Job ID = 11244931 sra ファイルのダウンロード中... Completed: 122214K bytes transferred in 5 seconds (193173K 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 4289015 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554668/SRR7696341.sra Written 4289015 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554668/SRR7696341.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: 00:02:38 4289015 reads; of these: 4289015 (100.00%) were paired; of these: 3092571 (72.10%) aligned concordantly 0 times 1014872 (23.66%) aligned concordantly exactly 1 time 181572 (4.23%) aligned concordantly >1 times ---- 3092571 pairs aligned concordantly 0 times; of these: 9719 (0.31%) aligned discordantly 1 time ---- 3082852 pairs aligned 0 times concordantly or discordantly; of these: 6165704 mates make up the pairs; of these: 4408246 (71.50%) aligned 0 times 1500141 (24.33%) aligned exactly 1 time 257317 (4.17%) aligned >1 times 48.61% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 71679 / 1205761 = 0.0594 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 22:55:32: # Command line: callpeak -t SRX4554668.bam -f BAM -g 12100000 -n SRX4554668.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554668.05 # format = BAM # ChIP-seq file = ['SRX4554668.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 22:55:32: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:55:32: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:55:32: # Command line: callpeak -t SRX4554668.bam -f BAM -g 12100000 -n SRX4554668.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554668.10 # format = BAM # ChIP-seq file = ['SRX4554668.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 22:55:32: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:55:32: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:55:32: # Command line: callpeak -t SRX4554668.bam -f BAM -g 12100000 -n SRX4554668.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554668.20 # format = BAM # ChIP-seq file = ['SRX4554668.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 22:55:32: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:55:32: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:55:38: 1000000 INFO @ Tue, 09 Oct 2018 22:55:38: 1000000 INFO @ Tue, 09 Oct 2018 22:55:38: 1000000 INFO @ Tue, 09 Oct 2018 22:55:43: 2000000 INFO @ Tue, 09 Oct 2018 22:55:43: 2000000 INFO @ Tue, 09 Oct 2018 22:55:43: 2000000 INFO @ Tue, 09 Oct 2018 22:55:49: 3000000 INFO @ Tue, 09 Oct 2018 22:55:49: 3000000 INFO @ Tue, 09 Oct 2018 22:55:49: 3000000 INFO @ Tue, 09 Oct 2018 22:55:54: 4000000 INFO @ Tue, 09 Oct 2018 22:55:55: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:55:55: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:55:55: #1 total tags in treatment: 1125053 INFO @ Tue, 09 Oct 2018 22:55:55: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:55:55: #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 22:55:55: #1 tags after filtering in treatment: 786613 INFO @ Tue, 09 Oct 2018 22:55:55: #1 Redundant rate of treatment: 0.30 INFO @ Tue, 09 Oct 2018 22:55:55: #1 finished! INFO @ Tue, 09 Oct 2018 22:55:55: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:55:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:55:55: #2 number of paired peaks: 535 WARNING @ Tue, 09 Oct 2018 22:55:55: Fewer paired peaks (535) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 535 pairs to build model! INFO @ Tue, 09 Oct 2018 22:55:55: start model_add_line... INFO @ Tue, 09 Oct 2018 22:55:55: start X-correlation... INFO @ Tue, 09 Oct 2018 22:55:55: end of X-cor INFO @ Tue, 09 Oct 2018 22:55:55: #2 finished! INFO @ Tue, 09 Oct 2018 22:55:55: #2 predicted fragment length is 196 bps INFO @ Tue, 09 Oct 2018 22:55:55: #2 alternative fragment length(s) may be 1,196,232,248 bps INFO @ Tue, 09 Oct 2018 22:55:55: #2.2 Generate R script for model : SRX4554668.10_model.r INFO @ Tue, 09 Oct 2018 22:55:55: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:55:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:55:55: 4000000 INFO @ Tue, 09 Oct 2018 22:55:55: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:55:55: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:55:55: #1 total tags in treatment: 1125053 INFO @ Tue, 09 Oct 2018 22:55:55: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:55:55: #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 22:55:55: #1 tags after filtering in treatment: 786613 INFO @ Tue, 09 Oct 2018 22:55:55: #1 Redundant rate of treatment: 0.30 INFO @ Tue, 09 Oct 2018 22:55:55: #1 finished! INFO @ Tue, 09 Oct 2018 22:55:55: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:55:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:55:55: #2 number of paired peaks: 535 WARNING @ Tue, 09 Oct 2018 22:55:55: Fewer paired peaks (535) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 535 pairs to build model! INFO @ Tue, 09 Oct 2018 22:55:55: start model_add_line... INFO @ Tue, 09 Oct 2018 22:55:55: start X-correlation... INFO @ Tue, 09 Oct 2018 22:55:55: end of X-cor INFO @ Tue, 09 Oct 2018 22:55:55: #2 finished! INFO @ Tue, 09 Oct 2018 22:55:55: #2 predicted fragment length is 196 bps INFO @ Tue, 09 Oct 2018 22:55:55: #2 alternative fragment length(s) may be 1,196,232,248 bps INFO @ Tue, 09 Oct 2018 22:55:55: #2.2 Generate R script for model : SRX4554668.20_model.r INFO @ Tue, 09 Oct 2018 22:55:55: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:55:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:55:55: 4000000 INFO @ Tue, 09 Oct 2018 22:55:56: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:55:56: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:55:56: #1 total tags in treatment: 1125053 INFO @ Tue, 09 Oct 2018 22:55:56: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:55:56: #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 22:55:56: #1 tags after filtering in treatment: 786613 INFO @ Tue, 09 Oct 2018 22:55:56: #1 Redundant rate of treatment: 0.30 INFO @ Tue, 09 Oct 2018 22:55:56: #1 finished! INFO @ Tue, 09 Oct 2018 22:55:56: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:55:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:55:56: #2 number of paired peaks: 535 WARNING @ Tue, 09 Oct 2018 22:55:56: Fewer paired peaks (535) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 535 pairs to build model! INFO @ Tue, 09 Oct 2018 22:55:56: start model_add_line... INFO @ Tue, 09 Oct 2018 22:55:56: start X-correlation... INFO @ Tue, 09 Oct 2018 22:55:56: end of X-cor INFO @ Tue, 09 Oct 2018 22:55:56: #2 finished! INFO @ Tue, 09 Oct 2018 22:55:56: #2 predicted fragment length is 196 bps INFO @ Tue, 09 Oct 2018 22:55:56: #2 alternative fragment length(s) may be 1,196,232,248 bps INFO @ Tue, 09 Oct 2018 22:55:56: #2.2 Generate R script for model : SRX4554668.05_model.r INFO @ Tue, 09 Oct 2018 22:55:56: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:55:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:56:00: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:56:01: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:56:01: #4 Write output xls file... SRX4554668.10_peaks.xls INFO @ Tue, 09 Oct 2018 22:56:01: #4 Write peak in narrowPeak format file... SRX4554668.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:56:01: #4 Write summits bed file... SRX4554668.10_summits.bed INFO @ Tue, 09 Oct 2018 22:56:01: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (312 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 22:56:01: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:56:01: #4 Write output xls file... SRX4554668.20_peaks.xls INFO @ Tue, 09 Oct 2018 22:56:01: #4 Write peak in narrowPeak format file... SRX4554668.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:56:01: #4 Write summits bed file... SRX4554668.20_summits.bed INFO @ Tue, 09 Oct 2018 22:56:01: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (259 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 22:56:02: #4 Write output xls file... SRX4554668.05_peaks.xls INFO @ Tue, 09 Oct 2018 22:56:02: #4 Write peak in narrowPeak format file... SRX4554668.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:56:02: #4 Write summits bed file... SRX4554668.05_summits.bed INFO @ Tue, 09 Oct 2018 22:56:02: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (389 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。