Job ID = 10194746 sra ファイルのダウンロード中... Completed: 898121K bytes transferred in 10 seconds (684384K 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 29376258 spots for /home/okishinya/chipatlas/results/rn6/SRX1074890/SRR2080217.sra Written 29376258 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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:21:20 29376258 reads; of these: 29376258 (100.00%) were unpaired; of these: 17365134 (59.11%) aligned 0 times 8563262 (29.15%) aligned exactly 1 time 3447862 (11.74%) aligned >1 times 40.89% overall alignment rate Time searching: 00:21:22 Overall time: 00:21:22 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 8 files... [bam_rmdupse_core] 1437904 / 12011124 = 0.1197 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, 10 Nov 2017 23:57:29: # Command line: callpeak -t SRX1074890.bam -f BAM -g 2.15e9 -n SRX1074890.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1074890.20 # format = BAM # ChIP-seq file = ['SRX1074890.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, 10 Nov 2017 23:57:29: # Command line: callpeak -t SRX1074890.bam -f BAM -g 2.15e9 -n SRX1074890.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1074890.05 # format = BAM # ChIP-seq file = ['SRX1074890.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, 10 Nov 2017 23:57:29: # Command line: callpeak -t SRX1074890.bam -f BAM -g 2.15e9 -n SRX1074890.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1074890.10 # format = BAM # ChIP-seq file = ['SRX1074890.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, 10 Nov 2017 23:57:29: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:57:29: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:57:29: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:57:29: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:57:29: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:57:29: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:57:37: 1000000 INFO @ Fri, 10 Nov 2017 23:57:37: 1000000 INFO @ Fri, 10 Nov 2017 23:57:40: 1000000 INFO @ Fri, 10 Nov 2017 23:57:45: 2000000 INFO @ Fri, 10 Nov 2017 23:57:45: 2000000 INFO @ Fri, 10 Nov 2017 23:57:49: 2000000 INFO @ Fri, 10 Nov 2017 23:57:53: 3000000 INFO @ Fri, 10 Nov 2017 23:57:55: 3000000 INFO @ Fri, 10 Nov 2017 23:57:57: 3000000 INFO @ Fri, 10 Nov 2017 23:58:03: 4000000 INFO @ Fri, 10 Nov 2017 23:58:06: 4000000 INFO @ Fri, 10 Nov 2017 23:58:07: 4000000 INFO @ Fri, 10 Nov 2017 23:58:12: 5000000 INFO @ Fri, 10 Nov 2017 23:58:16: 5000000 INFO @ Fri, 10 Nov 2017 23:58:17: 5000000 INFO @ Fri, 10 Nov 2017 23:58:21: 6000000 INFO @ Fri, 10 Nov 2017 23:58:27: 6000000 INFO @ Fri, 10 Nov 2017 23:58:28: 6000000 INFO @ Fri, 10 Nov 2017 23:58:31: 7000000 INFO @ Fri, 10 Nov 2017 23:58:36: 7000000 INFO @ Fri, 10 Nov 2017 23:58:38: 7000000 INFO @ Fri, 10 Nov 2017 23:58:39: 8000000 INFO @ Fri, 10 Nov 2017 23:58:46: 8000000 INFO @ Fri, 10 Nov 2017 23:58:47: 8000000 INFO @ Fri, 10 Nov 2017 23:58:48: 9000000 INFO @ Fri, 10 Nov 2017 23:58:55: 9000000 INFO @ Fri, 10 Nov 2017 23:58:56: 10000000 INFO @ Fri, 10 Nov 2017 23:58:58: 9000000 INFO @ Fri, 10 Nov 2017 23:59:02: #1 tag size is determined as 52 bps INFO @ Fri, 10 Nov 2017 23:59:02: #1 tag size = 52 INFO @ Fri, 10 Nov 2017 23:59:02: #1 total tags in treatment: 10573220 INFO @ Fri, 10 Nov 2017 23:59:02: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:59:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:59:02: #1 tags after filtering in treatment: 10573007 INFO @ Fri, 10 Nov 2017 23:59:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:59:02: #1 finished! INFO @ Fri, 10 Nov 2017 23:59:02: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:59:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:59:03: 10000000 INFO @ Fri, 10 Nov 2017 23:59:05: #2 number of paired peaks: 28899 INFO @ Fri, 10 Nov 2017 23:59:05: start model_add_line... INFO @ Fri, 10 Nov 2017 23:59:05: start X-correlation... INFO @ Fri, 10 Nov 2017 23:59:05: end of X-cor INFO @ Fri, 10 Nov 2017 23:59:05: #2 finished! INFO @ Fri, 10 Nov 2017 23:59:05: #2 predicted fragment length is 193 bps INFO @ Fri, 10 Nov 2017 23:59:05: #2 alternative fragment length(s) may be 193 bps INFO @ Fri, 10 Nov 2017 23:59:05: #2.2 Generate R script for model : SRX1074890.05_model.r INFO @ Fri, 10 Nov 2017 23:59:05: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:59:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:59:08: 10000000 INFO @ Fri, 10 Nov 2017 23:59:08: #1 tag size is determined as 52 bps INFO @ Fri, 10 Nov 2017 23:59:08: #1 tag size = 52 INFO @ Fri, 10 Nov 2017 23:59:08: #1 total tags in treatment: 10573220 INFO @ Fri, 10 Nov 2017 23:59:08: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:59:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:59:08: #1 tags after filtering in treatment: 10573007 INFO @ Fri, 10 Nov 2017 23:59:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:59:08: #1 finished! INFO @ Fri, 10 Nov 2017 23:59:08: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:59:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:59:10: #2 number of paired peaks: 28899 INFO @ Fri, 10 Nov 2017 23:59:10: start model_add_line... INFO @ Fri, 10 Nov 2017 23:59:10: start X-correlation... INFO @ Fri, 10 Nov 2017 23:59:10: end of X-cor INFO @ Fri, 10 Nov 2017 23:59:10: #2 finished! INFO @ Fri, 10 Nov 2017 23:59:10: #2 predicted fragment length is 193 bps INFO @ Fri, 10 Nov 2017 23:59:10: #2 alternative fragment length(s) may be 193 bps INFO @ Fri, 10 Nov 2017 23:59:10: #2.2 Generate R script for model : SRX1074890.10_model.r INFO @ Fri, 10 Nov 2017 23:59:10: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:59:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:59:13: #1 tag size is determined as 52 bps INFO @ Fri, 10 Nov 2017 23:59:13: #1 tag size = 52 INFO @ Fri, 10 Nov 2017 23:59:13: #1 total tags in treatment: 10573220 INFO @ Fri, 10 Nov 2017 23:59:13: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:59:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:59:14: #1 tags after filtering in treatment: 10573007 INFO @ Fri, 10 Nov 2017 23:59:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:59:14: #1 finished! INFO @ Fri, 10 Nov 2017 23:59:14: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:59:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:59:17: #2 number of paired peaks: 28899 INFO @ Fri, 10 Nov 2017 23:59:17: start model_add_line... INFO @ Fri, 10 Nov 2017 23:59:17: start X-correlation... INFO @ Fri, 10 Nov 2017 23:59:17: end of X-cor INFO @ Fri, 10 Nov 2017 23:59:17: #2 finished! INFO @ Fri, 10 Nov 2017 23:59:17: #2 predicted fragment length is 193 bps INFO @ Fri, 10 Nov 2017 23:59:17: #2 alternative fragment length(s) may be 193 bps INFO @ Fri, 10 Nov 2017 23:59:17: #2.2 Generate R script for model : SRX1074890.20_model.r INFO @ Fri, 10 Nov 2017 23:59:17: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:59:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:59:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:59:38: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:59:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:59:53: #4 Write output xls file... SRX1074890.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:59:53: #4 Write output xls file... SRX1074890.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:59:53: #4 Write peak in narrowPeak format file... SRX1074890.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:59:53: #4 Write summits bed file... SRX1074890.10_summits.bed INFO @ Fri, 10 Nov 2017 23:59:53: Done! INFO @ Fri, 10 Nov 2017 23:59:53: #4 Write peak in narrowPeak format file... SRX1074890.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:59:53: #4 Write summits bed file... SRX1074890.05_summits.bed INFO @ Fri, 10 Nov 2017 23:59:53: Done! pass1 - making usageList (50 chroms): 1 millis pass2 - checking and writing primary data (4086 records, 4 fields): 9 millis CompletedMACS2peakCalling pass1 - making usageList (60 chroms): 6 millis pass2 - checking and writing primary data (9282 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:00:05: #4 Write output xls file... SRX1074890.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:00:06: #4 Write peak in narrowPeak format file... SRX1074890.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:00:06: #4 Write summits bed file... SRX1074890.20_summits.bed INFO @ Sat, 11 Nov 2017 00:00:06: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (1243 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。