Job ID = 10194832 sra ファイルのダウンロード中... Completed: 1051947K bytes transferred in 21 seconds (399188K 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... Written 51426492 spots for /home/okishinya/chipatlas/results/rn6/SRX1977122/SRR3952254.sra Written 51426492 spots total 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: 01:29:17 51426492 reads; of these: 51426492 (100.00%) were unpaired; of these: 15169702 (29.50%) aligned 0 times 20448247 (39.76%) aligned exactly 1 time 15808543 (30.74%) aligned >1 times 70.50% overall alignment rate Time searching: 01:29:21 Overall time: 01:29:21 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] 3881252 / 36256790 = 0.1070 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, 11 Nov 2017 02:41:32: # Command line: callpeak -t SRX1977122.bam -f BAM -g 2.15e9 -n SRX1977122.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977122.20 # format = BAM # ChIP-seq file = ['SRX1977122.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, 11 Nov 2017 02:41:32: # Command line: callpeak -t SRX1977122.bam -f BAM -g 2.15e9 -n SRX1977122.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977122.10 # format = BAM # ChIP-seq file = ['SRX1977122.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, 11 Nov 2017 02:41:32: # Command line: callpeak -t SRX1977122.bam -f BAM -g 2.15e9 -n SRX1977122.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977122.05 # format = BAM # ChIP-seq file = ['SRX1977122.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, 11 Nov 2017 02:41:32: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:41:32: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:41:32: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:41:32: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:41:32: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:41:32: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:41:40: 1000000 INFO @ Sat, 11 Nov 2017 02:41:40: 1000000 INFO @ Sat, 11 Nov 2017 02:41:41: 1000000 INFO @ Sat, 11 Nov 2017 02:41:48: 2000000 INFO @ Sat, 11 Nov 2017 02:41:48: 2000000 INFO @ Sat, 11 Nov 2017 02:41:50: 2000000 INFO @ Sat, 11 Nov 2017 02:41:56: 3000000 INFO @ Sat, 11 Nov 2017 02:41:57: 3000000 INFO @ Sat, 11 Nov 2017 02:41:59: 3000000 INFO @ Sat, 11 Nov 2017 02:42:03: 4000000 INFO @ Sat, 11 Nov 2017 02:42:05: 4000000 INFO @ Sat, 11 Nov 2017 02:42:08: 4000000 INFO @ Sat, 11 Nov 2017 02:42:11: 5000000 INFO @ Sat, 11 Nov 2017 02:42:13: 5000000 INFO @ Sat, 11 Nov 2017 02:42:17: 5000000 INFO @ Sat, 11 Nov 2017 02:42:19: 6000000 INFO @ Sat, 11 Nov 2017 02:42:21: 6000000 INFO @ Sat, 11 Nov 2017 02:42:26: 6000000 INFO @ Sat, 11 Nov 2017 02:42:27: 7000000 INFO @ Sat, 11 Nov 2017 02:42:29: 7000000 INFO @ Sat, 11 Nov 2017 02:42:35: 8000000 INFO @ Sat, 11 Nov 2017 02:42:35: 7000000 INFO @ Sat, 11 Nov 2017 02:42:38: 8000000 INFO @ Sat, 11 Nov 2017 02:42:43: 8000000 INFO @ Sat, 11 Nov 2017 02:42:43: 9000000 INFO @ Sat, 11 Nov 2017 02:42:47: 9000000 INFO @ Sat, 11 Nov 2017 02:42:51: 9000000 INFO @ Sat, 11 Nov 2017 02:42:51: 10000000 INFO @ Sat, 11 Nov 2017 02:42:56: 10000000 INFO @ Sat, 11 Nov 2017 02:42:59: 10000000 INFO @ Sat, 11 Nov 2017 02:43:00: 11000000 INFO @ Sat, 11 Nov 2017 02:43:05: 11000000 INFO @ Sat, 11 Nov 2017 02:43:07: 11000000 INFO @ Sat, 11 Nov 2017 02:43:08: 12000000 INFO @ Sat, 11 Nov 2017 02:43:13: 12000000 INFO @ Sat, 11 Nov 2017 02:43:15: 12000000 INFO @ Sat, 11 Nov 2017 02:43:16: 13000000 INFO @ Sat, 11 Nov 2017 02:43:22: 13000000 INFO @ Sat, 11 Nov 2017 02:43:23: 13000000 INFO @ Sat, 11 Nov 2017 02:43:25: 14000000 INFO @ Sat, 11 Nov 2017 02:43:31: 14000000 INFO @ Sat, 11 Nov 2017 02:43:31: 14000000 INFO @ Sat, 11 Nov 2017 02:43:33: 15000000 INFO @ Sat, 11 Nov 2017 02:43:39: 15000000 INFO @ Sat, 11 Nov 2017 02:43:39: 15000000 INFO @ Sat, 11 Nov 2017 02:43:41: 16000000 INFO @ Sat, 11 Nov 2017 02:43:47: 16000000 INFO @ Sat, 11 Nov 2017 02:43:48: 16000000 INFO @ Sat, 11 Nov 2017 02:43:50: 17000000 INFO @ Sat, 11 Nov 2017 02:43:55: 17000000 INFO @ Sat, 11 Nov 2017 02:43:57: 17000000 INFO @ Sat, 11 Nov 2017 02:43:58: 18000000 INFO @ Sat, 11 Nov 2017 02:44:03: 18000000 INFO @ Sat, 11 Nov 2017 02:44:06: 18000000 INFO @ Sat, 11 Nov 2017 02:44:06: 19000000 INFO @ Sat, 11 Nov 2017 02:44:11: 19000000 INFO @ Sat, 11 Nov 2017 02:44:14: 19000000 INFO @ Sat, 11 Nov 2017 02:44:15: 20000000 INFO @ Sat, 11 Nov 2017 02:44:19: 20000000 INFO @ Sat, 11 Nov 2017 02:44:23: 21000000 INFO @ Sat, 11 Nov 2017 02:44:23: 20000000 INFO @ Sat, 11 Nov 2017 02:44:27: 21000000 INFO @ Sat, 11 Nov 2017 02:44:31: 22000000 INFO @ Sat, 11 Nov 2017 02:44:32: 21000000 INFO @ Sat, 11 Nov 2017 02:44:35: 22000000 INFO @ Sat, 11 Nov 2017 02:44:40: 23000000 INFO @ Sat, 11 Nov 2017 02:44:41: 22000000 INFO @ Sat, 11 Nov 2017 02:44:43: 23000000 INFO @ Sat, 11 Nov 2017 02:44:48: 24000000 INFO @ Sat, 11 Nov 2017 02:44:50: 23000000 INFO @ Sat, 11 Nov 2017 02:44:51: 24000000 INFO @ Sat, 11 Nov 2017 02:44:57: 25000000 INFO @ Sat, 11 Nov 2017 02:44:59: 24000000 INFO @ Sat, 11 Nov 2017 02:44:59: 25000000 INFO @ Sat, 11 Nov 2017 02:45:05: 26000000 INFO @ Sat, 11 Nov 2017 02:45:07: 26000000 INFO @ Sat, 11 Nov 2017 02:45:08: 25000000 INFO @ Sat, 11 Nov 2017 02:45:14: 27000000 INFO @ Sat, 11 Nov 2017 02:45:15: 27000000 INFO @ Sat, 11 Nov 2017 02:45:16: 26000000 INFO @ Sat, 11 Nov 2017 02:45:22: 28000000 INFO @ Sat, 11 Nov 2017 02:45:23: 28000000 INFO @ Sat, 11 Nov 2017 02:45:25: 27000000 INFO @ Sat, 11 Nov 2017 02:45:31: 29000000 INFO @ Sat, 11 Nov 2017 02:45:31: 29000000 INFO @ Sat, 11 Nov 2017 02:45:34: 28000000 INFO @ Sat, 11 Nov 2017 02:45:39: 30000000 INFO @ Sat, 11 Nov 2017 02:45:39: 30000000 INFO @ Sat, 11 Nov 2017 02:45:43: 29000000 INFO @ Sat, 11 Nov 2017 02:45:47: 31000000 INFO @ Sat, 11 Nov 2017 02:45:47: 31000000 INFO @ Sat, 11 Nov 2017 02:45:52: 30000000 INFO @ Sat, 11 Nov 2017 02:45:55: 32000000 INFO @ Sat, 11 Nov 2017 02:45:56: 32000000 INFO @ Sat, 11 Nov 2017 02:45:58: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:45:58: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:45:58: #1 total tags in treatment: 32375538 INFO @ Sat, 11 Nov 2017 02:45:58: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:45:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 02:45:59: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:45:59: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:45:59: #1 total tags in treatment: 32375538 INFO @ Sat, 11 Nov 2017 02:45:59: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:45:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 02:45:59: #1 tags after filtering in treatment: 32375451 INFO @ Sat, 11 Nov 2017 02:45:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:45:59: #1 finished! INFO @ Sat, 11 Nov 2017 02:45:59: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:45:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:46:00: #1 tags after filtering in treatment: 32375451 INFO @ Sat, 11 Nov 2017 02:46:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:46:00: #1 finished! INFO @ Sat, 11 Nov 2017 02:46:00: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:46:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:46:00: 31000000 INFO @ Sat, 11 Nov 2017 02:46:04: #2 number of paired peaks: 46256 INFO @ Sat, 11 Nov 2017 02:46:04: start model_add_line... INFO @ Sat, 11 Nov 2017 02:46:05: start X-correlation... INFO @ Sat, 11 Nov 2017 02:46:05: end of X-cor INFO @ Sat, 11 Nov 2017 02:46:05: #2 finished! INFO @ Sat, 11 Nov 2017 02:46:05: #2 predicted fragment length is 131 bps INFO @ Sat, 11 Nov 2017 02:46:05: #2 alternative fragment length(s) may be 131 bps INFO @ Sat, 11 Nov 2017 02:46:05: #2.2 Generate R script for model : SRX1977122.20_model.r INFO @ Sat, 11 Nov 2017 02:46:05: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:46:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:46:05: #2 number of paired peaks: 46256 INFO @ Sat, 11 Nov 2017 02:46:05: start model_add_line... INFO @ Sat, 11 Nov 2017 02:46:05: start X-correlation... INFO @ Sat, 11 Nov 2017 02:46:05: end of X-cor INFO @ Sat, 11 Nov 2017 02:46:05: #2 finished! INFO @ Sat, 11 Nov 2017 02:46:05: #2 predicted fragment length is 131 bps INFO @ Sat, 11 Nov 2017 02:46:05: #2 alternative fragment length(s) may be 131 bps INFO @ Sat, 11 Nov 2017 02:46:05: #2.2 Generate R script for model : SRX1977122.05_model.r INFO @ Sat, 11 Nov 2017 02:46:05: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:46:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:46:08: 32000000 INFO @ Sat, 11 Nov 2017 02:46:11: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:46:11: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:46:11: #1 total tags in treatment: 32375538 INFO @ Sat, 11 Nov 2017 02:46:11: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:46:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 02:46:12: #1 tags after filtering in treatment: 32375451 INFO @ Sat, 11 Nov 2017 02:46:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:46:12: #1 finished! INFO @ Sat, 11 Nov 2017 02:46:12: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:46:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:46:17: #2 number of paired peaks: 46256 INFO @ Sat, 11 Nov 2017 02:46:17: start model_add_line... INFO @ Sat, 11 Nov 2017 02:46:18: start X-correlation... INFO @ Sat, 11 Nov 2017 02:46:18: end of X-cor INFO @ Sat, 11 Nov 2017 02:46:18: #2 finished! INFO @ Sat, 11 Nov 2017 02:46:18: #2 predicted fragment length is 131 bps INFO @ Sat, 11 Nov 2017 02:46:18: #2 alternative fragment length(s) may be 131 bps INFO @ Sat, 11 Nov 2017 02:46:18: #2.2 Generate R script for model : SRX1977122.10_model.r INFO @ Sat, 11 Nov 2017 02:46:18: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:46:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:47:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:47:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:47:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:48:16: #4 Write output xls file... SRX1977122.05_peaks.xls INFO @ Sat, 11 Nov 2017 02:48:16: #4 Write peak in narrowPeak format file... SRX1977122.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:48:17: #4 Write summits bed file... SRX1977122.05_summits.bed INFO @ Sat, 11 Nov 2017 02:48:17: Done! pass1 - making usageList (226 chroms): 11 millis pass2 - checking and writing primary data (60250 records, 4 fields): 75 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 02:48:21: #4 Write output xls file... SRX1977122.20_peaks.xls INFO @ Sat, 11 Nov 2017 02:48:21: #4 Write peak in narrowPeak format file... SRX1977122.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:48:21: #4 Write summits bed file... SRX1977122.20_summits.bed INFO @ Sat, 11 Nov 2017 02:48:21: Done! pass1 - making usageList (81 chroms): 1 millis pass2 - checking and writing primary data (3741 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 02:48:36: #4 Write output xls file... SRX1977122.10_peaks.xls INFO @ Sat, 11 Nov 2017 02:48:37: #4 Write peak in narrowPeak format file... SRX1977122.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:48:37: #4 Write summits bed file... SRX1977122.10_summits.bed INFO @ Sat, 11 Nov 2017 02:48:37: Done! pass1 - making usageList (138 chroms): 4 millis pass2 - checking and writing primary data (20580 records, 4 fields): 30 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。