Job ID = 11192584 sra ファイルのダウンロード中... Completed: 510336K bytes transferred in 8 seconds (501697K 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 41945573 spots for /home/okishinya/chipatlas/results/rn6/SRX4014804/SRR7085053.sra Written 41945573 spots for /home/okishinya/chipatlas/results/rn6/SRX4014804/SRR7085053.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: 00:00:02 Multiseed full-index search: 00:36:31 41945573 reads; of these: 41945573 (100.00%) were unpaired; of these: 1340630 (3.20%) aligned 0 times 35693276 (85.09%) aligned exactly 1 time 4911667 (11.71%) aligned >1 times 96.80% overall alignment rate Time searching: 00:36:36 Overall time: 00:36:36 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 20 files... [bam_rmdupse_core] 8613046 / 40604943 = 0.2121 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 11:39:08: # Command line: callpeak -t SRX4014804.bam -f BAM -g 2.15e9 -n SRX4014804.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4014804.20 # format = BAM # ChIP-seq file = ['SRX4014804.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 11:39:08: # Command line: callpeak -t SRX4014804.bam -f BAM -g 2.15e9 -n SRX4014804.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4014804.10 # format = BAM # ChIP-seq file = ['SRX4014804.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 11:39:08: # Command line: callpeak -t SRX4014804.bam -f BAM -g 2.15e9 -n SRX4014804.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4014804.05 # format = BAM # ChIP-seq file = ['SRX4014804.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 11:39:08: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:39:08: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:39:08: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:39:08: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:39:08: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:39:08: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:39:17: 1000000 INFO @ Sat, 15 Sep 2018 11:39:17: 1000000 INFO @ Sat, 15 Sep 2018 11:39:17: 1000000 INFO @ Sat, 15 Sep 2018 11:39:26: 2000000 INFO @ Sat, 15 Sep 2018 11:39:26: 2000000 INFO @ Sat, 15 Sep 2018 11:39:26: 2000000 INFO @ Sat, 15 Sep 2018 11:39:35: 3000000 INFO @ Sat, 15 Sep 2018 11:39:35: 3000000 INFO @ Sat, 15 Sep 2018 11:39:35: 3000000 INFO @ Sat, 15 Sep 2018 11:39:44: 4000000 INFO @ Sat, 15 Sep 2018 11:39:44: 4000000 INFO @ Sat, 15 Sep 2018 11:39:45: 4000000 INFO @ Sat, 15 Sep 2018 11:39:52: 5000000 INFO @ Sat, 15 Sep 2018 11:39:52: 5000000 INFO @ Sat, 15 Sep 2018 11:39:54: 5000000 INFO @ Sat, 15 Sep 2018 11:40:01: 6000000 INFO @ Sat, 15 Sep 2018 11:40:01: 6000000 INFO @ Sat, 15 Sep 2018 11:40:03: 6000000 INFO @ Sat, 15 Sep 2018 11:40:11: 7000000 INFO @ Sat, 15 Sep 2018 11:40:11: 7000000 INFO @ Sat, 15 Sep 2018 11:40:12: 7000000 INFO @ Sat, 15 Sep 2018 11:40:20: 8000000 INFO @ Sat, 15 Sep 2018 11:40:20: 8000000 INFO @ Sat, 15 Sep 2018 11:40:20: 8000000 INFO @ Sat, 15 Sep 2018 11:40:29: 9000000 INFO @ Sat, 15 Sep 2018 11:40:29: 9000000 INFO @ Sat, 15 Sep 2018 11:40:30: 9000000 INFO @ Sat, 15 Sep 2018 11:40:38: 10000000 INFO @ Sat, 15 Sep 2018 11:40:38: 10000000 INFO @ Sat, 15 Sep 2018 11:40:39: 10000000 INFO @ Sat, 15 Sep 2018 11:40:47: 11000000 INFO @ Sat, 15 Sep 2018 11:40:47: 11000000 INFO @ Sat, 15 Sep 2018 11:40:48: 11000000 INFO @ Sat, 15 Sep 2018 11:40:56: 12000000 INFO @ Sat, 15 Sep 2018 11:40:56: 12000000 INFO @ Sat, 15 Sep 2018 11:40:56: 12000000 INFO @ Sat, 15 Sep 2018 11:41:05: 13000000 INFO @ Sat, 15 Sep 2018 11:41:05: 13000000 INFO @ Sat, 15 Sep 2018 11:41:05: 13000000 INFO @ Sat, 15 Sep 2018 11:41:14: 14000000 INFO @ Sat, 15 Sep 2018 11:41:14: 14000000 INFO @ Sat, 15 Sep 2018 11:41:15: 14000000 INFO @ Sat, 15 Sep 2018 11:41:23: 15000000 INFO @ Sat, 15 Sep 2018 11:41:23: 15000000 INFO @ Sat, 15 Sep 2018 11:41:23: 15000000 INFO @ Sat, 15 Sep 2018 11:41:32: 16000000 INFO @ Sat, 15 Sep 2018 11:41:32: 16000000 INFO @ Sat, 15 Sep 2018 11:41:32: 16000000 INFO @ Sat, 15 Sep 2018 11:41:41: 17000000 INFO @ Sat, 15 Sep 2018 11:41:41: 17000000 INFO @ Sat, 15 Sep 2018 11:41:41: 17000000 INFO @ Sat, 15 Sep 2018 11:41:50: 18000000 INFO @ Sat, 15 Sep 2018 11:41:50: 18000000 INFO @ Sat, 15 Sep 2018 11:41:51: 18000000 INFO @ Sat, 15 Sep 2018 11:41:59: 19000000 INFO @ Sat, 15 Sep 2018 11:41:59: 19000000 INFO @ Sat, 15 Sep 2018 11:42:00: 19000000 INFO @ Sat, 15 Sep 2018 11:42:07: 20000000 INFO @ Sat, 15 Sep 2018 11:42:07: 20000000 INFO @ Sat, 15 Sep 2018 11:42:10: 20000000 INFO @ Sat, 15 Sep 2018 11:42:17: 21000000 INFO @ Sat, 15 Sep 2018 11:42:17: 21000000 INFO @ Sat, 15 Sep 2018 11:42:18: 21000000 INFO @ Sat, 15 Sep 2018 11:42:26: 22000000 INFO @ Sat, 15 Sep 2018 11:42:26: 22000000 INFO @ Sat, 15 Sep 2018 11:42:27: 22000000 INFO @ Sat, 15 Sep 2018 11:42:35: 23000000 INFO @ Sat, 15 Sep 2018 11:42:35: 23000000 INFO @ Sat, 15 Sep 2018 11:42:36: 23000000 INFO @ Sat, 15 Sep 2018 11:42:44: 24000000 INFO @ Sat, 15 Sep 2018 11:42:44: 24000000 INFO @ Sat, 15 Sep 2018 11:42:45: 24000000 INFO @ Sat, 15 Sep 2018 11:42:54: 25000000 INFO @ Sat, 15 Sep 2018 11:42:54: 25000000 INFO @ Sat, 15 Sep 2018 11:42:54: 25000000 INFO @ Sat, 15 Sep 2018 11:43:03: 26000000 INFO @ Sat, 15 Sep 2018 11:43:03: 26000000 INFO @ Sat, 15 Sep 2018 11:43:03: 26000000 INFO @ Sat, 15 Sep 2018 11:43:11: 27000000 INFO @ Sat, 15 Sep 2018 11:43:11: 27000000 INFO @ Sat, 15 Sep 2018 11:43:13: 27000000 INFO @ Sat, 15 Sep 2018 11:43:20: 28000000 INFO @ Sat, 15 Sep 2018 11:43:20: 28000000 INFO @ Sat, 15 Sep 2018 11:43:22: 28000000 INFO @ Sat, 15 Sep 2018 11:43:30: 29000000 INFO @ Sat, 15 Sep 2018 11:43:30: 29000000 INFO @ Sat, 15 Sep 2018 11:43:31: 29000000 INFO @ Sat, 15 Sep 2018 11:43:39: 30000000 INFO @ Sat, 15 Sep 2018 11:43:39: 30000000 INFO @ Sat, 15 Sep 2018 11:43:40: 30000000 INFO @ Sat, 15 Sep 2018 11:43:48: 31000000 INFO @ Sat, 15 Sep 2018 11:43:48: 31000000 INFO @ Sat, 15 Sep 2018 11:43:48: 31000000 INFO @ Sat, 15 Sep 2018 11:43:58: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:43:58: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:43:58: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:43:58: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:43:58: #1 total tags in treatment: 31991897 INFO @ Sat, 15 Sep 2018 11:43:58: #1 total tags in treatment: 31991897 INFO @ Sat, 15 Sep 2018 11:43:58: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:43:58: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:43:58: #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 11:43:58: #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 11:43:58: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:43:58: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:43:58: #1 total tags in treatment: 31991897 INFO @ Sat, 15 Sep 2018 11:43:58: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:43:58: #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 11:43:58: #1 tags after filtering in treatment: 31991693 INFO @ Sat, 15 Sep 2018 11:43:58: #1 tags after filtering in treatment: 31991693 INFO @ Sat, 15 Sep 2018 11:43:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:43:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:43:58: #1 finished! INFO @ Sat, 15 Sep 2018 11:43:58: #1 finished! INFO @ Sat, 15 Sep 2018 11:43:58: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:43:58: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:43:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:43:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:43:59: #1 tags after filtering in treatment: 31991693 INFO @ Sat, 15 Sep 2018 11:43:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:43:59: #1 finished! INFO @ Sat, 15 Sep 2018 11:43:59: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:43:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:44:07: #2 number of paired peaks: 132425 INFO @ Sat, 15 Sep 2018 11:44:07: start model_add_line... INFO @ Sat, 15 Sep 2018 11:44:07: #2 number of paired peaks: 132425 INFO @ Sat, 15 Sep 2018 11:44:07: start model_add_line... INFO @ Sat, 15 Sep 2018 11:44:07: #2 number of paired peaks: 132425 INFO @ Sat, 15 Sep 2018 11:44:07: start model_add_line... INFO @ Sat, 15 Sep 2018 11:44:08: start X-correlation... INFO @ Sat, 15 Sep 2018 11:44:08: end of X-cor INFO @ Sat, 15 Sep 2018 11:44:08: #2 finished! INFO @ Sat, 15 Sep 2018 11:44:08: #2 predicted fragment length is 251 bps INFO @ Sat, 15 Sep 2018 11:44:08: #2 alternative fragment length(s) may be 251 bps INFO @ Sat, 15 Sep 2018 11:44:08: #2.2 Generate R script for model : SRX4014804.10_model.r INFO @ Sat, 15 Sep 2018 11:44:08: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:44:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:44:08: start X-correlation... INFO @ Sat, 15 Sep 2018 11:44:08: end of X-cor INFO @ Sat, 15 Sep 2018 11:44:08: #2 finished! INFO @ Sat, 15 Sep 2018 11:44:08: #2 predicted fragment length is 251 bps INFO @ Sat, 15 Sep 2018 11:44:08: #2 alternative fragment length(s) may be 251 bps INFO @ Sat, 15 Sep 2018 11:44:08: #2.2 Generate R script for model : SRX4014804.05_model.r INFO @ Sat, 15 Sep 2018 11:44:08: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:44:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:44:08: start X-correlation... INFO @ Sat, 15 Sep 2018 11:44:08: end of X-cor INFO @ Sat, 15 Sep 2018 11:44:08: #2 finished! INFO @ Sat, 15 Sep 2018 11:44:08: #2 predicted fragment length is 251 bps INFO @ Sat, 15 Sep 2018 11:44:08: #2 alternative fragment length(s) may be 251 bps INFO @ Sat, 15 Sep 2018 11:44:08: #2.2 Generate R script for model : SRX4014804.20_model.r INFO @ Sat, 15 Sep 2018 11:44:08: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:44:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:45:42: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:45:46: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:45:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:46:44: #4 Write output xls file... SRX4014804.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:46:45: #4 Write peak in narrowPeak format file... SRX4014804.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:46:45: #4 Write summits bed file... SRX4014804.20_summits.bed INFO @ Sat, 15 Sep 2018 11:46:45: Done! pass1 - making usageList (72 chroms): 3 millis pass2 - checking and writing primary data (9966 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:46:50: #4 Write output xls file... SRX4014804.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:46:50: #4 Write peak in narrowPeak format file... SRX4014804.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:46:50: #4 Write summits bed file... SRX4014804.10_summits.bed INFO @ Sat, 15 Sep 2018 11:46:50: Done! pass1 - making usageList (102 chroms): 3 millis pass2 - checking and writing primary data (17331 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:46:58: #4 Write output xls file... SRX4014804.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:46:59: #4 Write peak in narrowPeak format file... SRX4014804.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:46:59: #4 Write summits bed file... SRX4014804.05_summits.bed INFO @ Sat, 15 Sep 2018 11:46:59: Done! pass1 - making usageList (127 chroms): 6 millis pass2 - checking and writing primary data (26451 records, 4 fields): 36 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。