Job ID = 11192925 sra ファイルのダウンロード中... Completed: 518079K bytes transferred in 7 seconds (546257K 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 13642717 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3242040/SRR6129622.sra Written 13642717 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3242040/SRR6129622.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: 00:02:26 13642717 reads; of these: 13642717 (100.00%) were paired; of these: 13232294 (96.99%) aligned concordantly 0 times 333663 (2.45%) aligned concordantly exactly 1 time 76760 (0.56%) aligned concordantly >1 times ---- 13232294 pairs aligned concordantly 0 times; of these: 154730 (1.17%) aligned discordantly 1 time ---- 13077564 pairs aligned 0 times concordantly or discordantly; of these: 26155128 mates make up the pairs; of these: 24783563 (94.76%) aligned 0 times 1129718 (4.32%) aligned exactly 1 time 241847 (0.92%) aligned >1 times 9.17% overall alignment rate Time searching: 00:02:26 Overall time: 00:02:26 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] 132733 / 560611 = 0.2368 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 10:35:34: # Command line: callpeak -t SRX3242040.bam -f BAM -g 12100000 -n SRX3242040.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3242040.10 # format = BAM # ChIP-seq file = ['SRX3242040.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 10:35:34: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:35:34: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:35:34: # Command line: callpeak -t SRX3242040.bam -f BAM -g 12100000 -n SRX3242040.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3242040.20 # format = BAM # ChIP-seq file = ['SRX3242040.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 10:35:34: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:35:34: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:35:34: # Command line: callpeak -t SRX3242040.bam -f BAM -g 12100000 -n SRX3242040.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3242040.05 # format = BAM # ChIP-seq file = ['SRX3242040.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 10:35:34: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:35:34: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:35:38: 1000000 INFO @ Sat, 15 Sep 2018 10:35:38: 1000000 INFO @ Sat, 15 Sep 2018 10:35:38: 1000000 INFO @ Sat, 15 Sep 2018 10:35:43: 2000000 INFO @ Sat, 15 Sep 2018 10:35:43: 2000000 INFO @ Sat, 15 Sep 2018 10:35:43: 2000000 INFO @ Sat, 15 Sep 2018 10:35:44: #1 tag size is determined as 47 bps INFO @ Sat, 15 Sep 2018 10:35:44: #1 tag size = 47 INFO @ Sat, 15 Sep 2018 10:35:44: #1 total tags in treatment: 341893 INFO @ Sat, 15 Sep 2018 10:35:44: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:35:44: #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 10:35:44: #1 tags after filtering in treatment: 314273 INFO @ Sat, 15 Sep 2018 10:35:44: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Sep 2018 10:35:44: #1 finished! INFO @ Sat, 15 Sep 2018 10:35:44: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:35:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:35:44: #2 number of paired peaks: 188 WARNING @ Sat, 15 Sep 2018 10:35:44: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Sat, 15 Sep 2018 10:35:44: start model_add_line... INFO @ Sat, 15 Sep 2018 10:35:44: start X-correlation... INFO @ Sat, 15 Sep 2018 10:35:44: end of X-cor INFO @ Sat, 15 Sep 2018 10:35:44: #2 finished! INFO @ Sat, 15 Sep 2018 10:35:44: #2 predicted fragment length is 124 bps INFO @ Sat, 15 Sep 2018 10:35:44: #2 alternative fragment length(s) may be 124,525,568 bps INFO @ Sat, 15 Sep 2018 10:35:44: #2.2 Generate R script for model : SRX3242040.10_model.r INFO @ Sat, 15 Sep 2018 10:35:44: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:35:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:35:44: #1 tag size is determined as 47 bps INFO @ Sat, 15 Sep 2018 10:35:44: #1 tag size = 47 INFO @ Sat, 15 Sep 2018 10:35:44: #1 total tags in treatment: 341893 INFO @ Sat, 15 Sep 2018 10:35:44: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:35:44: #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 10:35:44: #1 tags after filtering in treatment: 314273 INFO @ Sat, 15 Sep 2018 10:35:44: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Sep 2018 10:35:44: #1 finished! INFO @ Sat, 15 Sep 2018 10:35:44: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:35:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:35:44: #2 number of paired peaks: 188 WARNING @ Sat, 15 Sep 2018 10:35:44: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Sat, 15 Sep 2018 10:35:44: start model_add_line... INFO @ Sat, 15 Sep 2018 10:35:44: start X-correlation... INFO @ Sat, 15 Sep 2018 10:35:45: end of X-cor INFO @ Sat, 15 Sep 2018 10:35:45: #2 finished! INFO @ Sat, 15 Sep 2018 10:35:45: #2 predicted fragment length is 124 bps INFO @ Sat, 15 Sep 2018 10:35:45: #2 alternative fragment length(s) may be 124,525,568 bps INFO @ Sat, 15 Sep 2018 10:35:45: #2.2 Generate R script for model : SRX3242040.05_model.r INFO @ Sat, 15 Sep 2018 10:35:45: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:35:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:35:45: #1 tag size is determined as 47 bps INFO @ Sat, 15 Sep 2018 10:35:45: #1 tag size = 47 INFO @ Sat, 15 Sep 2018 10:35:45: #1 total tags in treatment: 341893 INFO @ Sat, 15 Sep 2018 10:35:45: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:35:45: #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 10:35:45: #1 tags after filtering in treatment: 314273 INFO @ Sat, 15 Sep 2018 10:35:45: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Sep 2018 10:35:45: #1 finished! INFO @ Sat, 15 Sep 2018 10:35:45: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:35:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:35:45: #2 number of paired peaks: 188 WARNING @ Sat, 15 Sep 2018 10:35:45: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Sat, 15 Sep 2018 10:35:45: start model_add_line... INFO @ Sat, 15 Sep 2018 10:35:45: start X-correlation... INFO @ Sat, 15 Sep 2018 10:35:45: end of X-cor INFO @ Sat, 15 Sep 2018 10:35:45: #2 finished! INFO @ Sat, 15 Sep 2018 10:35:45: #2 predicted fragment length is 124 bps INFO @ Sat, 15 Sep 2018 10:35:45: #2 alternative fragment length(s) may be 124,525,568 bps INFO @ Sat, 15 Sep 2018 10:35:45: #2.2 Generate R script for model : SRX3242040.20_model.r INFO @ Sat, 15 Sep 2018 10:35:45: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:35:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:35:45: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:35:45: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:35:46: #4 Write output xls file... SRX3242040.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:35:46: #4 Write peak in narrowPeak format file... SRX3242040.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:35:46: #4 Write summits bed file... SRX3242040.10_summits.bed INFO @ Sat, 15 Sep 2018 10:35:46: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (62 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:35:46: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:35:46: #4 Write output xls file... SRX3242040.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:35:46: #4 Write peak in narrowPeak format file... SRX3242040.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:35:46: #4 Write summits bed file... SRX3242040.05_summits.bed INFO @ Sat, 15 Sep 2018 10:35:46: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (131 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:35:46: #4 Write output xls file... SRX3242040.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:35:46: #4 Write peak in narrowPeak format file... SRX3242040.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:35:46: #4 Write summits bed file... SRX3242040.20_summits.bed INFO @ Sat, 15 Sep 2018 10:35:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (34 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。