Job ID = 9160032 sra ファイルのダウンロード中... Completed: 33400K bytes transferred in 4 seconds (66008K bits/sec), in 1 file, 2 directories. 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... Written 1142427 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2574970/SRR5270919.sra Written 1142427 spots total 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: 00:01:23 1142427 reads; of these: 1142427 (100.00%) were paired; of these: 152270 (13.33%) aligned concordantly 0 times 179272 (15.69%) aligned concordantly exactly 1 time 810885 (70.98%) aligned concordantly >1 times ---- 152270 pairs aligned concordantly 0 times; of these: 1965 (1.29%) aligned discordantly 1 time ---- 150305 pairs aligned 0 times concordantly or discordantly; of these: 300610 mates make up the pairs; of these: 253250 (84.25%) aligned 0 times 8489 (2.82%) aligned exactly 1 time 38871 (12.93%) aligned >1 times 88.92% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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] 129327 / 944633 = 0.1369 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 @ Wed, 28 Jun 2017 01:44:01: # Command line: callpeak -t SRX2574970.bam -f BAM -g 12100000 -n SRX2574970.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2574970.10 # format = BAM # ChIP-seq file = ['SRX2574970.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 @ Wed, 28 Jun 2017 01:44:01: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:44:01: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:44:01: # Command line: callpeak -t SRX2574970.bam -f BAM -g 12100000 -n SRX2574970.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2574970.05 # format = BAM # ChIP-seq file = ['SRX2574970.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 @ Wed, 28 Jun 2017 01:44:01: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:44:01: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:44:01: # Command line: callpeak -t SRX2574970.bam -f BAM -g 12100000 -n SRX2574970.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2574970.20 # format = BAM # ChIP-seq file = ['SRX2574970.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 @ Wed, 28 Jun 2017 01:44:01: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:44:01: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:44:07: 1000000 INFO @ Wed, 28 Jun 2017 01:44:08: 1000000 INFO @ Wed, 28 Jun 2017 01:44:08: 1000000 INFO @ Wed, 28 Jun 2017 01:44:12: #1 tag size is determined as 26 bps INFO @ Wed, 28 Jun 2017 01:44:12: #1 tag size = 26 INFO @ Wed, 28 Jun 2017 01:44:12: #1 total tags in treatment: 860835 INFO @ Wed, 28 Jun 2017 01:44:12: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:44:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:44:12: #1 tags after filtering in treatment: 228679 INFO @ Wed, 28 Jun 2017 01:44:12: #1 Redundant rate of treatment: 0.73 INFO @ Wed, 28 Jun 2017 01:44:12: #1 finished! INFO @ Wed, 28 Jun 2017 01:44:12: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:44:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:44:12: #2 number of paired peaks: 286 WARNING @ Wed, 28 Jun 2017 01:44:12: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Wed, 28 Jun 2017 01:44:12: start model_add_line... INFO @ Wed, 28 Jun 2017 01:44:12: start X-correlation... INFO @ Wed, 28 Jun 2017 01:44:12: end of X-cor INFO @ Wed, 28 Jun 2017 01:44:12: #2 finished! INFO @ Wed, 28 Jun 2017 01:44:12: #2 predicted fragment length is 193 bps INFO @ Wed, 28 Jun 2017 01:44:12: #2 alternative fragment length(s) may be 193 bps INFO @ Wed, 28 Jun 2017 01:44:12: #2.2 Generate R script for model : SRX2574970.10_model.r INFO @ Wed, 28 Jun 2017 01:44:12: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:44:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:44:12: #1 tag size is determined as 26 bps INFO @ Wed, 28 Jun 2017 01:44:12: #1 tag size = 26 INFO @ Wed, 28 Jun 2017 01:44:12: #1 total tags in treatment: 860835 INFO @ Wed, 28 Jun 2017 01:44:12: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:44:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:44:12: #1 tags after filtering in treatment: 228679 INFO @ Wed, 28 Jun 2017 01:44:12: #1 Redundant rate of treatment: 0.73 INFO @ Wed, 28 Jun 2017 01:44:12: #1 finished! INFO @ Wed, 28 Jun 2017 01:44:12: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:44:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:44:12: #2 number of paired peaks: 286 WARNING @ Wed, 28 Jun 2017 01:44:12: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Wed, 28 Jun 2017 01:44:12: start model_add_line... INFO @ Wed, 28 Jun 2017 01:44:12: start X-correlation... INFO @ Wed, 28 Jun 2017 01:44:12: end of X-cor INFO @ Wed, 28 Jun 2017 01:44:12: #2 finished! INFO @ Wed, 28 Jun 2017 01:44:12: #2 predicted fragment length is 193 bps INFO @ Wed, 28 Jun 2017 01:44:12: #2 alternative fragment length(s) may be 193 bps INFO @ Wed, 28 Jun 2017 01:44:12: #2.2 Generate R script for model : SRX2574970.05_model.r INFO @ Wed, 28 Jun 2017 01:44:12: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:44:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:44:12: #1 tag size is determined as 26 bps INFO @ Wed, 28 Jun 2017 01:44:12: #1 tag size = 26 INFO @ Wed, 28 Jun 2017 01:44:12: #1 total tags in treatment: 860835 INFO @ Wed, 28 Jun 2017 01:44:12: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:44:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:44:12: #1 tags after filtering in treatment: 228679 INFO @ Wed, 28 Jun 2017 01:44:12: #1 Redundant rate of treatment: 0.73 INFO @ Wed, 28 Jun 2017 01:44:12: #1 finished! INFO @ Wed, 28 Jun 2017 01:44:12: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:44:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:44:13: #2 number of paired peaks: 286 WARNING @ Wed, 28 Jun 2017 01:44:13: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Wed, 28 Jun 2017 01:44:13: start model_add_line... INFO @ Wed, 28 Jun 2017 01:44:13: start X-correlation... INFO @ Wed, 28 Jun 2017 01:44:13: end of X-cor INFO @ Wed, 28 Jun 2017 01:44:13: #2 finished! INFO @ Wed, 28 Jun 2017 01:44:13: #2 predicted fragment length is 193 bps INFO @ Wed, 28 Jun 2017 01:44:13: #2 alternative fragment length(s) may be 193 bps INFO @ Wed, 28 Jun 2017 01:44:13: #2.2 Generate R script for model : SRX2574970.20_model.r INFO @ Wed, 28 Jun 2017 01:44:13: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:44:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:44:13: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 28 Jun 2017 01:44:13: #4 Write output xls file... SRX2574970.10_peaks.xls INFO @ Wed, 28 Jun 2017 01:44:13: #4 Write peak in narrowPeak format file... SRX2574970.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:44:13: #4 Write summits bed file... SRX2574970.10_summits.bed INFO @ Wed, 28 Jun 2017 01:44:13: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (326 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:44:13: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:44:14: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:44:14: #4 Write output xls file... SRX2574970.05_peaks.xls INFO @ Wed, 28 Jun 2017 01:44:14: #4 Write peak in narrowPeak format file... SRX2574970.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:44:14: #4 Write summits bed file... SRX2574970.05_summits.bed INFO @ Wed, 28 Jun 2017 01:44:14: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (468 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:44:14: #4 Write output xls file... SRX2574970.20_peaks.xls INFO @ Wed, 28 Jun 2017 01:44:14: #4 Write peak in narrowPeak format file... SRX2574970.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:44:14: #4 Write summits bed file... SRX2574970.20_summits.bed INFO @ Wed, 28 Jun 2017 01:44:14: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (135 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。