Job ID = 11388960 sra ファイルのダウンロード中... Completed: 203925K bytes transferred in 5 seconds (286385K 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 3509917 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5041903/SRR8223355.sra Written 3509917 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5041903/SRR8223355.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: 00:04:30 3509917 reads; of these: 3509917 (100.00%) were paired; of these: 1706807 (48.63%) aligned concordantly 0 times 1549061 (44.13%) aligned concordantly exactly 1 time 254049 (7.24%) aligned concordantly >1 times ---- 1706807 pairs aligned concordantly 0 times; of these: 8921 (0.52%) aligned discordantly 1 time ---- 1697886 pairs aligned 0 times concordantly or discordantly; of these: 3395772 mates make up the pairs; of these: 2986551 (87.95%) aligned 0 times 391706 (11.54%) aligned exactly 1 time 17515 (0.52%) aligned >1 times 57.46% overall alignment rate Time searching: 00:04:30 Overall time: 00:04:30 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] 1612545 / 1811458 = 0.8902 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 @ Thu, 13 Dec 2018 00:29:06: # Command line: callpeak -t SRX5041903.bam -f BAM -g 12100000 -n SRX5041903.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5041903.20 # format = BAM # ChIP-seq file = ['SRX5041903.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 @ Thu, 13 Dec 2018 00:29:06: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:29:06: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:29:06: # Command line: callpeak -t SRX5041903.bam -f BAM -g 12100000 -n SRX5041903.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5041903.10 # format = BAM # ChIP-seq file = ['SRX5041903.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 @ Thu, 13 Dec 2018 00:29:06: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:29:06: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:29:06: # Command line: callpeak -t SRX5041903.bam -f BAM -g 12100000 -n SRX5041903.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5041903.05 # format = BAM # ChIP-seq file = ['SRX5041903.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 @ Thu, 13 Dec 2018 00:29:06: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:29:06: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:29:13: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 00:29:13: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 00:29:13: #1 total tags in treatment: 195458 INFO @ Thu, 13 Dec 2018 00:29:13: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:29:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:29:13: #1 tags after filtering in treatment: 171440 INFO @ Thu, 13 Dec 2018 00:29:13: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 13 Dec 2018 00:29:13: #1 finished! INFO @ Thu, 13 Dec 2018 00:29:13: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:29:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:29:13: #2 number of paired peaks: 206 WARNING @ Thu, 13 Dec 2018 00:29:13: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Thu, 13 Dec 2018 00:29:13: start model_add_line... INFO @ Thu, 13 Dec 2018 00:29:13: start X-correlation... INFO @ Thu, 13 Dec 2018 00:29:13: end of X-cor INFO @ Thu, 13 Dec 2018 00:29:13: #2 finished! INFO @ Thu, 13 Dec 2018 00:29:13: #2 predicted fragment length is 174 bps INFO @ Thu, 13 Dec 2018 00:29:13: #2 alternative fragment length(s) may be 174 bps INFO @ Thu, 13 Dec 2018 00:29:13: #2.2 Generate R script for model : SRX5041903.10_model.r INFO @ Thu, 13 Dec 2018 00:29:13: #3 Call peaks... INFO @ Thu, 13 Dec 2018 00:29:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 00:29:14: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 00:29:14: #4 Write output xls file... SRX5041903.10_peaks.xls INFO @ Thu, 13 Dec 2018 00:29:14: #4 Write peak in narrowPeak format file... SRX5041903.10_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 00:29:14: #4 Write summits bed file... SRX5041903.10_summits.bed INFO @ Thu, 13 Dec 2018 00:29:14: Done! INFO @ Thu, 13 Dec 2018 00:29:14: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 00:29:14: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 00:29:14: #1 total tags in treatment: 195458 INFO @ Thu, 13 Dec 2018 00:29:14: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:29:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:29:14: #1 tags after filtering in treatment: 171440 INFO @ Thu, 13 Dec 2018 00:29:14: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 13 Dec 2018 00:29:14: #1 finished! INFO @ Thu, 13 Dec 2018 00:29:14: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:29:14: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (13 chroms): 2 millis INFO @ Thu, 13 Dec 2018 00:29:14: #2 number of paired peaks: 206 WARNING @ Thu, 13 Dec 2018 00:29:14: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Thu, 13 Dec 2018 00:29:14: start model_add_line... pass2 - checking and writing primary data (56 records, 4 fields): 4 millis INFO @ Thu, 13 Dec 2018 00:29:14: start X-correlation... CompletedMACS2peakCalling INFO @ Thu, 13 Dec 2018 00:29:14: end of X-cor INFO @ Thu, 13 Dec 2018 00:29:14: #2 finished! INFO @ Thu, 13 Dec 2018 00:29:14: #2 predicted fragment length is 174 bps INFO @ Thu, 13 Dec 2018 00:29:14: #2 alternative fragment length(s) may be 174 bps INFO @ Thu, 13 Dec 2018 00:29:14: #2.2 Generate R script for model : SRX5041903.20_model.r INFO @ Thu, 13 Dec 2018 00:29:14: #3 Call peaks... INFO @ Thu, 13 Dec 2018 00:29:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 00:29:15: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 00:29:15: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 00:29:15: #1 total tags in treatment: 195458 INFO @ Thu, 13 Dec 2018 00:29:15: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:29:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:29:15: #1 tags after filtering in treatment: 171440 INFO @ Thu, 13 Dec 2018 00:29:15: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 13 Dec 2018 00:29:15: #1 finished! INFO @ Thu, 13 Dec 2018 00:29:15: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:29:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:29:15: #2 number of paired peaks: 206 WARNING @ Thu, 13 Dec 2018 00:29:15: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Thu, 13 Dec 2018 00:29:15: start model_add_line... INFO @ Thu, 13 Dec 2018 00:29:15: start X-correlation... INFO @ Thu, 13 Dec 2018 00:29:15: end of X-cor INFO @ Thu, 13 Dec 2018 00:29:15: #2 finished! INFO @ Thu, 13 Dec 2018 00:29:15: #2 predicted fragment length is 174 bps INFO @ Thu, 13 Dec 2018 00:29:15: #2 alternative fragment length(s) may be 174 bps INFO @ Thu, 13 Dec 2018 00:29:15: #2.2 Generate R script for model : SRX5041903.05_model.r INFO @ Thu, 13 Dec 2018 00:29:15: #3 Call peaks... INFO @ Thu, 13 Dec 2018 00:29:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 00:29:15: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 00:29:16: #4 Write output xls file... SRX5041903.20_peaks.xls INFO @ Thu, 13 Dec 2018 00:29:16: #4 Write peak in narrowPeak format file... SRX5041903.20_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 00:29:16: #4 Write summits bed file... SRX5041903.20_summits.bed INFO @ Thu, 13 Dec 2018 00:29:16: Done! pass1 - making usageList (2 chroms): 2 millis pass2 - checking and writing primary data (4 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 13 Dec 2018 00:29:16: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 00:29:16: #4 Write output xls file... SRX5041903.05_peaks.xls INFO @ Thu, 13 Dec 2018 00:29:16: #4 Write peak in narrowPeak format file... SRX5041903.05_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 00:29:16: #4 Write summits bed file... SRX5041903.05_summits.bed INFO @ Thu, 13 Dec 2018 00:29:16: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (126 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。