Job ID = 9161793 sra ファイルのダウンロード中... Completed: 631843K bytes transferred in 9 seconds (571940K 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 15261900 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1044179/SRR2045660.sra Written 15261900 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: 00:06:59 15261900 reads; of these: 15261900 (100.00%) were paired; of these: 7154376 (46.88%) aligned concordantly 0 times 7461350 (48.89%) aligned concordantly exactly 1 time 646174 (4.23%) aligned concordantly >1 times ---- 7154376 pairs aligned concordantly 0 times; of these: 256079 (3.58%) aligned discordantly 1 time ---- 6898297 pairs aligned 0 times concordantly or discordantly; of these: 13796594 mates make up the pairs; of these: 13528689 (98.06%) aligned 0 times 201471 (1.46%) aligned exactly 1 time 66434 (0.48%) aligned >1 times 55.68% overall alignment rate Time searching: 00:06:59 Overall time: 00:06:59 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 4120411 / 8321895 = 0.4951 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 @ Wed, 28 Jun 2017 04:45:46: # Command line: callpeak -t SRX1044179.bam -f BAM -g 12100000 -n SRX1044179.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1044179.10 # format = BAM # ChIP-seq file = ['SRX1044179.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 28 Jun 2017 04:45:46: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:45:46: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:45:46: # Command line: callpeak -t SRX1044179.bam -f BAM -g 12100000 -n SRX1044179.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1044179.05 # format = BAM # ChIP-seq file = ['SRX1044179.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 28 Jun 2017 04:45:46: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:45:46: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:45:46: # Command line: callpeak -t SRX1044179.bam -f BAM -g 12100000 -n SRX1044179.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1044179.20 # format = BAM # ChIP-seq file = ['SRX1044179.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 28 Jun 2017 04:45:46: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:45:46: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:45:53: 1000000 INFO @ Wed, 28 Jun 2017 04:45:53: 1000000 INFO @ Wed, 28 Jun 2017 04:45:53: 1000000 INFO @ Wed, 28 Jun 2017 04:45:59: 2000000 INFO @ Wed, 28 Jun 2017 04:45:59: 2000000 INFO @ Wed, 28 Jun 2017 04:45:59: 2000000 INFO @ Wed, 28 Jun 2017 04:46:06: 3000000 INFO @ Wed, 28 Jun 2017 04:46:06: 3000000 INFO @ Wed, 28 Jun 2017 04:46:06: 3000000 INFO @ Wed, 28 Jun 2017 04:46:12: 4000000 INFO @ Wed, 28 Jun 2017 04:46:12: 4000000 INFO @ Wed, 28 Jun 2017 04:46:13: 4000000 INFO @ Wed, 28 Jun 2017 04:46:18: 5000000 INFO @ Wed, 28 Jun 2017 04:46:18: 5000000 INFO @ Wed, 28 Jun 2017 04:46:19: 5000000 INFO @ Wed, 28 Jun 2017 04:46:25: 6000000 INFO @ Wed, 28 Jun 2017 04:46:25: 6000000 INFO @ Wed, 28 Jun 2017 04:46:26: 6000000 INFO @ Wed, 28 Jun 2017 04:46:31: 7000000 INFO @ Wed, 28 Jun 2017 04:46:31: 7000000 INFO @ Wed, 28 Jun 2017 04:46:32: 7000000 INFO @ Wed, 28 Jun 2017 04:46:38: 8000000 INFO @ Wed, 28 Jun 2017 04:46:38: 8000000 INFO @ Wed, 28 Jun 2017 04:46:39: 8000000 INFO @ Wed, 28 Jun 2017 04:46:42: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 04:46:42: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 04:46:42: #1 total tags in treatment: 4072762 INFO @ Wed, 28 Jun 2017 04:46:42: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:46:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 04:46:42: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 04:46:42: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 04:46:42: #1 total tags in treatment: 4072762 INFO @ Wed, 28 Jun 2017 04:46:42: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:46:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 04:46:42: #1 tags after filtering in treatment: 3292870 INFO @ Wed, 28 Jun 2017 04:46:42: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 28 Jun 2017 04:46:42: #1 finished! INFO @ Wed, 28 Jun 2017 04:46:42: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:46:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:46:42: #1 tags after filtering in treatment: 3292870 INFO @ Wed, 28 Jun 2017 04:46:42: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 28 Jun 2017 04:46:42: #1 finished! INFO @ Wed, 28 Jun 2017 04:46:42: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:46:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:46:43: #2 number of paired peaks: 109 WARNING @ Wed, 28 Jun 2017 04:46:43: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Wed, 28 Jun 2017 04:46:43: start model_add_line... INFO @ Wed, 28 Jun 2017 04:46:43: #2 number of paired peaks: 109 WARNING @ Wed, 28 Jun 2017 04:46:43: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Wed, 28 Jun 2017 04:46:43: start model_add_line... INFO @ Wed, 28 Jun 2017 04:46:43: start X-correlation... INFO @ Wed, 28 Jun 2017 04:46:43: end of X-cor INFO @ Wed, 28 Jun 2017 04:46:43: #2 finished! INFO @ Wed, 28 Jun 2017 04:46:43: #2 predicted fragment length is 148 bps INFO @ Wed, 28 Jun 2017 04:46:43: #2 alternative fragment length(s) may be 3,106,135,148,172 bps INFO @ Wed, 28 Jun 2017 04:46:43: #2.2 Generate R script for model : SRX1044179.05_model.r INFO @ Wed, 28 Jun 2017 04:46:43: start X-correlation... INFO @ Wed, 28 Jun 2017 04:46:43: #3 Call peaks... INFO @ Wed, 28 Jun 2017 04:46:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 04:46:43: end of X-cor INFO @ Wed, 28 Jun 2017 04:46:43: #2 finished! INFO @ Wed, 28 Jun 2017 04:46:43: #2 predicted fragment length is 148 bps INFO @ Wed, 28 Jun 2017 04:46:43: #2 alternative fragment length(s) may be 3,106,135,148,172 bps INFO @ Wed, 28 Jun 2017 04:46:43: #2.2 Generate R script for model : SRX1044179.20_model.r INFO @ Wed, 28 Jun 2017 04:46:43: #3 Call peaks... INFO @ Wed, 28 Jun 2017 04:46:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 04:46:44: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 04:46:44: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 04:46:44: #1 total tags in treatment: 4072762 INFO @ Wed, 28 Jun 2017 04:46:44: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:46:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 04:46:44: #1 tags after filtering in treatment: 3292870 INFO @ Wed, 28 Jun 2017 04:46:44: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 28 Jun 2017 04:46:44: #1 finished! INFO @ Wed, 28 Jun 2017 04:46:44: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:46:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:46:44: #2 number of paired peaks: 109 WARNING @ Wed, 28 Jun 2017 04:46:44: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Wed, 28 Jun 2017 04:46:44: start model_add_line... INFO @ Wed, 28 Jun 2017 04:46:44: start X-correlation... INFO @ Wed, 28 Jun 2017 04:46:44: end of X-cor INFO @ Wed, 28 Jun 2017 04:46:44: #2 finished! INFO @ Wed, 28 Jun 2017 04:46:44: #2 predicted fragment length is 148 bps INFO @ Wed, 28 Jun 2017 04:46:44: #2 alternative fragment length(s) may be 3,106,135,148,172 bps INFO @ Wed, 28 Jun 2017 04:46:44: #2.2 Generate R script for model : SRX1044179.10_model.r INFO @ Wed, 28 Jun 2017 04:46:44: #3 Call peaks... INFO @ Wed, 28 Jun 2017 04:46:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 04:46:53: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 04:46:53: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 04:46:54: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 04:46:56: #4 Write output xls file... SRX1044179.05_peaks.xls INFO @ Wed, 28 Jun 2017 04:46:56: #4 Write peak in narrowPeak format file... SRX1044179.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 04:46:56: #4 Write summits bed file... SRX1044179.05_summits.bed INFO @ Wed, 28 Jun 2017 04:46:56: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1034 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 04:46:57: #4 Write output xls file... SRX1044179.20_peaks.xls INFO @ Wed, 28 Jun 2017 04:46:57: #4 Write peak in narrowPeak format file... SRX1044179.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 04:46:57: #4 Write summits bed file... SRX1044179.20_summits.bed INFO @ Wed, 28 Jun 2017 04:46:57: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (408 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 04:46:58: #4 Write output xls file... SRX1044179.10_peaks.xls INFO @ Wed, 28 Jun 2017 04:46:58: #4 Write peak in narrowPeak format file... SRX1044179.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 04:46:58: #4 Write summits bed file... SRX1044179.10_summits.bed INFO @ Wed, 28 Jun 2017 04:46:58: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (630 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。