Job ID = 9158161 sra ファイルのダウンロード中... Completed: 388526K bytes transferred in 6 seconds (517382K bits/sec), in 1 file, 2 directories. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Written 9362306 spots for /home/okishinya/chipatlas/results/dm3/SRX1056718/SRR2060652.sra Written 9362306 spots total 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:26:36 9362306 reads; of these: 9362306 (100.00%) were paired; of these: 1132736 (12.10%) aligned concordantly 0 times 5225502 (55.81%) aligned concordantly exactly 1 time 3004068 (32.09%) aligned concordantly >1 times ---- 1132736 pairs aligned concordantly 0 times; of these: 147885 (13.06%) aligned discordantly 1 time ---- 984851 pairs aligned 0 times concordantly or discordantly; of these: 1969702 mates make up the pairs; of these: 1254540 (63.69%) aligned 0 times 408215 (20.72%) aligned exactly 1 time 306947 (15.58%) aligned >1 times 93.30% overall alignment rate Time searching: 00:26:36 Overall time: 00:26:36 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 354796 / 8366264 = 0.0424 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 @ Tue, 27 Jun 2017 16:02:35: # Command line: callpeak -t SRX1056718.bam -f BAM -g dm -n SRX1056718.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1056718.20 # format = BAM # ChIP-seq file = ['SRX1056718.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 27 Jun 2017 16:02:35: #1 read tag files... INFO @ Tue, 27 Jun 2017 16:02:35: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 16:02:35: # Command line: callpeak -t SRX1056718.bam -f BAM -g dm -n SRX1056718.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1056718.10 # format = BAM # ChIP-seq file = ['SRX1056718.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 27 Jun 2017 16:02:35: #1 read tag files... INFO @ Tue, 27 Jun 2017 16:02:35: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 16:02:35: # Command line: callpeak -t SRX1056718.bam -f BAM -g dm -n SRX1056718.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1056718.05 # format = BAM # ChIP-seq file = ['SRX1056718.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 27 Jun 2017 16:02:35: #1 read tag files... INFO @ Tue, 27 Jun 2017 16:02:35: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 16:02:41: 1000000 INFO @ Tue, 27 Jun 2017 16:02:41: 1000000 INFO @ Tue, 27 Jun 2017 16:02:41: 1000000 INFO @ Tue, 27 Jun 2017 16:02:47: 2000000 INFO @ Tue, 27 Jun 2017 16:02:47: 2000000 INFO @ Tue, 27 Jun 2017 16:02:47: 2000000 INFO @ Tue, 27 Jun 2017 16:02:52: 3000000 INFO @ Tue, 27 Jun 2017 16:02:52: 3000000 INFO @ Tue, 27 Jun 2017 16:02:52: 3000000 INFO @ Tue, 27 Jun 2017 16:02:58: 4000000 INFO @ Tue, 27 Jun 2017 16:02:58: 4000000 INFO @ Tue, 27 Jun 2017 16:02:58: 4000000 INFO @ Tue, 27 Jun 2017 16:03:04: 5000000 INFO @ Tue, 27 Jun 2017 16:03:04: 5000000 INFO @ Tue, 27 Jun 2017 16:03:04: 5000000 INFO @ Tue, 27 Jun 2017 16:03:10: 6000000 INFO @ Tue, 27 Jun 2017 16:03:10: 6000000 INFO @ Tue, 27 Jun 2017 16:03:10: 6000000 INFO @ Tue, 27 Jun 2017 16:03:15: 7000000 INFO @ Tue, 27 Jun 2017 16:03:15: 7000000 INFO @ Tue, 27 Jun 2017 16:03:15: 7000000 INFO @ Tue, 27 Jun 2017 16:03:21: 8000000 INFO @ Tue, 27 Jun 2017 16:03:21: 8000000 INFO @ Tue, 27 Jun 2017 16:03:21: 8000000 INFO @ Tue, 27 Jun 2017 16:03:26: 9000000 INFO @ Tue, 27 Jun 2017 16:03:27: 9000000 INFO @ Tue, 27 Jun 2017 16:03:27: 9000000 INFO @ Tue, 27 Jun 2017 16:03:33: 10000000 INFO @ Tue, 27 Jun 2017 16:03:33: 10000000 INFO @ Tue, 27 Jun 2017 16:03:33: 10000000 INFO @ Tue, 27 Jun 2017 16:03:39: 11000000 INFO @ Tue, 27 Jun 2017 16:03:39: 11000000 INFO @ Tue, 27 Jun 2017 16:03:39: 11000000 INFO @ Tue, 27 Jun 2017 16:03:45: 12000000 INFO @ Tue, 27 Jun 2017 16:03:45: 12000000 INFO @ Tue, 27 Jun 2017 16:03:46: 12000000 INFO @ Tue, 27 Jun 2017 16:03:51: 13000000 INFO @ Tue, 27 Jun 2017 16:03:51: 13000000 INFO @ Tue, 27 Jun 2017 16:03:53: 13000000 INFO @ Tue, 27 Jun 2017 16:03:57: 14000000 INFO @ Tue, 27 Jun 2017 16:03:57: 14000000 INFO @ Tue, 27 Jun 2017 16:03:59: 14000000 INFO @ Tue, 27 Jun 2017 16:04:03: 15000000 INFO @ Tue, 27 Jun 2017 16:04:03: 15000000 INFO @ Tue, 27 Jun 2017 16:04:06: 15000000 INFO @ Tue, 27 Jun 2017 16:04:09: 16000000 INFO @ Tue, 27 Jun 2017 16:04:09: 16000000 INFO @ Tue, 27 Jun 2017 16:04:13: 16000000 INFO @ Tue, 27 Jun 2017 16:04:14: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 16:04:14: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 16:04:14: #1 total tags in treatment: 7878757 INFO @ Tue, 27 Jun 2017 16:04:14: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 16:04:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 16:04:14: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 16:04:14: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 16:04:14: #1 total tags in treatment: 7878757 INFO @ Tue, 27 Jun 2017 16:04:14: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 16:04:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 16:04:14: #1 tags after filtering in treatment: 7190591 INFO @ Tue, 27 Jun 2017 16:04:14: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 27 Jun 2017 16:04:14: #1 finished! INFO @ Tue, 27 Jun 2017 16:04:14: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 16:04:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 16:04:14: #1 tags after filtering in treatment: 7190591 INFO @ Tue, 27 Jun 2017 16:04:14: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 27 Jun 2017 16:04:14: #1 finished! INFO @ Tue, 27 Jun 2017 16:04:14: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 16:04:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 16:04:15: #2 number of paired peaks: 985 WARNING @ Tue, 27 Jun 2017 16:04:15: Fewer paired peaks (985) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 985 pairs to build model! INFO @ Tue, 27 Jun 2017 16:04:15: start model_add_line... INFO @ Tue, 27 Jun 2017 16:04:15: start X-correlation... INFO @ Tue, 27 Jun 2017 16:04:15: #2 number of paired peaks: 985 WARNING @ Tue, 27 Jun 2017 16:04:15: Fewer paired peaks (985) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 985 pairs to build model! INFO @ Tue, 27 Jun 2017 16:04:15: start model_add_line... INFO @ Tue, 27 Jun 2017 16:04:15: end of X-cor INFO @ Tue, 27 Jun 2017 16:04:15: #2 finished! INFO @ Tue, 27 Jun 2017 16:04:15: #2 predicted fragment length is 149 bps INFO @ Tue, 27 Jun 2017 16:04:15: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 27 Jun 2017 16:04:15: #2.2 Generate R script for model : SRX1056718.20_model.r INFO @ Tue, 27 Jun 2017 16:04:15: #3 Call peaks... INFO @ Tue, 27 Jun 2017 16:04:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 16:04:15: start X-correlation... INFO @ Tue, 27 Jun 2017 16:04:15: end of X-cor INFO @ Tue, 27 Jun 2017 16:04:15: #2 finished! INFO @ Tue, 27 Jun 2017 16:04:15: #2 predicted fragment length is 149 bps INFO @ Tue, 27 Jun 2017 16:04:15: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 27 Jun 2017 16:04:15: #2.2 Generate R script for model : SRX1056718.10_model.r INFO @ Tue, 27 Jun 2017 16:04:15: #3 Call peaks... INFO @ Tue, 27 Jun 2017 16:04:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 16:04:17: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 16:04:17: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 16:04:17: #1 total tags in treatment: 7878757 INFO @ Tue, 27 Jun 2017 16:04:17: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 16:04:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 16:04:18: #1 tags after filtering in treatment: 7190591 INFO @ Tue, 27 Jun 2017 16:04:18: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 27 Jun 2017 16:04:18: #1 finished! INFO @ Tue, 27 Jun 2017 16:04:18: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 16:04:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 16:04:18: #2 number of paired peaks: 985 WARNING @ Tue, 27 Jun 2017 16:04:18: Fewer paired peaks (985) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 985 pairs to build model! INFO @ Tue, 27 Jun 2017 16:04:18: start model_add_line... INFO @ Tue, 27 Jun 2017 16:04:18: start X-correlation... INFO @ Tue, 27 Jun 2017 16:04:18: end of X-cor INFO @ Tue, 27 Jun 2017 16:04:18: #2 finished! INFO @ Tue, 27 Jun 2017 16:04:18: #2 predicted fragment length is 149 bps INFO @ Tue, 27 Jun 2017 16:04:18: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 27 Jun 2017 16:04:18: #2.2 Generate R script for model : SRX1056718.05_model.r INFO @ Tue, 27 Jun 2017 16:04:18: #3 Call peaks... INFO @ Tue, 27 Jun 2017 16:04:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 16:04:32: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 16:04:33: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 16:04:36: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 16:04:41: #4 Write output xls file... SRX1056718.10_peaks.xls INFO @ Tue, 27 Jun 2017 16:04:41: #4 Write peak in narrowPeak format file... SRX1056718.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 16:04:41: #4 Write summits bed file... SRX1056718.10_summits.bed INFO @ Tue, 27 Jun 2017 16:04:41: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1457 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 16:04:42: #4 Write output xls file... SRX1056718.20_peaks.xls INFO @ Tue, 27 Jun 2017 16:04:42: #4 Write peak in narrowPeak format file... SRX1056718.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 16:04:42: #4 Write summits bed file... SRX1056718.20_summits.bed INFO @ Tue, 27 Jun 2017 16:04:42: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (912 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 16:04:45: #4 Write output xls file... SRX1056718.05_peaks.xls INFO @ Tue, 27 Jun 2017 16:04:45: #4 Write peak in narrowPeak format file... SRX1056718.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 16:04:45: #4 Write summits bed file... SRX1056718.05_summits.bed INFO @ Tue, 27 Jun 2017 16:04:45: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2075 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。