Job ID = 11632679 sra ファイルのダウンロード中... Completed: 836173K bytes transferred in 27 seconds (250041K 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 46814406 spots for /home/okishinya/chipatlas/results/rn6/SRX3360117/SRR6253223.sra Written 46814406 spots for /home/okishinya/chipatlas/results/rn6/SRX3360117/SRR6253223.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:20:42 46814406 reads; of these: 46814406 (100.00%) were unpaired; of these: 15879927 (33.92%) aligned 0 times 25136659 (53.69%) aligned exactly 1 time 5797820 (12.38%) aligned >1 times 66.08% overall alignment rate Time searching: 00:20:43 Overall time: 00:20:43 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] 7123400 / 30934479 = 0.2303 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 @ Fri, 15 Feb 2019 06:46:08: # Command line: callpeak -t SRX3360117.bam -f BAM -g 2.15e9 -n SRX3360117.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3360117.05 # format = BAM # ChIP-seq file = ['SRX3360117.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 @ Fri, 15 Feb 2019 06:46:08: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:46:08: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:46:08: # Command line: callpeak -t SRX3360117.bam -f BAM -g 2.15e9 -n SRX3360117.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3360117.20 # format = BAM # ChIP-seq file = ['SRX3360117.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 @ Fri, 15 Feb 2019 06:46:08: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:46:08: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:46:08: # Command line: callpeak -t SRX3360117.bam -f BAM -g 2.15e9 -n SRX3360117.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3360117.10 # format = BAM # ChIP-seq file = ['SRX3360117.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 @ Fri, 15 Feb 2019 06:46:08: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:46:08: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:46:15: 1000000 INFO @ Fri, 15 Feb 2019 06:46:16: 1000000 INFO @ Fri, 15 Feb 2019 06:46:16: 1000000 INFO @ Fri, 15 Feb 2019 06:46:23: 2000000 INFO @ Fri, 15 Feb 2019 06:46:23: 2000000 INFO @ Fri, 15 Feb 2019 06:46:23: 2000000 INFO @ Fri, 15 Feb 2019 06:46:30: 3000000 INFO @ Fri, 15 Feb 2019 06:46:30: 3000000 INFO @ Fri, 15 Feb 2019 06:46:30: 3000000 INFO @ Fri, 15 Feb 2019 06:46:37: 4000000 INFO @ Fri, 15 Feb 2019 06:46:37: 4000000 INFO @ Fri, 15 Feb 2019 06:46:38: 4000000 INFO @ Fri, 15 Feb 2019 06:46:44: 5000000 INFO @ Fri, 15 Feb 2019 06:46:44: 5000000 INFO @ Fri, 15 Feb 2019 06:46:45: 5000000 INFO @ Fri, 15 Feb 2019 06:46:51: 6000000 INFO @ Fri, 15 Feb 2019 06:46:51: 6000000 INFO @ Fri, 15 Feb 2019 06:46:53: 6000000 INFO @ Fri, 15 Feb 2019 06:46:58: 7000000 INFO @ Fri, 15 Feb 2019 06:46:59: 7000000 INFO @ Fri, 15 Feb 2019 06:47:00: 7000000 INFO @ Fri, 15 Feb 2019 06:47:05: 8000000 INFO @ Fri, 15 Feb 2019 06:47:06: 8000000 INFO @ Fri, 15 Feb 2019 06:47:08: 8000000 INFO @ Fri, 15 Feb 2019 06:47:12: 9000000 INFO @ Fri, 15 Feb 2019 06:47:12: 9000000 INFO @ Fri, 15 Feb 2019 06:47:16: 9000000 INFO @ Fri, 15 Feb 2019 06:47:19: 10000000 INFO @ Fri, 15 Feb 2019 06:47:20: 10000000 INFO @ Fri, 15 Feb 2019 06:47:23: 10000000 INFO @ Fri, 15 Feb 2019 06:47:26: 11000000 INFO @ Fri, 15 Feb 2019 06:47:27: 11000000 INFO @ Fri, 15 Feb 2019 06:47:31: 11000000 INFO @ Fri, 15 Feb 2019 06:47:33: 12000000 INFO @ Fri, 15 Feb 2019 06:47:35: 12000000 INFO @ Fri, 15 Feb 2019 06:47:39: 12000000 INFO @ Fri, 15 Feb 2019 06:47:40: 13000000 INFO @ Fri, 15 Feb 2019 06:47:42: 13000000 INFO @ Fri, 15 Feb 2019 06:47:46: 14000000 INFO @ Fri, 15 Feb 2019 06:47:46: 13000000 INFO @ Fri, 15 Feb 2019 06:47:50: 14000000 INFO @ Fri, 15 Feb 2019 06:47:53: 15000000 INFO @ Fri, 15 Feb 2019 06:47:54: 14000000 INFO @ Fri, 15 Feb 2019 06:47:58: 15000000 INFO @ Fri, 15 Feb 2019 06:48:01: 16000000 INFO @ Fri, 15 Feb 2019 06:48:02: 15000000 INFO @ Fri, 15 Feb 2019 06:48:05: 16000000 INFO @ Fri, 15 Feb 2019 06:48:09: 17000000 INFO @ Fri, 15 Feb 2019 06:48:10: 16000000 INFO @ Fri, 15 Feb 2019 06:48:13: 17000000 INFO @ Fri, 15 Feb 2019 06:48:16: 18000000 INFO @ Fri, 15 Feb 2019 06:48:19: 17000000 INFO @ Fri, 15 Feb 2019 06:48:21: 18000000 INFO @ Fri, 15 Feb 2019 06:48:23: 19000000 INFO @ Fri, 15 Feb 2019 06:48:27: 18000000 INFO @ Fri, 15 Feb 2019 06:48:29: 19000000 INFO @ Fri, 15 Feb 2019 06:48:29: 20000000 INFO @ Fri, 15 Feb 2019 06:48:35: 19000000 INFO @ Fri, 15 Feb 2019 06:48:36: 21000000 INFO @ Fri, 15 Feb 2019 06:48:36: 20000000 INFO @ Fri, 15 Feb 2019 06:48:43: 20000000 INFO @ Fri, 15 Feb 2019 06:48:43: 22000000 INFO @ Fri, 15 Feb 2019 06:48:44: 21000000 INFO @ Fri, 15 Feb 2019 06:48:50: 23000000 INFO @ Fri, 15 Feb 2019 06:48:50: 21000000 INFO @ Fri, 15 Feb 2019 06:48:51: 22000000 INFO @ Fri, 15 Feb 2019 06:48:55: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 06:48:55: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 06:48:55: #1 total tags in treatment: 23811079 INFO @ Fri, 15 Feb 2019 06:48:55: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:48:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:48:56: #1 tags after filtering in treatment: 23810923 INFO @ Fri, 15 Feb 2019 06:48:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:48:56: #1 finished! INFO @ Fri, 15 Feb 2019 06:48:56: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:48:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:48:58: 22000000 INFO @ Fri, 15 Feb 2019 06:48:59: 23000000 INFO @ Fri, 15 Feb 2019 06:49:01: #2 number of paired peaks: 48221 INFO @ Fri, 15 Feb 2019 06:49:01: start model_add_line... INFO @ Fri, 15 Feb 2019 06:49:01: start X-correlation... INFO @ Fri, 15 Feb 2019 06:49:01: end of X-cor INFO @ Fri, 15 Feb 2019 06:49:01: #2 finished! INFO @ Fri, 15 Feb 2019 06:49:01: #2 predicted fragment length is 162 bps INFO @ Fri, 15 Feb 2019 06:49:01: #2 alternative fragment length(s) may be 162 bps INFO @ Fri, 15 Feb 2019 06:49:01: #2.2 Generate R script for model : SRX3360117.20_model.r INFO @ Fri, 15 Feb 2019 06:49:02: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:49:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:49:05: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 06:49:05: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 06:49:05: #1 total tags in treatment: 23811079 INFO @ Fri, 15 Feb 2019 06:49:05: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:49:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:49:06: 23000000 INFO @ Fri, 15 Feb 2019 06:49:06: #1 tags after filtering in treatment: 23810923 INFO @ Fri, 15 Feb 2019 06:49:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:49:06: #1 finished! INFO @ Fri, 15 Feb 2019 06:49:06: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:49:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:49:10: #2 number of paired peaks: 48221 INFO @ Fri, 15 Feb 2019 06:49:10: start model_add_line... INFO @ Fri, 15 Feb 2019 06:49:11: start X-correlation... INFO @ Fri, 15 Feb 2019 06:49:11: end of X-cor INFO @ Fri, 15 Feb 2019 06:49:11: #2 finished! INFO @ Fri, 15 Feb 2019 06:49:11: #2 predicted fragment length is 162 bps INFO @ Fri, 15 Feb 2019 06:49:11: #2 alternative fragment length(s) may be 162 bps INFO @ Fri, 15 Feb 2019 06:49:11: #2.2 Generate R script for model : SRX3360117.10_model.r INFO @ Fri, 15 Feb 2019 06:49:11: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 06:49:11: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 06:49:11: #1 total tags in treatment: 23811079 INFO @ Fri, 15 Feb 2019 06:49:11: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:49:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:49:11: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:49:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:49:12: #1 tags after filtering in treatment: 23810923 INFO @ Fri, 15 Feb 2019 06:49:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:49:12: #1 finished! INFO @ Fri, 15 Feb 2019 06:49:12: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:49:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:49:17: #2 number of paired peaks: 48221 INFO @ Fri, 15 Feb 2019 06:49:17: start model_add_line... INFO @ Fri, 15 Feb 2019 06:49:17: start X-correlation... INFO @ Fri, 15 Feb 2019 06:49:17: end of X-cor INFO @ Fri, 15 Feb 2019 06:49:17: #2 finished! INFO @ Fri, 15 Feb 2019 06:49:17: #2 predicted fragment length is 162 bps INFO @ Fri, 15 Feb 2019 06:49:17: #2 alternative fragment length(s) may be 162 bps INFO @ Fri, 15 Feb 2019 06:49:17: #2.2 Generate R script for model : SRX3360117.05_model.r INFO @ Fri, 15 Feb 2019 06:49:17: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:49:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:50:06: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:50:07: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:50:20: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:50:42: #4 Write output xls file... SRX3360117.20_peaks.xls INFO @ Fri, 15 Feb 2019 06:50:42: #4 Write peak in narrowPeak format file... SRX3360117.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:50:42: #4 Write summits bed file... SRX3360117.20_summits.bed INFO @ Fri, 15 Feb 2019 06:50:42: Done! pass1 - making usageList (105 chroms): 5 millis pass2 - checking and writing primary data (21036 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:50:44: #4 Write output xls file... SRX3360117.10_peaks.xls INFO @ Fri, 15 Feb 2019 06:50:45: #4 Write peak in narrowPeak format file... SRX3360117.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:50:45: #4 Write summits bed file... SRX3360117.10_summits.bed INFO @ Fri, 15 Feb 2019 06:50:45: Done! pass1 - making usageList (122 chroms): 6 millis pass2 - checking and writing primary data (27142 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:50:57: #4 Write output xls file... SRX3360117.05_peaks.xls INFO @ Fri, 15 Feb 2019 06:50:57: #4 Write peak in narrowPeak format file... SRX3360117.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:50:58: #4 Write summits bed file... SRX3360117.05_summits.bed INFO @ Fri, 15 Feb 2019 06:50:58: Done! pass1 - making usageList (141 chroms): 7 millis pass2 - checking and writing primary data (32811 records, 4 fields): 45 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。