Job ID = 10254329 sra ファイルのダウンロード中... Completed: 32116K bytes transferred in 3 seconds (81757K 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: SINGLE fastq に変換中... Written 1011122 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2587956/SRR5284384.sra Written 1011122 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: 00:00:16 1011122 reads; of these: 1011122 (100.00%) were unpaired; of these: 277589 (27.45%) aligned 0 times 535733 (52.98%) aligned exactly 1 time 197800 (19.56%) aligned >1 times 72.55% overall alignment rate Time searching: 00:00:16 Overall time: 00:00:16 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_rmdupse_core] 330584 / 733533 = 0.4507 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 17:27:23: # Command line: callpeak -t SRX2587956.bam -f BAM -g 12100000 -n SRX2587956.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2587956.05 # format = BAM # ChIP-seq file = ['SRX2587956.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 17:27:23: #1 read tag files... INFO @ Wed, 06 Dec 2017 17:27:23: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 17:27:23: # Command line: callpeak -t SRX2587956.bam -f BAM -g 12100000 -n SRX2587956.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2587956.10 # format = BAM # ChIP-seq file = ['SRX2587956.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 17:27:23: #1 read tag files... INFO @ Wed, 06 Dec 2017 17:27:23: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 17:27:23: # Command line: callpeak -t SRX2587956.bam -f BAM -g 12100000 -n SRX2587956.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2587956.20 # format = BAM # ChIP-seq file = ['SRX2587956.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 17:27:23: #1 read tag files... INFO @ Wed, 06 Dec 2017 17:27:23: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 17:27:26: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 17:27:26: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 17:27:26: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 17:27:26: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 17:27:26: #1 total tags in treatment: 402949 INFO @ Wed, 06 Dec 2017 17:27:26: #1 total tags in treatment: 402949 INFO @ Wed, 06 Dec 2017 17:27:26: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 17:27:26: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 17:27:26: #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 17:27:26: #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 17:27:26: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 17:27:26: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 17:27:26: #1 total tags in treatment: 402949 INFO @ Wed, 06 Dec 2017 17:27:26: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 17:27:26: #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 17:27:26: #1 tags after filtering in treatment: 402949 INFO @ Wed, 06 Dec 2017 17:27:26: #1 tags after filtering in treatment: 402949 INFO @ Wed, 06 Dec 2017 17:27:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 17:27:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 17:27:26: #1 finished! INFO @ Wed, 06 Dec 2017 17:27:26: #1 finished! INFO @ Wed, 06 Dec 2017 17:27:26: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 17:27:26: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 17:27:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 17:27:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 17:27:26: #1 tags after filtering in treatment: 402949 INFO @ Wed, 06 Dec 2017 17:27:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 17:27:26: #1 finished! INFO @ Wed, 06 Dec 2017 17:27:26: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 17:27:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 17:27:26: #2 number of paired peaks: 159 WARNING @ Wed, 06 Dec 2017 17:27:26: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Wed, 06 Dec 2017 17:27:26: start model_add_line... INFO @ Wed, 06 Dec 2017 17:27:26: #2 number of paired peaks: 159 WARNING @ Wed, 06 Dec 2017 17:27:26: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Wed, 06 Dec 2017 17:27:26: start model_add_line... INFO @ Wed, 06 Dec 2017 17:27:26: start X-correlation... INFO @ Wed, 06 Dec 2017 17:27:26: start X-correlation... INFO @ Wed, 06 Dec 2017 17:27:26: #2 number of paired peaks: 159 WARNING @ Wed, 06 Dec 2017 17:27:26: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Wed, 06 Dec 2017 17:27:26: end of X-cor INFO @ Wed, 06 Dec 2017 17:27:26: #2 finished! INFO @ Wed, 06 Dec 2017 17:27:26: start model_add_line... INFO @ Wed, 06 Dec 2017 17:27:26: #2 predicted fragment length is 112 bps INFO @ Wed, 06 Dec 2017 17:27:26: #2 alternative fragment length(s) may be 48,70,112,561,581 bps INFO @ Wed, 06 Dec 2017 17:27:26: #2.2 Generate R script for model : SRX2587956.05_model.r INFO @ Wed, 06 Dec 2017 17:27:26: end of X-cor INFO @ Wed, 06 Dec 2017 17:27:26: #2 finished! INFO @ Wed, 06 Dec 2017 17:27:26: #2 predicted fragment length is 112 bps INFO @ Wed, 06 Dec 2017 17:27:26: #2 alternative fragment length(s) may be 48,70,112,561,581 bps INFO @ Wed, 06 Dec 2017 17:27:26: #2.2 Generate R script for model : SRX2587956.10_model.r INFO @ Wed, 06 Dec 2017 17:27:26: start X-correlation... INFO @ Wed, 06 Dec 2017 17:27:26: #3 Call peaks... INFO @ Wed, 06 Dec 2017 17:27:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 06 Dec 2017 17:27:26: #3 Call peaks... INFO @ Wed, 06 Dec 2017 17:27:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 06 Dec 2017 17:27:26: end of X-cor INFO @ Wed, 06 Dec 2017 17:27:26: #2 finished! INFO @ Wed, 06 Dec 2017 17:27:26: #2 predicted fragment length is 112 bps INFO @ Wed, 06 Dec 2017 17:27:26: #2 alternative fragment length(s) may be 48,70,112,561,581 bps INFO @ Wed, 06 Dec 2017 17:27:26: #2.2 Generate R script for model : SRX2587956.20_model.r INFO @ Wed, 06 Dec 2017 17:27:26: #3 Call peaks... INFO @ Wed, 06 Dec 2017 17:27:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 06 Dec 2017 17:27:27: #3 Call peaks for each chromosome... INFO @ Wed, 06 Dec 2017 17:27:27: #3 Call peaks for each chromosome... INFO @ Wed, 06 Dec 2017 17:27:27: #3 Call peaks for each chromosome... INFO @ Wed, 06 Dec 2017 17:27:27: #4 Write output xls file... SRX2587956.10_peaks.xls INFO @ Wed, 06 Dec 2017 17:27:27: #4 Write peak in narrowPeak format file... SRX2587956.10_peaks.narrowPeak INFO @ Wed, 06 Dec 2017 17:27:27: #4 Write summits bed file... SRX2587956.10_summits.bed INFO @ Wed, 06 Dec 2017 17:27:27: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (159 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 06 Dec 2017 17:27:28: #4 Write output xls file... SRX2587956.05_peaks.xls INFO @ Wed, 06 Dec 2017 17:27:28: #4 Write output xls file... SRX2587956.20_peaks.xls INFO @ Wed, 06 Dec 2017 17:27:28: #4 Write peak in narrowPeak format file... SRX2587956.20_peaks.narrowPeak INFO @ Wed, 06 Dec 2017 17:27:28: #4 Write summits bed file... SRX2587956.20_summits.bed INFO @ Wed, 06 Dec 2017 17:27:28: #4 Write peak in narrowPeak format file... SRX2587956.05_peaks.narrowPeak INFO @ Wed, 06 Dec 2017 17:27:28: Done! INFO @ Wed, 06 Dec 2017 17:27:28: #4 Write summits bed file... SRX2587956.05_summits.bed INFO @ Wed, 06 Dec 2017 17:27:28: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (6 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (904 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。