Job ID = 11244899 sra ファイルのダウンロード中... Completed: 86989K bytes transferred in 4 seconds (172939K 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 1724314 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4456768/SRR7591553.sra Written 1724314 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4456768/SRR7591553.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: 00:01:22 1724314 reads; of these: 1724314 (100.00%) were paired; of these: 258476 (14.99%) aligned concordantly 0 times 1353611 (78.50%) aligned concordantly exactly 1 time 112227 (6.51%) aligned concordantly >1 times ---- 258476 pairs aligned concordantly 0 times; of these: 53237 (20.60%) aligned discordantly 1 time ---- 205239 pairs aligned 0 times concordantly or discordantly; of these: 410478 mates make up the pairs; of these: 372620 (90.78%) aligned 0 times 23301 (5.68%) aligned exactly 1 time 14557 (3.55%) aligned >1 times 89.20% overall alignment rate Time searching: 00:01:22 Overall time: 00:01:22 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] 36081 / 1517163 = 0.0238 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 22:41:59: # Command line: callpeak -t SRX4456768.bam -f BAM -g 12100000 -n SRX4456768.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4456768.10 # format = BAM # ChIP-seq file = ['SRX4456768.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 22:41:59: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:41:59: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:41:59: # Command line: callpeak -t SRX4456768.bam -f BAM -g 12100000 -n SRX4456768.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4456768.05 # format = BAM # ChIP-seq file = ['SRX4456768.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 22:41:59: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:41:59: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:41:59: # Command line: callpeak -t SRX4456768.bam -f BAM -g 12100000 -n SRX4456768.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4456768.20 # format = BAM # ChIP-seq file = ['SRX4456768.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 22:41:59: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:41:59: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:42:05: 1000000 INFO @ Tue, 09 Oct 2018 22:42:06: 1000000 INFO @ Tue, 09 Oct 2018 22:42:06: 1000000 INFO @ Tue, 09 Oct 2018 22:42:12: 2000000 INFO @ Tue, 09 Oct 2018 22:42:13: 2000000 INFO @ Tue, 09 Oct 2018 22:42:13: 2000000 INFO @ Tue, 09 Oct 2018 22:42:19: 3000000 INFO @ Tue, 09 Oct 2018 22:42:19: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:42:19: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:42:19: #1 total tags in treatment: 1429957 INFO @ Tue, 09 Oct 2018 22:42:19: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:42:19: #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 22:42:19: #1 tags after filtering in treatment: 1128103 INFO @ Tue, 09 Oct 2018 22:42:19: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 09 Oct 2018 22:42:19: #1 finished! INFO @ Tue, 09 Oct 2018 22:42:19: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:42:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:42:19: #2 number of paired peaks: 309 WARNING @ Tue, 09 Oct 2018 22:42:19: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Tue, 09 Oct 2018 22:42:19: start model_add_line... INFO @ Tue, 09 Oct 2018 22:42:19: start X-correlation... INFO @ Tue, 09 Oct 2018 22:42:19: end of X-cor INFO @ Tue, 09 Oct 2018 22:42:19: #2 finished! INFO @ Tue, 09 Oct 2018 22:42:19: #2 predicted fragment length is 217 bps INFO @ Tue, 09 Oct 2018 22:42:19: #2 alternative fragment length(s) may be 217 bps INFO @ Tue, 09 Oct 2018 22:42:19: #2.2 Generate R script for model : SRX4456768.05_model.r INFO @ Tue, 09 Oct 2018 22:42:19: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:42:19: 3000000 INFO @ Tue, 09 Oct 2018 22:42:19: 3000000 INFO @ Tue, 09 Oct 2018 22:42:19: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:42:19: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:42:19: #1 total tags in treatment: 1429957 INFO @ Tue, 09 Oct 2018 22:42:19: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:42:19: #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 22:42:19: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:42:19: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:42:19: #1 total tags in treatment: 1429957 INFO @ Tue, 09 Oct 2018 22:42:19: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:42:19: #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 22:42:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:42:20: #1 tags after filtering in treatment: 1128103 INFO @ Tue, 09 Oct 2018 22:42:20: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 09 Oct 2018 22:42:20: #1 finished! INFO @ Tue, 09 Oct 2018 22:42:20: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:42:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:42:20: #1 tags after filtering in treatment: 1128103 INFO @ Tue, 09 Oct 2018 22:42:20: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 09 Oct 2018 22:42:20: #1 finished! INFO @ Tue, 09 Oct 2018 22:42:20: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:42:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:42:20: #2 number of paired peaks: 309 WARNING @ Tue, 09 Oct 2018 22:42:20: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Tue, 09 Oct 2018 22:42:20: start model_add_line... INFO @ Tue, 09 Oct 2018 22:42:20: #2 number of paired peaks: 309 WARNING @ Tue, 09 Oct 2018 22:42:20: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Tue, 09 Oct 2018 22:42:20: start model_add_line... INFO @ Tue, 09 Oct 2018 22:42:20: start X-correlation... INFO @ Tue, 09 Oct 2018 22:42:20: start X-correlation... INFO @ Tue, 09 Oct 2018 22:42:20: end of X-cor INFO @ Tue, 09 Oct 2018 22:42:20: #2 finished! INFO @ Tue, 09 Oct 2018 22:42:20: #2 predicted fragment length is 217 bps INFO @ Tue, 09 Oct 2018 22:42:20: #2 alternative fragment length(s) may be 217 bps INFO @ Tue, 09 Oct 2018 22:42:20: #2.2 Generate R script for model : SRX4456768.20_model.r INFO @ Tue, 09 Oct 2018 22:42:20: end of X-cor INFO @ Tue, 09 Oct 2018 22:42:20: #2 finished! INFO @ Tue, 09 Oct 2018 22:42:20: #2 predicted fragment length is 217 bps INFO @ Tue, 09 Oct 2018 22:42:20: #2 alternative fragment length(s) may be 217 bps INFO @ Tue, 09 Oct 2018 22:42:20: #2.2 Generate R script for model : SRX4456768.10_model.r INFO @ Tue, 09 Oct 2018 22:42:20: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:42:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:42:20: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:42:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:42:24: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:42:24: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:42:24: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:42:26: #4 Write output xls file... SRX4456768.05_peaks.xls INFO @ Tue, 09 Oct 2018 22:42:26: #4 Write peak in narrowPeak format file... SRX4456768.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:42:26: #4 Write summits bed file... SRX4456768.05_summits.bed INFO @ Tue, 09 Oct 2018 22:42:26: Done! INFO @ Tue, 09 Oct 2018 22:42:26: #4 Write output xls file... SRX4456768.20_peaks.xls INFO @ Tue, 09 Oct 2018 22:42:26: #4 Write peak in narrowPeak format file... SRX4456768.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:42:26: #4 Write summits bed file... SRX4456768.20_summits.bed INFO @ Tue, 09 Oct 2018 22:42:26: Done! pass1 - making usageList (17 chroms): 0 millis pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (276 records, 4 fields): 27 millis pass2 - checking and writing primary data (801 records, 4 fields): 47 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 22:42:26: #4 Write output xls file... SRX4456768.10_peaks.xls INFO @ Tue, 09 Oct 2018 22:42:26: #4 Write peak in narrowPeak format file... SRX4456768.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:42:26: #4 Write summits bed file... SRX4456768.10_summits.bed INFO @ Tue, 09 Oct 2018 22:42:26: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (526 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。