Job ID = 11192596 sra ファイルのダウンロード中... Completed: 333892K bytes transferred in 33 seconds (80940K 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 32600947 spots for /home/okishinya/chipatlas/results/rn6/SRX4014816/SRR7085065.sra Written 32600947 spots for /home/okishinya/chipatlas/results/rn6/SRX4014816/SRR7085065.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: 00:00:02 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:40:24 32600947 reads; of these: 32600947 (100.00%) were unpaired; of these: 1014709 (3.11%) aligned 0 times 27934463 (85.69%) aligned exactly 1 time 3651775 (11.20%) aligned >1 times 96.89% overall alignment rate Time searching: 00:40:29 Overall time: 00:40:29 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 16 files... [bam_rmdupse_core] 2810219 / 31586238 = 0.0890 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 11:40:16: # Command line: callpeak -t SRX4014816.bam -f BAM -g 2.15e9 -n SRX4014816.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4014816.10 # format = BAM # ChIP-seq file = ['SRX4014816.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 11:40:16: # Command line: callpeak -t SRX4014816.bam -f BAM -g 2.15e9 -n SRX4014816.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4014816.20 # format = BAM # ChIP-seq file = ['SRX4014816.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 11:40:16: # Command line: callpeak -t SRX4014816.bam -f BAM -g 2.15e9 -n SRX4014816.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4014816.05 # format = BAM # ChIP-seq file = ['SRX4014816.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 11:40:16: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:40:16: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:40:16: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:40:16: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:40:16: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:40:16: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:40:24: 1000000 INFO @ Sat, 15 Sep 2018 11:40:24: 1000000 INFO @ Sat, 15 Sep 2018 11:40:24: 1000000 INFO @ Sat, 15 Sep 2018 11:40:32: 2000000 INFO @ Sat, 15 Sep 2018 11:40:32: 2000000 INFO @ Sat, 15 Sep 2018 11:40:32: 2000000 INFO @ Sat, 15 Sep 2018 11:40:39: 3000000 INFO @ Sat, 15 Sep 2018 11:40:39: 3000000 INFO @ Sat, 15 Sep 2018 11:40:39: 3000000 INFO @ Sat, 15 Sep 2018 11:40:47: 4000000 INFO @ Sat, 15 Sep 2018 11:40:47: 4000000 INFO @ Sat, 15 Sep 2018 11:40:47: 4000000 INFO @ Sat, 15 Sep 2018 11:40:55: 5000000 INFO @ Sat, 15 Sep 2018 11:40:55: 5000000 INFO @ Sat, 15 Sep 2018 11:40:55: 5000000 INFO @ Sat, 15 Sep 2018 11:41:03: 6000000 INFO @ Sat, 15 Sep 2018 11:41:03: 6000000 INFO @ Sat, 15 Sep 2018 11:41:03: 6000000 INFO @ Sat, 15 Sep 2018 11:41:10: 7000000 INFO @ Sat, 15 Sep 2018 11:41:10: 7000000 INFO @ Sat, 15 Sep 2018 11:41:11: 7000000 INFO @ Sat, 15 Sep 2018 11:41:18: 8000000 INFO @ Sat, 15 Sep 2018 11:41:18: 8000000 INFO @ Sat, 15 Sep 2018 11:41:18: 8000000 INFO @ Sat, 15 Sep 2018 11:41:26: 9000000 INFO @ Sat, 15 Sep 2018 11:41:26: 9000000 INFO @ Sat, 15 Sep 2018 11:41:26: 9000000 INFO @ Sat, 15 Sep 2018 11:41:33: 10000000 INFO @ Sat, 15 Sep 2018 11:41:33: 10000000 INFO @ Sat, 15 Sep 2018 11:41:35: 10000000 INFO @ Sat, 15 Sep 2018 11:41:41: 11000000 INFO @ Sat, 15 Sep 2018 11:41:41: 11000000 INFO @ Sat, 15 Sep 2018 11:41:43: 11000000 INFO @ Sat, 15 Sep 2018 11:41:49: 12000000 INFO @ Sat, 15 Sep 2018 11:41:49: 12000000 INFO @ Sat, 15 Sep 2018 11:41:51: 12000000 INFO @ Sat, 15 Sep 2018 11:41:56: 13000000 INFO @ Sat, 15 Sep 2018 11:41:56: 13000000 INFO @ Sat, 15 Sep 2018 11:41:59: 13000000 INFO @ Sat, 15 Sep 2018 11:42:04: 14000000 INFO @ Sat, 15 Sep 2018 11:42:04: 14000000 INFO @ Sat, 15 Sep 2018 11:42:07: 14000000 INFO @ Sat, 15 Sep 2018 11:42:12: 15000000 INFO @ Sat, 15 Sep 2018 11:42:12: 15000000 INFO @ Sat, 15 Sep 2018 11:42:14: 15000000 INFO @ Sat, 15 Sep 2018 11:42:20: 16000000 INFO @ Sat, 15 Sep 2018 11:42:20: 16000000 INFO @ Sat, 15 Sep 2018 11:42:23: 16000000 INFO @ Sat, 15 Sep 2018 11:42:27: 17000000 INFO @ Sat, 15 Sep 2018 11:42:27: 17000000 INFO @ Sat, 15 Sep 2018 11:42:31: 17000000 INFO @ Sat, 15 Sep 2018 11:42:35: 18000000 INFO @ Sat, 15 Sep 2018 11:42:35: 18000000 INFO @ Sat, 15 Sep 2018 11:42:39: 18000000 INFO @ Sat, 15 Sep 2018 11:42:43: 19000000 INFO @ Sat, 15 Sep 2018 11:42:43: 19000000 INFO @ Sat, 15 Sep 2018 11:42:46: 19000000 INFO @ Sat, 15 Sep 2018 11:42:51: 20000000 INFO @ Sat, 15 Sep 2018 11:42:51: 20000000 INFO @ Sat, 15 Sep 2018 11:42:55: 20000000 INFO @ Sat, 15 Sep 2018 11:42:58: 21000000 INFO @ Sat, 15 Sep 2018 11:42:58: 21000000 INFO @ Sat, 15 Sep 2018 11:43:03: 21000000 INFO @ Sat, 15 Sep 2018 11:43:05: 22000000 INFO @ Sat, 15 Sep 2018 11:43:05: 22000000 INFO @ Sat, 15 Sep 2018 11:43:11: 22000000 INFO @ Sat, 15 Sep 2018 11:43:13: 23000000 INFO @ Sat, 15 Sep 2018 11:43:13: 23000000 INFO @ Sat, 15 Sep 2018 11:43:20: 24000000 INFO @ Sat, 15 Sep 2018 11:43:20: 24000000 INFO @ Sat, 15 Sep 2018 11:43:21: 23000000 INFO @ Sat, 15 Sep 2018 11:43:27: 25000000 INFO @ Sat, 15 Sep 2018 11:43:27: 25000000 INFO @ Sat, 15 Sep 2018 11:43:29: 24000000 INFO @ Sat, 15 Sep 2018 11:43:34: 26000000 INFO @ Sat, 15 Sep 2018 11:43:34: 26000000 INFO @ Sat, 15 Sep 2018 11:43:38: 25000000 INFO @ Sat, 15 Sep 2018 11:43:41: 27000000 INFO @ Sat, 15 Sep 2018 11:43:41: 27000000 INFO @ Sat, 15 Sep 2018 11:43:46: 26000000 INFO @ Sat, 15 Sep 2018 11:43:48: 28000000 INFO @ Sat, 15 Sep 2018 11:43:48: 28000000 INFO @ Sat, 15 Sep 2018 11:43:54: 27000000 INFO @ Sat, 15 Sep 2018 11:43:55: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:43:55: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:43:55: #1 total tags in treatment: 28776019 INFO @ Sat, 15 Sep 2018 11:43:55: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:43:55: #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 11:43:55: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:43:55: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:43:55: #1 total tags in treatment: 28776019 INFO @ Sat, 15 Sep 2018 11:43:55: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:43:55: #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 11:43:55: #1 tags after filtering in treatment: 28775833 INFO @ Sat, 15 Sep 2018 11:43:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:43:55: #1 finished! INFO @ Sat, 15 Sep 2018 11:43:55: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:43:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:43:55: #1 tags after filtering in treatment: 28775833 INFO @ Sat, 15 Sep 2018 11:43:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:43:55: #1 finished! INFO @ Sat, 15 Sep 2018 11:43:55: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:43:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:44:02: 28000000 INFO @ Sat, 15 Sep 2018 11:44:04: #2 number of paired peaks: 157949 INFO @ Sat, 15 Sep 2018 11:44:04: start model_add_line... INFO @ Sat, 15 Sep 2018 11:44:04: #2 number of paired peaks: 157949 INFO @ Sat, 15 Sep 2018 11:44:04: start model_add_line... INFO @ Sat, 15 Sep 2018 11:44:05: start X-correlation... INFO @ Sat, 15 Sep 2018 11:44:05: start X-correlation... INFO @ Sat, 15 Sep 2018 11:44:05: end of X-cor INFO @ Sat, 15 Sep 2018 11:44:05: end of X-cor INFO @ Sat, 15 Sep 2018 11:44:05: #2 finished! INFO @ Sat, 15 Sep 2018 11:44:05: #2 finished! INFO @ Sat, 15 Sep 2018 11:44:05: #2 predicted fragment length is 229 bps INFO @ Sat, 15 Sep 2018 11:44:05: #2 predicted fragment length is 229 bps INFO @ Sat, 15 Sep 2018 11:44:05: #2 alternative fragment length(s) may be 229 bps INFO @ Sat, 15 Sep 2018 11:44:05: #2 alternative fragment length(s) may be 229 bps INFO @ Sat, 15 Sep 2018 11:44:05: #2.2 Generate R script for model : SRX4014816.10_model.r INFO @ Sat, 15 Sep 2018 11:44:05: #2.2 Generate R script for model : SRX4014816.05_model.r INFO @ Sat, 15 Sep 2018 11:44:05: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:44:05: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:44:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:44:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:44:09: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:44:09: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:44:09: #1 total tags in treatment: 28776019 INFO @ Sat, 15 Sep 2018 11:44:09: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:44:09: #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 11:44:10: #1 tags after filtering in treatment: 28775833 INFO @ Sat, 15 Sep 2018 11:44:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:44:10: #1 finished! INFO @ Sat, 15 Sep 2018 11:44:10: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:44:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:44:18: #2 number of paired peaks: 157949 INFO @ Sat, 15 Sep 2018 11:44:18: start model_add_line... INFO @ Sat, 15 Sep 2018 11:44:19: start X-correlation... INFO @ Sat, 15 Sep 2018 11:44:19: end of X-cor INFO @ Sat, 15 Sep 2018 11:44:19: #2 finished! INFO @ Sat, 15 Sep 2018 11:44:19: #2 predicted fragment length is 229 bps INFO @ Sat, 15 Sep 2018 11:44:19: #2 alternative fragment length(s) may be 229 bps INFO @ Sat, 15 Sep 2018 11:44:19: #2.2 Generate R script for model : SRX4014816.20_model.r INFO @ Sat, 15 Sep 2018 11:44:19: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:44:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:45:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:45:30: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:45:38: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:46:15: #4 Write output xls file... SRX4014816.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:46:15: #4 Write peak in narrowPeak format file... SRX4014816.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:46:15: #4 Write summits bed file... SRX4014816.05_summits.bed INFO @ Sat, 15 Sep 2018 11:46:15: Done! pass1 - making usageList (123 chroms): 14 millis pass2 - checking and writing primary data (18443 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:46:22: #4 Write output xls file... SRX4014816.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:46:22: #4 Write peak in narrowPeak format file... SRX4014816.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:46:22: #4 Write summits bed file... SRX4014816.10_summits.bed INFO @ Sat, 15 Sep 2018 11:46:22: Done! pass1 - making usageList (69 chroms): 1 millis pass2 - checking and writing primary data (4552 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:46:26: #4 Write output xls file... SRX4014816.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:46:26: #4 Write peak in narrowPeak format file... SRX4014816.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:46:26: #4 Write summits bed file... SRX4014816.20_summits.bed INFO @ Sat, 15 Sep 2018 11:46:26: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (652 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。