Job ID = 9160034 sra ファイルのダウンロード中... Completed: 57453K bytes transferred in 3 seconds (124304K 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 1963738 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2574972/SRR5270921.sra Written 1963738 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: 00:01:05 1963738 reads; of these: 1963738 (100.00%) were paired; of these: 386616 (19.69%) aligned concordantly 0 times 1286987 (65.54%) aligned concordantly exactly 1 time 290135 (14.77%) aligned concordantly >1 times ---- 386616 pairs aligned concordantly 0 times; of these: 29189 (7.55%) aligned discordantly 1 time ---- 357427 pairs aligned 0 times concordantly or discordantly; of these: 714854 mates make up the pairs; of these: 663760 (92.85%) aligned 0 times 28922 (4.05%) aligned exactly 1 time 22172 (3.10%) aligned >1 times 83.10% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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_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] 15385 / 1605524 = 0.0096 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 01:44:53: # Command line: callpeak -t SRX2574972.bam -f BAM -g 12100000 -n SRX2574972.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2574972.10 # format = BAM # ChIP-seq file = ['SRX2574972.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 01:44:53: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:44:53: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:44:53: # Command line: callpeak -t SRX2574972.bam -f BAM -g 12100000 -n SRX2574972.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2574972.20 # format = BAM # ChIP-seq file = ['SRX2574972.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 01:44:53: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:44:53: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:44:53: # Command line: callpeak -t SRX2574972.bam -f BAM -g 12100000 -n SRX2574972.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2574972.05 # format = BAM # ChIP-seq file = ['SRX2574972.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 01:44:53: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:44:53: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:44:58: 1000000 INFO @ Wed, 28 Jun 2017 01:44:58: 1000000 INFO @ Wed, 28 Jun 2017 01:44:58: 1000000 INFO @ Wed, 28 Jun 2017 01:45:03: 2000000 INFO @ Wed, 28 Jun 2017 01:45:04: 2000000 INFO @ Wed, 28 Jun 2017 01:45:04: 2000000 INFO @ Wed, 28 Jun 2017 01:45:08: 3000000 INFO @ Wed, 28 Jun 2017 01:45:09: #1 tag size is determined as 26 bps INFO @ Wed, 28 Jun 2017 01:45:09: #1 tag size = 26 INFO @ Wed, 28 Jun 2017 01:45:09: #1 total tags in treatment: 1561791 INFO @ Wed, 28 Jun 2017 01:45:09: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:45:09: #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 01:45:09: #1 tags after filtering in treatment: 1265864 INFO @ Wed, 28 Jun 2017 01:45:09: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 28 Jun 2017 01:45:09: #1 finished! INFO @ Wed, 28 Jun 2017 01:45:09: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:45:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:45:09: #2 number of paired peaks: 307 WARNING @ Wed, 28 Jun 2017 01:45:09: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Wed, 28 Jun 2017 01:45:09: start model_add_line... INFO @ Wed, 28 Jun 2017 01:45:09: start X-correlation... INFO @ Wed, 28 Jun 2017 01:45:09: end of X-cor INFO @ Wed, 28 Jun 2017 01:45:09: #2 finished! INFO @ Wed, 28 Jun 2017 01:45:09: #2 predicted fragment length is 171 bps INFO @ Wed, 28 Jun 2017 01:45:09: #2 alternative fragment length(s) may be 171 bps INFO @ Wed, 28 Jun 2017 01:45:09: #2.2 Generate R script for model : SRX2574972.10_model.r INFO @ Wed, 28 Jun 2017 01:45:09: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:45:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:45:09: 3000000 INFO @ Wed, 28 Jun 2017 01:45:10: 3000000 INFO @ Wed, 28 Jun 2017 01:45:10: #1 tag size is determined as 26 bps INFO @ Wed, 28 Jun 2017 01:45:10: #1 tag size = 26 INFO @ Wed, 28 Jun 2017 01:45:10: #1 total tags in treatment: 1561791 INFO @ Wed, 28 Jun 2017 01:45:10: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:45:10: #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 01:45:11: #1 tags after filtering in treatment: 1265864 INFO @ Wed, 28 Jun 2017 01:45:11: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 28 Jun 2017 01:45:11: #1 finished! INFO @ Wed, 28 Jun 2017 01:45:11: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:45:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:45:11: #2 number of paired peaks: 307 WARNING @ Wed, 28 Jun 2017 01:45:11: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Wed, 28 Jun 2017 01:45:11: start model_add_line... INFO @ Wed, 28 Jun 2017 01:45:11: start X-correlation... INFO @ Wed, 28 Jun 2017 01:45:11: end of X-cor INFO @ Wed, 28 Jun 2017 01:45:11: #2 finished! INFO @ Wed, 28 Jun 2017 01:45:11: #2 predicted fragment length is 171 bps INFO @ Wed, 28 Jun 2017 01:45:11: #2 alternative fragment length(s) may be 171 bps INFO @ Wed, 28 Jun 2017 01:45:11: #2.2 Generate R script for model : SRX2574972.20_model.r INFO @ Wed, 28 Jun 2017 01:45:11: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:45:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:45:11: #1 tag size is determined as 26 bps INFO @ Wed, 28 Jun 2017 01:45:11: #1 tag size = 26 INFO @ Wed, 28 Jun 2017 01:45:11: #1 total tags in treatment: 1561791 INFO @ Wed, 28 Jun 2017 01:45:11: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:45:11: #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 01:45:11: #1 tags after filtering in treatment: 1265864 INFO @ Wed, 28 Jun 2017 01:45:11: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 28 Jun 2017 01:45:11: #1 finished! INFO @ Wed, 28 Jun 2017 01:45:11: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:45:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:45:11: #2 number of paired peaks: 307 WARNING @ Wed, 28 Jun 2017 01:45:11: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Wed, 28 Jun 2017 01:45:11: start model_add_line... INFO @ Wed, 28 Jun 2017 01:45:11: start X-correlation... INFO @ Wed, 28 Jun 2017 01:45:11: end of X-cor INFO @ Wed, 28 Jun 2017 01:45:11: #2 finished! INFO @ Wed, 28 Jun 2017 01:45:11: #2 predicted fragment length is 171 bps INFO @ Wed, 28 Jun 2017 01:45:11: #2 alternative fragment length(s) may be 171 bps INFO @ Wed, 28 Jun 2017 01:45:11: #2.2 Generate R script for model : SRX2574972.05_model.r INFO @ Wed, 28 Jun 2017 01:45:11: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:45:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:45:14: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:45:15: #4 Write output xls file... SRX2574972.10_peaks.xls INFO @ Wed, 28 Jun 2017 01:45:15: #4 Write peak in narrowPeak format file... SRX2574972.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:45:15: #4 Write summits bed file... SRX2574972.10_summits.bed INFO @ Wed, 28 Jun 2017 01:45:15: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:45:15: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (800 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:45:15: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:45:17: #4 Write output xls file... SRX2574972.20_peaks.xls INFO @ Wed, 28 Jun 2017 01:45:17: #4 Write peak in narrowPeak format file... SRX2574972.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:45:17: #4 Write summits bed file... SRX2574972.20_summits.bed INFO @ Wed, 28 Jun 2017 01:45:17: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (570 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:45:17: #4 Write output xls file... SRX2574972.05_peaks.xls INFO @ Wed, 28 Jun 2017 01:45:17: #4 Write peak in narrowPeak format file... SRX2574972.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:45:17: #4 Write summits bed file... SRX2574972.05_summits.bed INFO @ Wed, 28 Jun 2017 01:45:17: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1053 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。