 finished! INFO @ Sat, 15 Sep 2018 09:14:46: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:14:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:14:46: #1 tags after filtering in treatment: 10723656 INFO @ Sat, 15 Sep 2018 09:14:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:14:46: #1 finished! INFO @ Sat, 15 Sep 2018 09:14:46: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:14:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:14:47: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:14:47: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:14:47: #1 total tags in treatment: 10723825 INFO @ Sat, 15 Sep 2018 09:14:47: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:14:47: #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 09:14:48: #1 tags after filtering in treatment: 10723656 INFO @ Sat, 15 Sep 2018 09:14:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:14:48: #1 finished! INFO @ Sat, 15 Sep 2018 09:14:48: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:14:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:14:49: #2 number of paired peaks: 42231 INFO @ Sat, 15 Sep 2018 09:14:49: start model_add_line... INFO @ Sat, 15 Sep 2018 09:14:49: start X-correlation... INFO @ Sat, 15 Sep 2018 09:14:49: end of X-cor INFO @ Sat, 15 Sep 2018 09:14:49: #2 finished! INFO @ Sat, 15 Sep 2018 09:14:49: #2 predicted fragment length is 227 bps INFO @ Sat, 15 Sep 2018 09:14:49: #2 alternative fragment length(s) may be 227 bps INFO @ Sat, 15 Sep 2018 09:14:49: #2.2 Generate R script for model : SRX2226578.10_model.r INFO @ Sat, 15 Sep 2018 09:14:49: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:14:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:14:49: #2 number of paired peaks: 42231 INFO @ Sat, 15 Sep 2018 09:14:49: start model_add_line... INFO @ Sat, 15 Sep 2018 09:14:49: start X-correlation... INFO @ Sat, 15 Sep 2018 09:14:49: end of X-cor INFO @ Sat, 15 Sep 2018 09:14:49: #2 finished! INFO @ Sat, 15 Sep 2018 09:14:49: #2 predicted fragment length is 227 bps INFO @ Sat, 15 Sep 2018 09:14:49: #2 alternative fragment length(s) may be 227 bps INFO @ Sat, 15 Sep 2018 09:14:49: #2.2 Generate R script for model : SRX2226578.20_model.r INFO @ Sat, 15 Sep 2018 09:14:49: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:14:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:14:50: #2 number of paired peaks: 42231 INFO @ Sat, 15 Sep 2018 09:14:50: start model_add_line... INFO @ Sat, 15 Sep 2018 09:14:50: start X-correlation... INFO @ Sat, 15 Sep 2018 09:14:50: end of X-cor INFO @ Sat, 15 Sep 2018 09:14:50: #2 finished! INFO @ Sat, 15 Sep 2018 09:14:50: #2 predicted fragment length is 227 bps INFO @ Sat, 15 Sep 2018 09:14:50: #2 alternative fragment length(s) may be 227 bps INFO @ Sat, 15 Sep 2018 09:14:50: #2.2 Generate R script for model : SRX2226578.05_model.r INFO @ Sat, 15 Sep 2018 09:14:50: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:14:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:15:18: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:15:18: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:15:19: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:15:34: #4 Write output xls file... SRX2226578.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:15:34: #4 Write peak in narrowPeak format file... SRX2226578.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:15:34: #4 Write summits bed file... SRX2226578.10_summits.bed INFO @ Sat, 15 Sep 2018 09:15:34: Done! pass1 - making usageList (70 chroms): 2 millis pass2 - checking and writing primary data (8086 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:15:35: #4 Write output xls file... SRX2226578.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:15:35: #4 Write peak in narrowPeak format file... SRX2226578.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:15:35: #4 Write summits bed file... SRX2226578.20_summits.bed INFO @ Sat, 15 Sep 2018 09:15:35: #4 Write output xls file... SRX2226578.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:15:35: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (4987 records, 4 fields): 10 millis INFO @ Sat, 15 Sep 2018 09:15:35: #4 Write peak in narrowPeak format file... SRX2226578.05_peaks.narrowPeak CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:15:35: #4 Write summits bed file... SRX2226578.05_summits.bed INFO @ Sat, 15 Sep 2018 09:15:35: Done! pass1 - making usageList (88 chroms): 3 millis pass2 - checking and writing primary data (11643 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。