Job ID = 11192915 sra ファイルのダウンロード中... Completed: 312478K bytes transferred in 6 seconds (411035K 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... Read 8472342 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3242030/SRR6129632.sra Written 8472342 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3242030/SRR6129632.sra 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: 00:02:42 8472342 reads; of these: 8472342 (100.00%) were paired; of these: 7653482 (90.33%) aligned concordantly 0 times 713668 (8.42%) aligned concordantly exactly 1 time 105192 (1.24%) aligned concordantly >1 times ---- 7653482 pairs aligned concordantly 0 times; of these: 281809 (3.68%) aligned discordantly 1 time ---- 7371673 pairs aligned 0 times concordantly or discordantly; of these: 14743346 mates make up the pairs; of these: 12486922 (84.70%) aligned 0 times 1948790 (13.22%) aligned exactly 1 time 307634 (2.09%) aligned >1 times 26.31% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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] 331093 / 966544 = 0.3426 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 @ Sat, 15 Sep 2018 10:28:31: # Command line: callpeak -t SRX3242030.bam -f BAM -g 12100000 -n SRX3242030.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3242030.10 # format = BAM # ChIP-seq file = ['SRX3242030.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 @ Sat, 15 Sep 2018 10:28:31: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:28:31: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:28:31: # Command line: callpeak -t SRX3242030.bam -f BAM -g 12100000 -n SRX3242030.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3242030.05 # format = BAM # ChIP-seq file = ['SRX3242030.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 @ Sat, 15 Sep 2018 10:28:31: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:28:31: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:28:31: # Command line: callpeak -t SRX3242030.bam -f BAM -g 12100000 -n SRX3242030.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3242030.20 # format = BAM # ChIP-seq file = ['SRX3242030.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 @ Sat, 15 Sep 2018 10:28:31: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:28:31: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:28:36: 1000000 INFO @ Sat, 15 Sep 2018 10:28:36: 1000000 INFO @ Sat, 15 Sep 2018 10:28:36: 1000000 INFO @ Sat, 15 Sep 2018 10:28:41: 2000000 INFO @ Sat, 15 Sep 2018 10:28:41: 2000000 INFO @ Sat, 15 Sep 2018 10:28:41: 2000000 INFO @ Sat, 15 Sep 2018 10:28:46: 3000000 INFO @ Sat, 15 Sep 2018 10:28:46: 3000000 INFO @ Sat, 15 Sep 2018 10:28:46: 3000000 INFO @ Sat, 15 Sep 2018 10:28:50: #1 tag size is determined as 37 bps INFO @ Sat, 15 Sep 2018 10:28:50: #1 tag size = 37 INFO @ Sat, 15 Sep 2018 10:28:50: #1 total tags in treatment: 534814 INFO @ Sat, 15 Sep 2018 10:28:50: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:28:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:28:50: #1 tags after filtering in treatment: 491520 INFO @ Sat, 15 Sep 2018 10:28:50: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Sep 2018 10:28:50: #1 finished! INFO @ Sat, 15 Sep 2018 10:28:50: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:28:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:28:50: #1 tag size is determined as 37 bps INFO @ Sat, 15 Sep 2018 10:28:50: #1 tag size = 37 INFO @ Sat, 15 Sep 2018 10:28:50: #1 total tags in treatment: 534814 INFO @ Sat, 15 Sep 2018 10:28:50: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:28:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:28:50: #1 tags after filtering in treatment: 491520 INFO @ Sat, 15 Sep 2018 10:28:50: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Sep 2018 10:28:50: #1 finished! INFO @ Sat, 15 Sep 2018 10:28:50: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:28:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:28:50: #2 number of paired peaks: 158 WARNING @ Sat, 15 Sep 2018 10:28:50: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 15 Sep 2018 10:28:50: start model_add_line... INFO @ Sat, 15 Sep 2018 10:28:50: start X-correlation... INFO @ Sat, 15 Sep 2018 10:28:50: end of X-cor INFO @ Sat, 15 Sep 2018 10:28:50: #2 finished! INFO @ Sat, 15 Sep 2018 10:28:50: #2 predicted fragment length is 160 bps INFO @ Sat, 15 Sep 2018 10:28:50: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 15 Sep 2018 10:28:50: #2.2 Generate R script for model : SRX3242030.20_model.r INFO @ Sat, 15 Sep 2018 10:28:50: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:28:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:28:50: #2 number of paired peaks: 158 WARNING @ Sat, 15 Sep 2018 10:28:50: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 15 Sep 2018 10:28:50: start model_add_line... INFO @ Sat, 15 Sep 2018 10:28:50: start X-correlation... INFO @ Sat, 15 Sep 2018 10:28:50: end of X-cor INFO @ Sat, 15 Sep 2018 10:28:50: #2 finished! INFO @ Sat, 15 Sep 2018 10:28:50: #2 predicted fragment length is 160 bps INFO @ Sat, 15 Sep 2018 10:28:50: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 15 Sep 2018 10:28:50: #2.2 Generate R script for model : SRX3242030.05_model.r INFO @ Sat, 15 Sep 2018 10:28:50: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:28:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:28:50: #1 tag size is determined as 37 bps INFO @ Sat, 15 Sep 2018 10:28:50: #1 tag size = 37 INFO @ Sat, 15 Sep 2018 10:28:50: #1 total tags in treatment: 534814 INFO @ Sat, 15 Sep 2018 10:28:50: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:28:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:28:50: #1 tags after filtering in treatment: 491520 INFO @ Sat, 15 Sep 2018 10:28:50: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Sep 2018 10:28:50: #1 finished! INFO @ Sat, 15 Sep 2018 10:28:50: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:28:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:28:50: #2 number of paired peaks: 158 WARNING @ Sat, 15 Sep 2018 10:28:50: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 15 Sep 2018 10:28:50: start model_add_line... INFO @ Sat, 15 Sep 2018 10:28:50: start X-correlation... INFO @ Sat, 15 Sep 2018 10:28:50: end of X-cor INFO @ Sat, 15 Sep 2018 10:28:50: #2 finished! INFO @ Sat, 15 Sep 2018 10:28:50: #2 predicted fragment length is 160 bps INFO @ Sat, 15 Sep 2018 10:28:50: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 15 Sep 2018 10:28:50: #2.2 Generate R script for model : SRX3242030.10_model.r INFO @ Sat, 15 Sep 2018 10:28:50: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:28:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:28:51: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:28:51: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:28:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:28:52: #4 Write output xls file... SRX3242030.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:28:52: #4 Write peak in narrowPeak format file... SRX3242030.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:28:52: #4 Write summits bed file... SRX3242030.20_summits.bed INFO @ Sat, 15 Sep 2018 10:28:52: Done! INFO @ Sat, 15 Sep 2018 10:28:52: #4 Write output xls file... SRX3242030.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:28:52: #4 Write peak in narrowPeak format file... SRX3242030.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:28:52: #4 Write summits bed file... SRX3242030.05_summits.bed INFO @ Sat, 15 Sep 2018 10:28:52: Done! INFO @ Sat, 15 Sep 2018 10:28:52: #4 Write output xls file... SRX3242030.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:28:52: #4 Write peak in narrowPeak format file... SRX3242030.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:28:52: #4 Write summits bed file... SRX3242030.10_summits.bed INFO @ Sat, 15 Sep 2018 10:28:52: Done! pass1 - making usageList (17 chroms): 12 millis pass1 - making usageList (17 chroms)pass1 - making usageList (17 chroms): 12 millis : 12 millis pass2 - checking and writing primary data (213 records, 4 fields): 11 millis pass2 - checking and writing primary data (471 records, 4 fields): 12 millis pass2 - checking and writing primary data (859 records, 4 fields): 12 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。