Job ID = 11632729 sra ファイルのダウンロード中... Completed: 490249K bytes transferred in 8 seconds (485864K 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 25857434 spots for /home/okishinya/chipatlas/results/rn6/SRX4497199/SRR7633469.sra Written 25857434 spots for /home/okishinya/chipatlas/results/rn6/SRX4497199/SRR7633469.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: 00:19:32 25857434 reads; of these: 25857434 (100.00%) were unpaired; of these: 961180 (3.72%) aligned 0 times 18125984 (70.10%) aligned exactly 1 time 6770270 (26.18%) aligned >1 times 96.28% overall alignment rate Time searching: 00:19:36 Overall time: 00:19:36 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 12 files... [bam_rmdupse_core] 3335268 / 24896254 = 0.1340 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 07:39:35: # Command line: callpeak -t SRX4497199.bam -f BAM -g 2.15e9 -n SRX4497199.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4497199.10 # format = BAM # ChIP-seq file = ['SRX4497199.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 07:39:35: # Command line: callpeak -t SRX4497199.bam -f BAM -g 2.15e9 -n SRX4497199.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4497199.20 # format = BAM # ChIP-seq file = ['SRX4497199.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 07:39:35: # Command line: callpeak -t SRX4497199.bam -f BAM -g 2.15e9 -n SRX4497199.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4497199.05 # format = BAM # ChIP-seq file = ['SRX4497199.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 07:39:35: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:39:35: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:39:35: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:39:35: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:39:35: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:39:35: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:39:41: 1000000 INFO @ Fri, 15 Feb 2019 07:39:41: 1000000 INFO @ Fri, 15 Feb 2019 07:39:42: 1000000 INFO @ Fri, 15 Feb 2019 07:39:48: 2000000 INFO @ Fri, 15 Feb 2019 07:39:48: 2000000 INFO @ Fri, 15 Feb 2019 07:39:49: 2000000 INFO @ Fri, 15 Feb 2019 07:39:55: 3000000 INFO @ Fri, 15 Feb 2019 07:39:55: 3000000 INFO @ Fri, 15 Feb 2019 07:39:55: 3000000 INFO @ Fri, 15 Feb 2019 07:40:01: 4000000 INFO @ Fri, 15 Feb 2019 07:40:01: 4000000 INFO @ Fri, 15 Feb 2019 07:40:02: 4000000 INFO @ Fri, 15 Feb 2019 07:40:08: 5000000 INFO @ Fri, 15 Feb 2019 07:40:08: 5000000 INFO @ Fri, 15 Feb 2019 07:40:09: 5000000 INFO @ Fri, 15 Feb 2019 07:40:14: 6000000 INFO @ Fri, 15 Feb 2019 07:40:15: 6000000 INFO @ Fri, 15 Feb 2019 07:40:17: 6000000 INFO @ Fri, 15 Feb 2019 07:40:21: 7000000 INFO @ Fri, 15 Feb 2019 07:40:21: 7000000 INFO @ Fri, 15 Feb 2019 07:40:24: 7000000 INFO @ Fri, 15 Feb 2019 07:40:28: 8000000 INFO @ Fri, 15 Feb 2019 07:40:28: 8000000 INFO @ Fri, 15 Feb 2019 07:40:32: 8000000 INFO @ Fri, 15 Feb 2019 07:40:35: 9000000 INFO @ Fri, 15 Feb 2019 07:40:35: 9000000 INFO @ Fri, 15 Feb 2019 07:40:39: 9000000 INFO @ Fri, 15 Feb 2019 07:40:41: 10000000 INFO @ Fri, 15 Feb 2019 07:40:42: 10000000 INFO @ Fri, 15 Feb 2019 07:40:46: 10000000 INFO @ Fri, 15 Feb 2019 07:40:48: 11000000 INFO @ Fri, 15 Feb 2019 07:40:48: 11000000 INFO @ Fri, 15 Feb 2019 07:40:53: 11000000 INFO @ Fri, 15 Feb 2019 07:40:55: 12000000 INFO @ Fri, 15 Feb 2019 07:40:55: 12000000 INFO @ Fri, 15 Feb 2019 07:41:00: 12000000 INFO @ Fri, 15 Feb 2019 07:41:02: 13000000 INFO @ Fri, 15 Feb 2019 07:41:02: 13000000 INFO @ Fri, 15 Feb 2019 07:41:06: 13000000 INFO @ Fri, 15 Feb 2019 07:41:09: 14000000 INFO @ Fri, 15 Feb 2019 07:41:09: 14000000 INFO @ Fri, 15 Feb 2019 07:41:13: 14000000 INFO @ Fri, 15 Feb 2019 07:41:15: 15000000 INFO @ Fri, 15 Feb 2019 07:41:16: 15000000 INFO @ Fri, 15 Feb 2019 07:41:20: 15000000 INFO @ Fri, 15 Feb 2019 07:41:22: 16000000 INFO @ Fri, 15 Feb 2019 07:41:23: 16000000 INFO @ Fri, 15 Feb 2019 07:41:27: 16000000 INFO @ Fri, 15 Feb 2019 07:41:29: 17000000 INFO @ Fri, 15 Feb 2019 07:41:29: 17000000 INFO @ Fri, 15 Feb 2019 07:41:34: 17000000 INFO @ Fri, 15 Feb 2019 07:41:36: 18000000 INFO @ Fri, 15 Feb 2019 07:41:36: 18000000 INFO @ Fri, 15 Feb 2019 07:41:40: 18000000 INFO @ Fri, 15 Feb 2019 07:41:43: 19000000 INFO @ Fri, 15 Feb 2019 07:41:43: 19000000 INFO @ Fri, 15 Feb 2019 07:41:48: 19000000 INFO @ Fri, 15 Feb 2019 07:41:50: 20000000 INFO @ Fri, 15 Feb 2019 07:41:50: 20000000 INFO @ Fri, 15 Feb 2019 07:41:55: 20000000 INFO @ Fri, 15 Feb 2019 07:41:57: 21000000 INFO @ Fri, 15 Feb 2019 07:41:57: 21000000 INFO @ Fri, 15 Feb 2019 07:42:01: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:42:01: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:42:01: #1 total tags in treatment: 21560986 INFO @ Fri, 15 Feb 2019 07:42:01: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:42:01: #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 07:42:01: #1 tags after filtering in treatment: 21560835 INFO @ Fri, 15 Feb 2019 07:42:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:42:01: #1 finished! INFO @ Fri, 15 Feb 2019 07:42:01: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:42:02: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:42:02: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:42:02: #1 total tags in treatment: 21560986 INFO @ Fri, 15 Feb 2019 07:42:02: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:42:02: #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 07:42:02: #1 tags after filtering in treatment: 21560835 INFO @ Fri, 15 Feb 2019 07:42:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:42:02: #1 finished! INFO @ Fri, 15 Feb 2019 07:42:02: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:42:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:42:03: 21000000 INFO @ Fri, 15 Feb 2019 07:42:05: #2 number of paired peaks: 39577 INFO @ Fri, 15 Feb 2019 07:42:05: start model_add_line... INFO @ Fri, 15 Feb 2019 07:42:05: start X-correlation... INFO @ Fri, 15 Feb 2019 07:42:06: end of X-cor INFO @ Fri, 15 Feb 2019 07:42:06: #2 finished! INFO @ Fri, 15 Feb 2019 07:42:06: #2 predicted fragment length is 250 bps INFO @ Fri, 15 Feb 2019 07:42:06: #2 alternative fragment length(s) may be 250 bps INFO @ Fri, 15 Feb 2019 07:42:06: #2.2 Generate R script for model : SRX4497199.20_model.r INFO @ Fri, 15 Feb 2019 07:42:06: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:42:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:42:06: #2 number of paired peaks: 39577 INFO @ Fri, 15 Feb 2019 07:42:06: start model_add_line... INFO @ Fri, 15 Feb 2019 07:42:06: start X-correlation... INFO @ Fri, 15 Feb 2019 07:42:06: end of X-cor INFO @ Fri, 15 Feb 2019 07:42:06: #2 finished! INFO @ Fri, 15 Feb 2019 07:42:06: #2 predicted fragment length is 250 bps INFO @ Fri, 15 Feb 2019 07:42:06: #2 alternative fragment length(s) may be 250 bps INFO @ Fri, 15 Feb 2019 07:42:06: #2.2 Generate R script for model : SRX4497199.10_model.r INFO @ Fri, 15 Feb 2019 07:42:06: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:42:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:42:08: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:42:08: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:42:08: #1 total tags in treatment: 21560986 INFO @ Fri, 15 Feb 2019 07:42:08: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:42:08: #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 07:42:08: #1 tags after filtering in treatment: 21560835 INFO @ Fri, 15 Feb 2019 07:42:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:42:08: #1 finished! INFO @ Fri, 15 Feb 2019 07:42:08: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:42:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:42:12: #2 number of paired peaks: 39577 INFO @ Fri, 15 Feb 2019 07:42:12: start model_add_line... INFO @ Fri, 15 Feb 2019 07:42:13: start X-correlation... INFO @ Fri, 15 Feb 2019 07:42:13: end of X-cor INFO @ Fri, 15 Feb 2019 07:42:13: #2 finished! INFO @ Fri, 15 Feb 2019 07:42:13: #2 predicted fragment length is 250 bps INFO @ Fri, 15 Feb 2019 07:42:13: #2 alternative fragment length(s) may be 250 bps INFO @ Fri, 15 Feb 2019 07:42:13: #2.2 Generate R script for model : SRX4497199.05_model.r INFO @ Fri, 15 Feb 2019 07:42:13: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:42:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:43:00: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:43:02: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:43:06: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:43:29: #4 Write output xls file... SRX4497199.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:43:29: #4 Write peak in narrowPeak format file... SRX4497199.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:43:29: #4 Write summits bed file... SRX4497199.10_summits.bed INFO @ Fri, 15 Feb 2019 07:43:29: Done! pass1 - making usageList (38 chroms): 2 millis pass2 - checking and writing primary data (508 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:43:30: #4 Write output xls file... SRX4497199.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:43:30: #4 Write peak in narrowPeak format file... SRX4497199.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:43:30: #4 Write summits bed file... SRX4497199.20_summits.bed INFO @ Fri, 15 Feb 2019 07:43:30: Done! pass1 - making usageList (26 chroms): 3 millis pass2 - checking and writing primary data (229 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:43:38: #4 Write output xls file... SRX4497199.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:43:38: #4 Write peak in narrowPeak format file... SRX4497199.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:43:38: #4 Write summits bed file... SRX4497199.05_summits.bed INFO @ Fri, 15 Feb 2019 07:43:39: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (1009 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。