Job ID = 11192592 sra ファイルのダウンロード中... Completed: 650714K bytes transferred in 51 seconds (103258K 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 53423760 spots for /home/okishinya/chipatlas/results/rn6/SRX4014812/SRR7085061.sra Written 53423760 spots for /home/okishinya/chipatlas/results/rn6/SRX4014812/SRR7085061.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: 00:41:51 53423760 reads; of these: 53423760 (100.00%) were unpaired; of these: 1664653 (3.12%) aligned 0 times 46130407 (86.35%) aligned exactly 1 time 5628700 (10.54%) aligned >1 times 96.88% overall alignment rate Time searching: 00:41:55 Overall time: 00:41:55 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 24 files... [bam_rmdupse_core] 15658633 / 51759107 = 0.3025 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 11:35:18: # Command line: callpeak -t SRX4014812.bam -f BAM -g 2.15e9 -n SRX4014812.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4014812.10 # format = BAM # ChIP-seq file = ['SRX4014812.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 11:35:18: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:35:18: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:35:18: # Command line: callpeak -t SRX4014812.bam -f BAM -g 2.15e9 -n SRX4014812.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4014812.20 # format = BAM # ChIP-seq file = ['SRX4014812.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 11:35:18: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:35:18: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:35:18: # Command line: callpeak -t SRX4014812.bam -f BAM -g 2.15e9 -n SRX4014812.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4014812.05 # format = BAM # ChIP-seq file = ['SRX4014812.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 11:35:18: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:35:18: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:35:25: 1000000 INFO @ Sat, 15 Sep 2018 11:35:25: 1000000 INFO @ Sat, 15 Sep 2018 11:35:25: 1000000 INFO @ Sat, 15 Sep 2018 11:35:31: 2000000 INFO @ Sat, 15 Sep 2018 11:35:31: 2000000 INFO @ Sat, 15 Sep 2018 11:35:31: 2000000 INFO @ Sat, 15 Sep 2018 11:35:38: 3000000 INFO @ Sat, 15 Sep 2018 11:35:38: 3000000 INFO @ Sat, 15 Sep 2018 11:35:38: 3000000 INFO @ Sat, 15 Sep 2018 11:35:44: 4000000 INFO @ Sat, 15 Sep 2018 11:35:44: 4000000 INFO @ Sat, 15 Sep 2018 11:35:45: 4000000 INFO @ Sat, 15 Sep 2018 11:35:51: 5000000 INFO @ Sat, 15 Sep 2018 11:35:51: 5000000 INFO @ Sat, 15 Sep 2018 11:35:51: 5000000 INFO @ Sat, 15 Sep 2018 11:35:58: 6000000 INFO @ Sat, 15 Sep 2018 11:35:58: 6000000 INFO @ Sat, 15 Sep 2018 11:35:58: 6000000 INFO @ Sat, 15 Sep 2018 11:36:04: 7000000 INFO @ Sat, 15 Sep 2018 11:36:04: 7000000 INFO @ Sat, 15 Sep 2018 11:36:05: 7000000 INFO @ Sat, 15 Sep 2018 11:36:11: 8000000 INFO @ Sat, 15 Sep 2018 11:36:11: 8000000 INFO @ Sat, 15 Sep 2018 11:36:11: 8000000 INFO @ Sat, 15 Sep 2018 11:36:18: 9000000 INFO @ Sat, 15 Sep 2018 11:36:18: 9000000 INFO @ Sat, 15 Sep 2018 11:36:18: 9000000 INFO @ Sat, 15 Sep 2018 11:36:24: 10000000 INFO @ Sat, 15 Sep 2018 11:36:24: 10000000 INFO @ Sat, 15 Sep 2018 11:36:25: 10000000 INFO @ Sat, 15 Sep 2018 11:36:31: 11000000 INFO @ Sat, 15 Sep 2018 11:36:31: 11000000 INFO @ Sat, 15 Sep 2018 11:36:31: 11000000 INFO @ Sat, 15 Sep 2018 11:36:37: 12000000 INFO @ Sat, 15 Sep 2018 11:36:38: 12000000 INFO @ Sat, 15 Sep 2018 11:36:38: 12000000 INFO @ Sat, 15 Sep 2018 11:36:44: 13000000 INFO @ Sat, 15 Sep 2018 11:36:44: 13000000 INFO @ Sat, 15 Sep 2018 11:36:44: 13000000 INFO @ Sat, 15 Sep 2018 11:36:51: 14000000 INFO @ Sat, 15 Sep 2018 11:36:51: 14000000 INFO @ Sat, 15 Sep 2018 11:36:51: 14000000 INFO @ Sat, 15 Sep 2018 11:36:57: 15000000 INFO @ Sat, 15 Sep 2018 11:36:57: 15000000 INFO @ Sat, 15 Sep 2018 11:36:58: 15000000 INFO @ Sat, 15 Sep 2018 11:37:04: 16000000 INFO @ Sat, 15 Sep 2018 11:37:04: 16000000 INFO @ Sat, 15 Sep 2018 11:37:04: 16000000 INFO @ Sat, 15 Sep 2018 11:37:11: 17000000 INFO @ Sat, 15 Sep 2018 11:37:11: 17000000 INFO @ Sat, 15 Sep 2018 11:37:11: 17000000 INFO @ Sat, 15 Sep 2018 11:37:17: 18000000 INFO @ Sat, 15 Sep 2018 11:37:17: 18000000 INFO @ Sat, 15 Sep 2018 11:37:18: 18000000 INFO @ Sat, 15 Sep 2018 11:37:24: 19000000 INFO @ Sat, 15 Sep 2018 11:37:24: 19000000 INFO @ Sat, 15 Sep 2018 11:37:24: 19000000 INFO @ Sat, 15 Sep 2018 11:37:31: 20000000 INFO @ Sat, 15 Sep 2018 11:37:31: 20000000 INFO @ Sat, 15 Sep 2018 11:37:31: 20000000 INFO @ Sat, 15 Sep 2018 11:37:37: 21000000 INFO @ Sat, 15 Sep 2018 11:37:38: 21000000 INFO @ Sat, 15 Sep 2018 11:37:38: 21000000 INFO @ Sat, 15 Sep 2018 11:37:44: 22000000 INFO @ Sat, 15 Sep 2018 11:37:44: 22000000 INFO @ Sat, 15 Sep 2018 11:37:45: 22000000 INFO @ Sat, 15 Sep 2018 11:37:51: 23000000 INFO @ Sat, 15 Sep 2018 11:37:51: 23000000 INFO @ Sat, 15 Sep 2018 11:37:51: 23000000 INFO @ Sat, 15 Sep 2018 11:37:57: 24000000 INFO @ Sat, 15 Sep 2018 11:37:58: 24000000 INFO @ Sat, 15 Sep 2018 11:37:58: 24000000 INFO @ Sat, 15 Sep 2018 11:38:04: 25000000 INFO @ Sat, 15 Sep 2018 11:38:04: 25000000 INFO @ Sat, 15 Sep 2018 11:38:05: 25000000 INFO @ Sat, 15 Sep 2018 11:38:11: 26000000 INFO @ Sat, 15 Sep 2018 11:38:11: 26000000 INFO @ Sat, 15 Sep 2018 11:38:12: 26000000 INFO @ Sat, 15 Sep 2018 11:38:17: 27000000 INFO @ Sat, 15 Sep 2018 11:38:18: 27000000 INFO @ Sat, 15 Sep 2018 11:38:18: 27000000 INFO @ Sat, 15 Sep 2018 11:38:24: 28000000 INFO @ Sat, 15 Sep 2018 11:38:25: 28000000 INFO @ Sat, 15 Sep 2018 11:38:25: 28000000 INFO @ Sat, 15 Sep 2018 11:38:30: 29000000 INFO @ Sat, 15 Sep 2018 11:38:31: 29000000 INFO @ Sat, 15 Sep 2018 11:38:31: 29000000 INFO @ Sat, 15 Sep 2018 11:38:37: 30000000 INFO @ Sat, 15 Sep 2018 11:38:38: 30000000 INFO @ Sat, 15 Sep 2018 11:38:38: 30000000 INFO @ Sat, 15 Sep 2018 11:38:43: 31000000 INFO @ Sat, 15 Sep 2018 11:38:45: 31000000 INFO @ Sat, 15 Sep 2018 11:38:45: 31000000 INFO @ Sat, 15 Sep 2018 11:38:50: 32000000 INFO @ Sat, 15 Sep 2018 11:38:51: 32000000 INFO @ Sat, 15 Sep 2018 11:38:51: 32000000 INFO @ Sat, 15 Sep 2018 11:38:56: 33000000 INFO @ Sat, 15 Sep 2018 11:38:58: 33000000 INFO @ Sat, 15 Sep 2018 11:38:58: 33000000 INFO @ Sat, 15 Sep 2018 11:39:03: 34000000 INFO @ Sat, 15 Sep 2018 11:39:04: 34000000 INFO @ Sat, 15 Sep 2018 11:39:04: 34000000 INFO @ Sat, 15 Sep 2018 11:39:09: 35000000 INFO @ Sat, 15 Sep 2018 11:39:11: 35000000 INFO @ Sat, 15 Sep 2018 11:39:11: 35000000 INFO @ Sat, 15 Sep 2018 11:39:16: 36000000 INFO @ Sat, 15 Sep 2018 11:39:17: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:39:17: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:39:17: #1 total tags in treatment: 36100474 INFO @ Sat, 15 Sep 2018 11:39:17: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:39:17: #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 11:39:17: 36000000 INFO @ Sat, 15 Sep 2018 11:39:18: 36000000 INFO @ Sat, 15 Sep 2018 11:39:18: #1 tags after filtering in treatment: 36100303 INFO @ Sat, 15 Sep 2018 11:39:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:39:18: #1 finished! INFO @ Sat, 15 Sep 2018 11:39:18: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:39:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:39:18: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:39:18: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:39:18: #1 total tags in treatment: 36100474 INFO @ Sat, 15 Sep 2018 11:39:18: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:39:18: #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 11:39:19: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:39:19: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:39:19: #1 total tags in treatment: 36100474 INFO @ Sat, 15 Sep 2018 11:39:19: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:39:19: #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 11:39:19: #1 tags after filtering in treatment: 36100303 INFO @ Sat, 15 Sep 2018 11:39:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:39:19: #1 finished! INFO @ Sat, 15 Sep 2018 11:39:19: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:39:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:39:19: #1 tags after filtering in treatment: 36100303 INFO @ Sat, 15 Sep 2018 11:39:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:39:19: #1 finished! INFO @ Sat, 15 Sep 2018 11:39:19: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:39:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:39:28: #2 number of paired peaks: 137002 INFO @ Sat, 15 Sep 2018 11:39:28: start model_add_line... INFO @ Sat, 15 Sep 2018 11:39:29: start X-correlation... INFO @ Sat, 15 Sep 2018 11:39:29: end of X-cor INFO @ Sat, 15 Sep 2018 11:39:29: #2 finished! INFO @ Sat, 15 Sep 2018 11:39:29: #2 predicted fragment length is 267 bps INFO @ Sat, 15 Sep 2018 11:39:29: #2 alternative fragment length(s) may be 4,267 bps INFO @ Sat, 15 Sep 2018 11:39:29: #2.2 Generate R script for model : SRX4014812.20_model.r INFO @ Sat, 15 Sep 2018 11:39:29: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:39:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:39:29: #2 number of paired peaks: 137002 INFO @ Sat, 15 Sep 2018 11:39:29: start model_add_line... INFO @ Sat, 15 Sep 2018 11:39:29: #2 number of paired peaks: 137002 INFO @ Sat, 15 Sep 2018 11:39:29: start model_add_line... INFO @ Sat, 15 Sep 2018 11:39:30: start X-correlation... INFO @ Sat, 15 Sep 2018 11:39:30: end of X-cor INFO @ Sat, 15 Sep 2018 11:39:30: #2 finished! INFO @ Sat, 15 Sep 2018 11:39:30: #2 predicted fragment length is 267 bps INFO @ Sat, 15 Sep 2018 11:39:30: #2 alternative fragment length(s) may be 4,267 bps INFO @ Sat, 15 Sep 2018 11:39:30: #2.2 Generate R script for model : SRX4014812.10_model.r INFO @ Sat, 15 Sep 2018 11:39:30: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:39:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:39:30: start X-correlation... INFO @ Sat, 15 Sep 2018 11:39:30: end of X-cor INFO @ Sat, 15 Sep 2018 11:39:30: #2 finished! INFO @ Sat, 15 Sep 2018 11:39:30: #2 predicted fragment length is 267 bps INFO @ Sat, 15 Sep 2018 11:39:30: #2 alternative fragment length(s) may be 4,267 bps INFO @ Sat, 15 Sep 2018 11:39:30: #2.2 Generate R script for model : SRX4014812.05_model.r INFO @ Sat, 15 Sep 2018 11:39:30: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:39:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:41:13: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:41:20: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:41:21: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:42:22: #4 Write output xls file... SRX4014812.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:42:22: #4 Write peak in narrowPeak format file... SRX4014812.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:42:22: #4 Write summits bed file... SRX4014812.20_summits.bed INFO @ Sat, 15 Sep 2018 11:42:22: Done! pass1 - making usageList (84 chroms): 3 millis pass2 - checking and writing primary data (12403 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:42:25: #4 Write output xls file... SRX4014812.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:42:25: #4 Write peak in narrowPeak format file... SRX4014812.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:42:25: #4 Write summits bed file... SRX4014812.10_summits.bed INFO @ Sat, 15 Sep 2018 11:42:25: Done! pass1 - making usageList (110 chroms): 4 millis pass2 - checking and writing primary data (20375 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:42:27: #4 Write output xls file... SRX4014812.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:42:28: #4 Write peak in narrowPeak format file... SRX4014812.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:42:28: #4 Write summits bed file... SRX4014812.05_summits.bed INFO @ Sat, 15 Sep 2018 11:42:28: Done! pass1 - making usageList (132 chroms): 6 millis pass2 - checking and writing primary data (30282 records, 4 fields): 40 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。