Job ID = 10937548 sra ファイルのダウンロード中... Completed: 557883K bytes transferred in 80 seconds (56867K bits/sec), in 1 file. Completed: 1021548K bytes transferred in 52 seconds (160180K 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 5710765 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010338/SRR5833337.sra Written 5710765 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010338/SRR5833337.sra Read 11100383 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010338/SRR5833338.sra Written 11100383 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010338/SRR5833338.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 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: 00:04:22 16811148 reads; of these: 16811148 (100.00%) were paired; of these: 15603222 (92.81%) aligned concordantly 0 times 926317 (5.51%) aligned concordantly exactly 1 time 281609 (1.68%) aligned concordantly >1 times ---- 15603222 pairs aligned concordantly 0 times; of these: 9000 (0.06%) aligned discordantly 1 time ---- 15594222 pairs aligned 0 times concordantly or discordantly; of these: 31188444 mates make up the pairs; of these: 31160205 (99.91%) aligned 0 times 16953 (0.05%) aligned exactly 1 time 11286 (0.04%) aligned >1 times 7.32% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 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] 171058 / 1216340 = 0.1406 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 @ Fri, 10 Aug 2018 02:42:14: # Command line: callpeak -t SRX3010338.bam -f BAM -g 12100000 -n SRX3010338.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3010338.20 # format = BAM # ChIP-seq file = ['SRX3010338.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 @ Fri, 10 Aug 2018 02:42:14: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:42:14: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:42:14: # Command line: callpeak -t SRX3010338.bam -f BAM -g 12100000 -n SRX3010338.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3010338.05 # format = BAM # ChIP-seq file = ['SRX3010338.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 @ Fri, 10 Aug 2018 02:42:14: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:42:14: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:42:14: # Command line: callpeak -t SRX3010338.bam -f BAM -g 12100000 -n SRX3010338.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3010338.10 # format = BAM # ChIP-seq file = ['SRX3010338.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 @ Fri, 10 Aug 2018 02:42:14: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:42:14: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:42:23: 1000000 INFO @ Fri, 10 Aug 2018 02:42:25: 1000000 INFO @ Fri, 10 Aug 2018 02:42:25: 1000000 INFO @ Fri, 10 Aug 2018 02:42:32: 2000000 INFO @ Fri, 10 Aug 2018 02:42:33: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:42:33: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:42:33: #1 total tags in treatment: 1037490 INFO @ Fri, 10 Aug 2018 02:42:33: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:42:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:42:33: #1 tags after filtering in treatment: 802270 INFO @ Fri, 10 Aug 2018 02:42:33: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 10 Aug 2018 02:42:33: #1 finished! INFO @ Fri, 10 Aug 2018 02:42:33: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:42:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:42:33: #2 number of paired peaks: 179 WARNING @ Fri, 10 Aug 2018 02:42:33: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Fri, 10 Aug 2018 02:42:33: start model_add_line... INFO @ Fri, 10 Aug 2018 02:42:33: start X-correlation... INFO @ Fri, 10 Aug 2018 02:42:33: end of X-cor INFO @ Fri, 10 Aug 2018 02:42:33: #2 finished! INFO @ Fri, 10 Aug 2018 02:42:33: #2 predicted fragment length is 217 bps INFO @ Fri, 10 Aug 2018 02:42:33: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 10 Aug 2018 02:42:33: #2.2 Generate R script for model : SRX3010338.20_model.r INFO @ Fri, 10 Aug 2018 02:42:33: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:42:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:42:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:42:37: #4 Write output xls file... SRX3010338.20_peaks.xls INFO @ Fri, 10 Aug 2018 02:42:37: #4 Write peak in narrowPeak format file... SRX3010338.20_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:42:37: #4 Write summits bed file... SRX3010338.20_summits.bed INFO @ Fri, 10 Aug 2018 02:42:37: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (61 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:42:37: 2000000 INFO @ Fri, 10 Aug 2018 02:42:37: 2000000 INFO @ Fri, 10 Aug 2018 02:42:38: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:42:38: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:42:38: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:42:38: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:42:38: #1 total tags in treatment: 1037490 INFO @ Fri, 10 Aug 2018 02:42:38: #1 total tags in treatment: 1037490 INFO @ Fri, 10 Aug 2018 02:42:38: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:42:38: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:42:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:42:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:42:38: #1 tags after filtering in treatment: 802270 INFO @ Fri, 10 Aug 2018 02:42:38: #1 tags after filtering in treatment: 802270 INFO @ Fri, 10 Aug 2018 02:42:38: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 10 Aug 2018 02:42:38: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 10 Aug 2018 02:42:38: #1 finished! INFO @ Fri, 10 Aug 2018 02:42:38: #1 finished! INFO @ Fri, 10 Aug 2018 02:42:38: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:42:38: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:42:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:42:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:42:38: #2 number of paired peaks: 179 INFO @ Fri, 10 Aug 2018 02:42:38: #2 number of paired peaks: 179 WARNING @ Fri, 10 Aug 2018 02:42:38: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! WARNING @ Fri, 10 Aug 2018 02:42:38: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Fri, 10 Aug 2018 02:42:38: start model_add_line... INFO @ Fri, 10 Aug 2018 02:42:38: start model_add_line... INFO @ Fri, 10 Aug 2018 02:42:38: start X-correlation... INFO @ Fri, 10 Aug 2018 02:42:38: start X-correlation... INFO @ Fri, 10 Aug 2018 02:42:38: end of X-cor INFO @ Fri, 10 Aug 2018 02:42:38: end of X-cor INFO @ Fri, 10 Aug 2018 02:42:38: #2 finished! INFO @ Fri, 10 Aug 2018 02:42:38: #2 finished! INFO @ Fri, 10 Aug 2018 02:42:38: #2 predicted fragment length is 217 bps INFO @ Fri, 10 Aug 2018 02:42:38: #2 predicted fragment length is 217 bps INFO @ Fri, 10 Aug 2018 02:42:38: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 10 Aug 2018 02:42:38: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 10 Aug 2018 02:42:38: #2.2 Generate R script for model : SRX3010338.05_model.r INFO @ Fri, 10 Aug 2018 02:42:38: #2.2 Generate R script for model : SRX3010338.10_model.r INFO @ Fri, 10 Aug 2018 02:42:38: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:42:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:42:38: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:42:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:42:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:42:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:42:42: #4 Write output xls file... SRX3010338.10_peaks.xls INFO @ Fri, 10 Aug 2018 02:42:42: #4 Write peak in narrowPeak format file... SRX3010338.10_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:42:42: #4 Write summits bed file... SRX3010338.10_summits.bed INFO @ Fri, 10 Aug 2018 02:42:42: Done! INFO @ Fri, 10 Aug 2018 02:42:42: #4 Write output xls file... SRX3010338.05_peaks.xls INFO @ Fri, 10 Aug 2018 02:42:42: #4 Write peak in narrowPeak format file... SRX3010338.05_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:42:42: #4 Write summits bed file... SRX3010338.05_summits.bed INFO @ Fri, 10 Aug 2018 02:42:42: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (149 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (353 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。