Job ID = 11192563 sra ファイルのダウンロード中... Completed: 755984K bytes transferred in 9 seconds (665745K 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 24069099 spots for /home/okishinya/chipatlas/results/rn6/SRX2226577/SRR4374827.sra Written 24069099 spots for /home/okishinya/chipatlas/results/rn6/SRX2226577/SRR4374827.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:13:01 24069099 reads; of these: 24069099 (100.00%) were unpaired; of these: 6082645 (25.27%) aligned 0 times 13813012 (57.39%) aligned exactly 1 time 4173442 (17.34%) aligned >1 times 74.73% overall alignment rate Time searching: 00:13:04 Overall time: 00:13:04 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] 9958564 / 17986454 = 0.5537 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 09:10:27: # Command line: callpeak -t SRX2226577.bam -f BAM -g 2.15e9 -n SRX2226577.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2226577.20 # format = BAM # ChIP-seq file = ['SRX2226577.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 09:10:27: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:10:27: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:10:27: # Command line: callpeak -t SRX2226577.bam -f BAM -g 2.15e9 -n SRX2226577.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2226577.05 # format = BAM # ChIP-seq file = ['SRX2226577.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 09:10:27: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:10:27: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:10:27: # Command line: callpeak -t SRX2226577.bam -f BAM -g 2.15e9 -n SRX2226577.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2226577.10 # format = BAM # ChIP-seq file = ['SRX2226577.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 09:10:27: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:10:27: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:10:33: 1000000 INFO @ Sat, 15 Sep 2018 09:10:34: 1000000 INFO @ Sat, 15 Sep 2018 09:10:34: 1000000 INFO @ Sat, 15 Sep 2018 09:10:40: 2000000 INFO @ Sat, 15 Sep 2018 09:10:41: 2000000 INFO @ Sat, 15 Sep 2018 09:10:41: 2000000 INFO @ Sat, 15 Sep 2018 09:10:47: 3000000 INFO @ Sat, 15 Sep 2018 09:10:48: 3000000 INFO @ Sat, 15 Sep 2018 09:10:48: 3000000 INFO @ Sat, 15 Sep 2018 09:10:54: 4000000 INFO @ Sat, 15 Sep 2018 09:10:55: 4000000 INFO @ Sat, 15 Sep 2018 09:10:55: 4000000 INFO @ Sat, 15 Sep 2018 09:11:01: 5000000 INFO @ Sat, 15 Sep 2018 09:11:02: 5000000 INFO @ Sat, 15 Sep 2018 09:11:02: 5000000 INFO @ Sat, 15 Sep 2018 09:11:08: 6000000 INFO @ Sat, 15 Sep 2018 09:11:10: 6000000 INFO @ Sat, 15 Sep 2018 09:11:10: 6000000 INFO @ Sat, 15 Sep 2018 09:11:14: 7000000 INFO @ Sat, 15 Sep 2018 09:11:17: 7000000 INFO @ Sat, 15 Sep 2018 09:11:17: 7000000 INFO @ Sat, 15 Sep 2018 09:11:21: 8000000 INFO @ Sat, 15 Sep 2018 09:11:22: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:11:22: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:11:22: #1 total tags in treatment: 8027890 INFO @ Sat, 15 Sep 2018 09:11:22: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:11:22: #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 09:11:22: #1 tags after filtering in treatment: 8027691 INFO @ Sat, 15 Sep 2018 09:11:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:11:22: #1 finished! INFO @ Sat, 15 Sep 2018 09:11:22: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:11:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:11:24: #2 number of paired peaks: 30810 INFO @ Sat, 15 Sep 2018 09:11:24: start model_add_line... INFO @ Sat, 15 Sep 2018 09:11:24: start X-correlation... INFO @ Sat, 15 Sep 2018 09:11:24: end of X-cor INFO @ Sat, 15 Sep 2018 09:11:24: #2 finished! INFO @ Sat, 15 Sep 2018 09:11:24: #2 predicted fragment length is 229 bps INFO @ Sat, 15 Sep 2018 09:11:24: #2 alternative fragment length(s) may be 229 bps INFO @ Sat, 15 Sep 2018 09:11:24: #2.2 Generate R script for model : SRX2226577.10_model.r INFO @ Sat, 15 Sep 2018 09:11:24: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:11:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:11:24: 8000000 INFO @ Sat, 15 Sep 2018 09:11:24: 8000000 INFO @ Sat, 15 Sep 2018 09:11:24: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:11:24: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:11:24: #1 total tags in treatment: 8027890 INFO @ Sat, 15 Sep 2018 09:11:24: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:11:24: #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 09:11:24: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:11:24: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:11:24: #1 total tags in treatment: 8027890 INFO @ Sat, 15 Sep 2018 09:11:24: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:11:24: #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 09:11:25: #1 tags after filtering in treatment: 8027691 INFO @ Sat, 15 Sep 2018 09:11:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:11:25: #1 finished! INFO @ Sat, 15 Sep 2018 09:11:25: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:11:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:11:25: #1 tags after filtering in treatment: 8027691 INFO @ Sat, 15 Sep 2018 09:11:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:11:25: #1 finished! INFO @ Sat, 15 Sep 2018 09:11:25: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:11:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:11:27: #2 number of paired peaks: 30810 INFO @ Sat, 15 Sep 2018 09:11:27: start model_add_line... INFO @ Sat, 15 Sep 2018 09:11:27: #2 number of paired peaks: 30810 INFO @ Sat, 15 Sep 2018 09:11:27: start model_add_line... INFO @ Sat, 15 Sep 2018 09:11:27: start X-correlation... INFO @ Sat, 15 Sep 2018 09:11:27: end of X-cor INFO @ Sat, 15 Sep 2018 09:11:27: #2 finished! INFO @ Sat, 15 Sep 2018 09:11:27: #2 predicted fragment length is 229 bps INFO @ Sat, 15 Sep 2018 09:11:27: #2 alternative fragment length(s) may be 229 bps INFO @ Sat, 15 Sep 2018 09:11:27: #2.2 Generate R script for model : SRX2226577.05_model.r INFO @ Sat, 15 Sep 2018 09:11:27: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:11:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:11:27: start X-correlation... INFO @ Sat, 15 Sep 2018 09:11:27: end of X-cor INFO @ Sat, 15 Sep 2018 09:11:27: #2 finished! INFO @ Sat, 15 Sep 2018 09:11:27: #2 predicted fragment length is 229 bps INFO @ Sat, 15 Sep 2018 09:11:27: #2 alternative fragment length(s) may be 229 bps INFO @ Sat, 15 Sep 2018 09:11:27: #2.2 Generate R script for model : SRX2226577.20_model.r INFO @ Sat, 15 Sep 2018 09:11:27: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:11:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:11:44: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:11:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:11:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:11:57: #4 Write output xls file... SRX2226577.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:11:57: #4 Write peak in narrowPeak format file... SRX2226577.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:11:57: #4 Write summits bed file... SRX2226577.10_summits.bed INFO @ Sat, 15 Sep 2018 09:11:57: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (3664 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:12:00: #4 Write output xls file... SRX2226577.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:12:00: #4 Write peak in narrowPeak format file... SRX2226577.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:12:00: #4 Write summits bed file... SRX2226577.20_summits.bed INFO @ Sat, 15 Sep 2018 09:12:00: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (1391 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:12:01: #4 Write output xls file... SRX2226577.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:12:01: #4 Write peak in narrowPeak format file... SRX2226577.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:12:01: #4 Write summits bed file... SRX2226577.05_summits.bed INFO @ Sat, 15 Sep 2018 09:12:01: Done! pass1 - making usageList (70 chroms): 1 millis pass2 - checking and writing primary data (6535 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。