Job ID = 11244953 sra ファイルのダウンロード中... Completed: 77296K bytes transferred in 4 seconds (146966K 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 2376110 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554683/SRR7696356.sra Written 2376110 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554683/SRR7696356.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: 00:00:41 2376110 reads; of these: 2376110 (100.00%) were paired; of these: 1660569 (69.89%) aligned concordantly 0 times 418758 (17.62%) aligned concordantly exactly 1 time 296783 (12.49%) aligned concordantly >1 times ---- 1660569 pairs aligned concordantly 0 times; of these: 10520 (0.63%) aligned discordantly 1 time ---- 1650049 pairs aligned 0 times concordantly or discordantly; of these: 3300098 mates make up the pairs; of these: 3259297 (98.76%) aligned 0 times 15032 (0.46%) aligned exactly 1 time 25769 (0.78%) aligned >1 times 31.42% overall alignment rate Time searching: 00:00:41 Overall time: 00:00:41 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] 20376 / 723508 = 0.0282 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 @ Tue, 09 Oct 2018 22:56:48: # Command line: callpeak -t SRX4554683.bam -f BAM -g 12100000 -n SRX4554683.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554683.05 # format = BAM # ChIP-seq file = ['SRX4554683.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 @ Tue, 09 Oct 2018 22:56:48: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:56:48: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:56:48: # Command line: callpeak -t SRX4554683.bam -f BAM -g 12100000 -n SRX4554683.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554683.20 # format = BAM # ChIP-seq file = ['SRX4554683.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 @ Tue, 09 Oct 2018 22:56:48: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:56:48: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:56:48: # Command line: callpeak -t SRX4554683.bam -f BAM -g 12100000 -n SRX4554683.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554683.10 # format = BAM # ChIP-seq file = ['SRX4554683.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 @ Tue, 09 Oct 2018 22:56:48: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:56:48: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:56:53: 1000000 INFO @ Tue, 09 Oct 2018 22:56:53: 1000000 INFO @ Tue, 09 Oct 2018 22:56:53: 1000000 INFO @ Tue, 09 Oct 2018 22:56:56: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:56:56: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:56:56: #1 total tags in treatment: 695318 INFO @ Tue, 09 Oct 2018 22:56:56: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:56:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:56:56: #1 tags after filtering in treatment: 433388 INFO @ Tue, 09 Oct 2018 22:56:56: #1 Redundant rate of treatment: 0.38 INFO @ Tue, 09 Oct 2018 22:56:56: #1 finished! INFO @ Tue, 09 Oct 2018 22:56:56: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:56:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:56:56: #2 number of paired peaks: 168 WARNING @ Tue, 09 Oct 2018 22:56:56: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Tue, 09 Oct 2018 22:56:56: start model_add_line... INFO @ Tue, 09 Oct 2018 22:56:56: start X-correlation... INFO @ Tue, 09 Oct 2018 22:56:56: end of X-cor INFO @ Tue, 09 Oct 2018 22:56:56: #2 finished! INFO @ Tue, 09 Oct 2018 22:56:56: #2 predicted fragment length is 113 bps INFO @ Tue, 09 Oct 2018 22:56:56: #2 alternative fragment length(s) may be 3,113,549 bps INFO @ Tue, 09 Oct 2018 22:56:56: #2.2 Generate R script for model : SRX4554683.10_model.r INFO @ Tue, 09 Oct 2018 22:56:56: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:56:56: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:56:56: #1 total tags in treatment: 695318 INFO @ Tue, 09 Oct 2018 22:56:56: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:56:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:56:56: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:56:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:56:56: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:56:56: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:56:56: #1 total tags in treatment: 695318 INFO @ Tue, 09 Oct 2018 22:56:56: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:56:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:56:56: #1 tags after filtering in treatment: 433388 INFO @ Tue, 09 Oct 2018 22:56:56: #1 Redundant rate of treatment: 0.38 INFO @ Tue, 09 Oct 2018 22:56:56: #1 finished! INFO @ Tue, 09 Oct 2018 22:56:56: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:56:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:56:56: #1 tags after filtering in treatment: 433388 INFO @ Tue, 09 Oct 2018 22:56:56: #1 Redundant rate of treatment: 0.38 INFO @ Tue, 09 Oct 2018 22:56:56: #1 finished! INFO @ Tue, 09 Oct 2018 22:56:56: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:56:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:56:56: #2 number of paired peaks: 168 WARNING @ Tue, 09 Oct 2018 22:56:56: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Tue, 09 Oct 2018 22:56:56: start model_add_line... INFO @ Tue, 09 Oct 2018 22:56:56: start X-correlation... INFO @ Tue, 09 Oct 2018 22:56:56: #2 number of paired peaks: 168 INFO @ Tue, 09 Oct 2018 22:56:56: end of X-cor WARNING @ Tue, 09 Oct 2018 22:56:56: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Tue, 09 Oct 2018 22:56:56: #2 finished! INFO @ Tue, 09 Oct 2018 22:56:56: start model_add_line... INFO @ Tue, 09 Oct 2018 22:56:56: #2 predicted fragment length is 113 bps INFO @ Tue, 09 Oct 2018 22:56:56: #2 alternative fragment length(s) may be 3,113,549 bps INFO @ Tue, 09 Oct 2018 22:56:56: #2.2 Generate R script for model : SRX4554683.20_model.r INFO @ Tue, 09 Oct 2018 22:56:56: start X-correlation... INFO @ Tue, 09 Oct 2018 22:56:56: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:56:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:56:56: end of X-cor INFO @ Tue, 09 Oct 2018 22:56:56: #2 finished! INFO @ Tue, 09 Oct 2018 22:56:56: #2 predicted fragment length is 113 bps INFO @ Tue, 09 Oct 2018 22:56:56: #2 alternative fragment length(s) may be 3,113,549 bps INFO @ Tue, 09 Oct 2018 22:56:56: #2.2 Generate R script for model : SRX4554683.05_model.r INFO @ Tue, 09 Oct 2018 22:56:56: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:56:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:56:57: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:56:57: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:56:58: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:56:58: #4 Write output xls file... SRX4554683.10_peaks.xls INFO @ Tue, 09 Oct 2018 22:56:58: #4 Write peak in narrowPeak format file... SRX4554683.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:56:58: #4 Write summits bed file... SRX4554683.10_summits.bed INFO @ Tue, 09 Oct 2018 22:56:58: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (27 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 22:56:58: #4 Write output xls file... SRX4554683.20_peaks.xls INFO @ Tue, 09 Oct 2018 22:56:58: #4 Write peak in narrowPeak format file... SRX4554683.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:56:58: #4 Write summits bed file... SRX4554683.20_summits.bed INFO @ Tue, 09 Oct 2018 22:56:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 22:56:58: #4 Write output xls file... SRX4554683.05_peaks.xls INFO @ Tue, 09 Oct 2018 22:56:58: #4 Write peak in narrowPeak format file... SRX4554683.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:56:58: #4 Write summits bed file... SRX4554683.05_summits.bed INFO @ Tue, 09 Oct 2018 22:56:58: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (79 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。