Job ID = 9162006 sra ファイルのダウンロード中... Completed: 1511658K bytes transferred in 15 seconds (794350K 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 24057383 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423738/SRR2931027.sra Written 24057383 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: 00:12:37 24057383 reads; of these: 24057383 (100.00%) were paired; of these: 8716038 (36.23%) aligned concordantly 0 times 13528305 (56.23%) aligned concordantly exactly 1 time 1813040 (7.54%) aligned concordantly >1 times ---- 8716038 pairs aligned concordantly 0 times; of these: 43409 (0.50%) aligned discordantly 1 time ---- 8672629 pairs aligned 0 times concordantly or discordantly; of these: 17345258 mates make up the pairs; of these: 17024540 (98.15%) aligned 0 times 263958 (1.52%) aligned exactly 1 time 56760 (0.33%) aligned >1 times 64.62% overall alignment rate Time searching: 00:12:37 Overall time: 00:12:37 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 16 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] 12574821 / 15355686 = 0.8189 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 05:34:59: # Command line: callpeak -t SRX1423738.bam -f BAM -g 12100000 -n SRX1423738.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423738.05 # format = BAM # ChIP-seq file = ['SRX1423738.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 05:34:59: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:34:59: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:34:59: # Command line: callpeak -t SRX1423738.bam -f BAM -g 12100000 -n SRX1423738.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423738.10 # format = BAM # ChIP-seq file = ['SRX1423738.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 05:34:59: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:34:59: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:34:59: # Command line: callpeak -t SRX1423738.bam -f BAM -g 12100000 -n SRX1423738.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423738.20 # format = BAM # ChIP-seq file = ['SRX1423738.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 05:34:59: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:34:59: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:35:06: 1000000 INFO @ Wed, 28 Jun 2017 05:35:06: 1000000 INFO @ Wed, 28 Jun 2017 05:35:07: 1000000 INFO @ Wed, 28 Jun 2017 05:35:13: 2000000 INFO @ Wed, 28 Jun 2017 05:35:13: 2000000 INFO @ Wed, 28 Jun 2017 05:35:14: 2000000 INFO @ Wed, 28 Jun 2017 05:35:19: 3000000 INFO @ Wed, 28 Jun 2017 05:35:19: 3000000 INFO @ Wed, 28 Jun 2017 05:35:20: 3000000 INFO @ Wed, 28 Jun 2017 05:35:25: 4000000 INFO @ Wed, 28 Jun 2017 05:35:25: 4000000 INFO @ Wed, 28 Jun 2017 05:35:27: 4000000 INFO @ Wed, 28 Jun 2017 05:35:31: 5000000 INFO @ Wed, 28 Jun 2017 05:35:31: 5000000 INFO @ Wed, 28 Jun 2017 05:35:34: 5000000 INFO @ Wed, 28 Jun 2017 05:35:36: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:35:36: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:35:36: #1 total tags in treatment: 2781565 INFO @ Wed, 28 Jun 2017 05:35:36: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:35:36: #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 05:35:36: #1 tags after filtering in treatment: 2346027 INFO @ Wed, 28 Jun 2017 05:35:36: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 28 Jun 2017 05:35:36: #1 finished! INFO @ Wed, 28 Jun 2017 05:35:36: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:35:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:35:36: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:35:36: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:35:36: #1 total tags in treatment: 2781565 INFO @ Wed, 28 Jun 2017 05:35:36: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:35:36: #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 05:35:36: #1 tags after filtering in treatment: 2346027 INFO @ Wed, 28 Jun 2017 05:35:36: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 28 Jun 2017 05:35:36: #1 finished! INFO @ Wed, 28 Jun 2017 05:35:36: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:35:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:35:36: #2 number of paired peaks: 127 WARNING @ Wed, 28 Jun 2017 05:35:36: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Wed, 28 Jun 2017 05:35:36: start model_add_line... INFO @ Wed, 28 Jun 2017 05:35:36: start X-correlation... INFO @ Wed, 28 Jun 2017 05:35:36: end of X-cor INFO @ Wed, 28 Jun 2017 05:35:36: #2 finished! INFO @ Wed, 28 Jun 2017 05:35:36: #2 predicted fragment length is 111 bps INFO @ Wed, 28 Jun 2017 05:35:36: #2 alternative fragment length(s) may be 2,25,53,68,94,111,158,570 bps INFO @ Wed, 28 Jun 2017 05:35:36: #2.2 Generate R script for model : SRX1423738.05_model.r INFO @ Wed, 28 Jun 2017 05:35:36: #3 Call peaks... INFO @ Wed, 28 Jun 2017 05:35:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 05:35:37: #2 number of paired peaks: 127 WARNING @ Wed, 28 Jun 2017 05:35:37: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Wed, 28 Jun 2017 05:35:37: start model_add_line... INFO @ Wed, 28 Jun 2017 05:35:37: start X-correlation... INFO @ Wed, 28 Jun 2017 05:35:37: end of X-cor INFO @ Wed, 28 Jun 2017 05:35:37: #2 finished! INFO @ Wed, 28 Jun 2017 05:35:37: #2 predicted fragment length is 111 bps INFO @ Wed, 28 Jun 2017 05:35:37: #2 alternative fragment length(s) may be 2,25,53,68,94,111,158,570 bps INFO @ Wed, 28 Jun 2017 05:35:37: #2.2 Generate R script for model : SRX1423738.10_model.r INFO @ Wed, 28 Jun 2017 05:35:37: #3 Call peaks... INFO @ Wed, 28 Jun 2017 05:35:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 05:35:40: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:35:40: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:35:40: #1 total tags in treatment: 2781565 INFO @ Wed, 28 Jun 2017 05:35:40: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:35:40: #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 05:35:40: #1 tags after filtering in treatment: 2346027 INFO @ Wed, 28 Jun 2017 05:35:40: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 28 Jun 2017 05:35:40: #1 finished! INFO @ Wed, 28 Jun 2017 05:35:40: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:35:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:35:40: #2 number of paired peaks: 127 WARNING @ Wed, 28 Jun 2017 05:35:40: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Wed, 28 Jun 2017 05:35:40: start model_add_line... INFO @ Wed, 28 Jun 2017 05:35:40: start X-correlation... INFO @ Wed, 28 Jun 2017 05:35:40: end of X-cor INFO @ Wed, 28 Jun 2017 05:35:40: #2 finished! INFO @ Wed, 28 Jun 2017 05:35:40: #2 predicted fragment length is 111 bps INFO @ Wed, 28 Jun 2017 05:35:40: #2 alternative fragment length(s) may be 2,25,53,68,94,111,158,570 bps INFO @ Wed, 28 Jun 2017 05:35:40: #2.2 Generate R script for model : SRX1423738.20_model.r INFO @ Wed, 28 Jun 2017 05:35:40: #3 Call peaks... INFO @ Wed, 28 Jun 2017 05:35:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 05:35:42: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 05:35:43: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 05:35:45: #4 Write output xls file... SRX1423738.05_peaks.xls INFO @ Wed, 28 Jun 2017 05:35:45: #4 Write peak in narrowPeak format file... SRX1423738.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 05:35:45: #4 Write summits bed file... SRX1423738.05_summits.bed INFO @ Wed, 28 Jun 2017 05:35:45: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (787 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 05:35:45: #4 Write output xls file... SRX1423738.10_peaks.xls INFO @ Wed, 28 Jun 2017 05:35:45: #4 Write peak in narrowPeak format file... SRX1423738.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 05:35:45: #4 Write summits bed file... SRX1423738.10_summits.bed INFO @ Wed, 28 Jun 2017 05:35:45: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (321 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 05:35:47: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 05:35:49: #4 Write output xls file... SRX1423738.20_peaks.xls INFO @ Wed, 28 Jun 2017 05:35:49: #4 Write peak in narrowPeak format file... SRX1423738.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 05:35:49: #4 Write summits bed file... SRX1423738.20_summits.bed INFO @ Wed, 28 Jun 2017 05:35:49: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (152 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。