Job ID = 10254411 sra ファイルのダウンロード中... Completed: 943579K bytes transferred in 14 seconds (520360K 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: PAIRED fastq に変換中... Written 20126486 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2658705/SRR5363221.sra Written 20126486 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:37 20126486 reads; of these: 20126486 (100.00%) were paired; of these: 5315751 (26.41%) aligned concordantly 0 times 11639804 (57.83%) aligned concordantly exactly 1 time 3170931 (15.76%) aligned concordantly >1 times ---- 5315751 pairs aligned concordantly 0 times; of these: 840528 (15.81%) aligned discordantly 1 time ---- 4475223 pairs aligned 0 times concordantly or discordantly; of these: 8950446 mates make up the pairs; of these: 8134410 (90.88%) aligned 0 times 258862 (2.89%) aligned exactly 1 time 557174 (6.23%) aligned >1 times 79.79% overall alignment rate Time searching: 00:13:37 Overall time: 00:13:37 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] 14272839 / 15641230 = 0.9125 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, 06 Dec 2017 18:08:33: # Command line: callpeak -t SRX2658705.bam -f BAM -g 12100000 -n SRX2658705.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2658705.10 # format = BAM # ChIP-seq file = ['SRX2658705.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, 06 Dec 2017 18:08:33: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:08:33: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:08:33: # Command line: callpeak -t SRX2658705.bam -f BAM -g 12100000 -n SRX2658705.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2658705.20 # format = BAM # ChIP-seq file = ['SRX2658705.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, 06 Dec 2017 18:08:33: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:08:33: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:08:33: # Command line: callpeak -t SRX2658705.bam -f BAM -g 12100000 -n SRX2658705.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2658705.05 # format = BAM # ChIP-seq file = ['SRX2658705.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, 06 Dec 2017 18:08:33: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:08:33: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:08:39: 1000000 INFO @ Wed, 06 Dec 2017 18:08:40: 1000000 INFO @ Wed, 06 Dec 2017 18:08:40: 1000000 INFO @ Wed, 06 Dec 2017 18:08:45: 2000000 INFO @ Wed, 06 Dec 2017 18:08:47: 2000000 INFO @ Wed, 06 Dec 2017 18:08:47: 2000000 INFO @ Wed, 06 Dec 2017 18:08:51: 3000000 INFO @ Wed, 06 Dec 2017 18:08:54: 3000000 INFO @ Wed, 06 Dec 2017 18:08:54: 3000000 INFO @ Wed, 06 Dec 2017 18:08:55: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 18:08:55: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 18:08:55: #1 total tags in treatment: 1265751 INFO @ Wed, 06 Dec 2017 18:08:55: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:08:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:08:55: #1 tags after filtering in treatment: 874781 INFO @ Wed, 06 Dec 2017 18:08:55: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 06 Dec 2017 18:08:55: #1 finished! INFO @ Wed, 06 Dec 2017 18:08:55: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:08:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:08:55: #2 number of paired peaks: 292 WARNING @ Wed, 06 Dec 2017 18:08:55: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Wed, 06 Dec 2017 18:08:55: start model_add_line... INFO @ Wed, 06 Dec 2017 18:08:55: start X-correlation... INFO @ Wed, 06 Dec 2017 18:08:55: end of X-cor INFO @ Wed, 06 Dec 2017 18:08:55: #2 finished! INFO @ Wed, 06 Dec 2017 18:08:55: #2 predicted fragment length is 192 bps INFO @ Wed, 06 Dec 2017 18:08:55: #2 alternative fragment length(s) may be 192 bps INFO @ Wed, 06 Dec 2017 18:08:55: #2.2 Generate R script for model : SRX2658705.05_model.r INFO @ Wed, 06 Dec 2017 18:08:55: #3 Call peaks... INFO @ Wed, 06 Dec 2017 18:08:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 06 Dec 2017 18:08:57: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 18:08:57: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 18:08:57: #1 total tags in treatment: 1265751 INFO @ Wed, 06 Dec 2017 18:08:57: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:08:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:08:57: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 18:08:57: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 18:08:57: #1 total tags in treatment: 1265751 INFO @ Wed, 06 Dec 2017 18:08:57: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:08:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:08:57: #1 tags after filtering in treatment: 874781 INFO @ Wed, 06 Dec 2017 18:08:57: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 06 Dec 2017 18:08:57: #1 finished! INFO @ Wed, 06 Dec 2017 18:08:57: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:08:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:08:57: #1 tags after filtering in treatment: 874781 INFO @ Wed, 06 Dec 2017 18:08:57: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 06 Dec 2017 18:08:57: #1 finished! INFO @ Wed, 06 Dec 2017 18:08:57: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:08:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:08:57: #2 number of paired peaks: 292 WARNING @ Wed, 06 Dec 2017 18:08:57: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Wed, 06 Dec 2017 18:08:57: start model_add_line... INFO @ Wed, 06 Dec 2017 18:08:57: start X-correlation... INFO @ Wed, 06 Dec 2017 18:08:57: end of X-cor INFO @ Wed, 06 Dec 2017 18:08:57: #2 finished! INFO @ Wed, 06 Dec 2017 18:08:57: #2 predicted fragment length is 192 bps INFO @ Wed, 06 Dec 2017 18:08:57: #2 alternative fragment length(s) may be 192 bps INFO @ Wed, 06 Dec 2017 18:08:57: #2.2 Generate R script for model : SRX2658705.20_model.r INFO @ Wed, 06 Dec 2017 18:08:57: #2 number of paired peaks: 292 WARNING @ Wed, 06 Dec 2017 18:08:57: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Wed, 06 Dec 2017 18:08:57: start model_add_line... INFO @ Wed, 06 Dec 2017 18:08:57: #3 Call peaks... INFO @ Wed, 06 Dec 2017 18:08:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 06 Dec 2017 18:08:57: start X-correlation... INFO @ Wed, 06 Dec 2017 18:08:57: end of X-cor INFO @ Wed, 06 Dec 2017 18:08:57: #2 finished! INFO @ Wed, 06 Dec 2017 18:08:57: #2 predicted fragment length is 192 bps INFO @ Wed, 06 Dec 2017 18:08:57: #2 alternative fragment length(s) may be 192 bps INFO @ Wed, 06 Dec 2017 18:08:57: #2.2 Generate R script for model : SRX2658705.10_model.r INFO @ Wed, 06 Dec 2017 18:08:57: #3 Call peaks... INFO @ Wed, 06 Dec 2017 18:08:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 06 Dec 2017 18:08:58: #3 Call peaks for each chromosome... INFO @ Wed, 06 Dec 2017 18:08:59: #4 Write output xls file... SRX2658705.05_peaks.xls INFO @ Wed, 06 Dec 2017 18:08:59: #4 Write peak in narrowPeak format file... SRX2658705.05_peaks.narrowPeak INFO @ Wed, 06 Dec 2017 18:08:59: #4 Write summits bed file... SRX2658705.05_summits.bed INFO @ Wed, 06 Dec 2017 18:08:59: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (870 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 06 Dec 2017 18:09:01: #3 Call peaks for each chromosome... INFO @ Wed, 06 Dec 2017 18:09:01: #3 Call peaks for each chromosome... INFO @ Wed, 06 Dec 2017 18:09:02: #4 Write output xls file... SRX2658705.20_peaks.xls INFO @ Wed, 06 Dec 2017 18:09:02: #4 Write peak in narrowPeak format file... SRX2658705.20_peaks.narrowPeak INFO @ Wed, 06 Dec 2017 18:09:02: #4 Write summits bed file... SRX2658705.20_summits.bed INFO @ Wed, 06 Dec 2017 18:09:02: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (243 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 06 Dec 2017 18:09:02: #4 Write output xls file... SRX2658705.10_peaks.xls INFO @ Wed, 06 Dec 2017 18:09:02: #4 Write peak in narrowPeak format file... SRX2658705.10_peaks.narrowPeak INFO @ Wed, 06 Dec 2017 18:09:02: #4 Write summits bed file... SRX2658705.10_summits.bed INFO @ Wed, 06 Dec 2017 18:09:02: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (527 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。