Job ID = 9162518 sra ファイルのダウンロード中... Completed: 193122K bytes transferred in 4 seconds (318806K 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 2767539 spots for /home/okishinya/chipatlas/results/sacCer3/SRX360915/SRR1003637.sra Written 2767539 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: 00:01:42 2767539 reads; of these: 2767539 (100.00%) were paired; of these: 1934461 (69.90%) aligned concordantly 0 times 730152 (26.38%) aligned concordantly exactly 1 time 102926 (3.72%) aligned concordantly >1 times ---- 1934461 pairs aligned concordantly 0 times; of these: 16600 (0.86%) aligned discordantly 1 time ---- 1917861 pairs aligned 0 times concordantly or discordantly; of these: 3835722 mates make up the pairs; of these: 2481733 (64.70%) aligned 0 times 1209975 (31.54%) aligned exactly 1 time 144014 (3.75%) aligned >1 times 55.16% overall alignment rate Time searching: 00:01:43 Overall time: 00:01:43 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] 802421 / 842271 = 0.9527 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 08:03:24: # Command line: callpeak -t SRX360915.bam -f BAM -g 12100000 -n SRX360915.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX360915.10 # format = BAM # ChIP-seq file = ['SRX360915.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 08:03:24: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:03:24: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:03:24: # Command line: callpeak -t SRX360915.bam -f BAM -g 12100000 -n SRX360915.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX360915.20 # format = BAM # ChIP-seq file = ['SRX360915.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 08:03:24: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:03:24: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:03:24: # Command line: callpeak -t SRX360915.bam -f BAM -g 12100000 -n SRX360915.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX360915.05 # format = BAM # ChIP-seq file = ['SRX360915.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 08:03:24: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:03:24: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:03:30: 1000000 INFO @ Wed, 28 Jun 2017 08:03:30: 1000000 INFO @ Wed, 28 Jun 2017 08:03:30: 1000000 INFO @ Wed, 28 Jun 2017 08:03:32: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 08:03:32: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 08:03:32: #1 total tags in treatment: 35292 INFO @ Wed, 28 Jun 2017 08:03:32: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:03:32: #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 08:03:32: #1 tags after filtering in treatment: 33903 INFO @ Wed, 28 Jun 2017 08:03:32: #1 Redundant rate of treatment: 0.04 INFO @ Wed, 28 Jun 2017 08:03:32: #1 finished! INFO @ Wed, 28 Jun 2017 08:03:32: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:03:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:03:32: #2 number of paired peaks: 332 WARNING @ Wed, 28 Jun 2017 08:03:32: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Wed, 28 Jun 2017 08:03:32: start model_add_line... INFO @ Wed, 28 Jun 2017 08:03:32: start X-correlation... INFO @ Wed, 28 Jun 2017 08:03:32: end of X-cor INFO @ Wed, 28 Jun 2017 08:03:32: #2 finished! INFO @ Wed, 28 Jun 2017 08:03:32: #2 predicted fragment length is 179 bps INFO @ Wed, 28 Jun 2017 08:03:32: #2 alternative fragment length(s) may be 147,179,203,231,300,551,571,590 bps INFO @ Wed, 28 Jun 2017 08:03:32: #2.2 Generate R script for model : SRX360915.10_model.r INFO @ Wed, 28 Jun 2017 08:03:32: #3 Call peaks... INFO @ Wed, 28 Jun 2017 08:03:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 08:03:32: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 08:03:32: #4 Write output xls file... SRX360915.10_peaks.xls INFO @ Wed, 28 Jun 2017 08:03:32: #4 Write peak in narrowPeak format file... SRX360915.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 08:03:32: #4 Write summits bed file... SRX360915.10_summits.bed INFO @ Wed, 28 Jun 2017 08:03:32: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (11 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 08:03:33: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 08:03:33: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 08:03:33: #1 total tags in treatment: 35292 INFO @ Wed, 28 Jun 2017 08:03:33: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:03:33: #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 08:03:33: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 08:03:33: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 08:03:33: #1 total tags in treatment: 35292 INFO @ Wed, 28 Jun 2017 08:03:33: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:03:33: #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 08:03:33: #1 tags after filtering in treatment: 33903 INFO @ Wed, 28 Jun 2017 08:03:33: #1 Redundant rate of treatment: 0.04 INFO @ Wed, 28 Jun 2017 08:03:33: #1 finished! INFO @ Wed, 28 Jun 2017 08:03:33: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:03:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:03:33: #1 tags after filtering in treatment: 33903 INFO @ Wed, 28 Jun 2017 08:03:33: #1 Redundant rate of treatment: 0.04 INFO @ Wed, 28 Jun 2017 08:03:33: #1 finished! INFO @ Wed, 28 Jun 2017 08:03:33: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:03:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:03:33: #2 number of paired peaks: 332 WARNING @ Wed, 28 Jun 2017 08:03:33: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Wed, 28 Jun 2017 08:03:33: start model_add_line... INFO @ Wed, 28 Jun 2017 08:03:33: start X-correlation... INFO @ Wed, 28 Jun 2017 08:03:33: #2 number of paired peaks: 332 WARNING @ Wed, 28 Jun 2017 08:03:33: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Wed, 28 Jun 2017 08:03:33: start model_add_line... INFO @ Wed, 28 Jun 2017 08:03:33: start X-correlation... INFO @ Wed, 28 Jun 2017 08:03:33: end of X-cor INFO @ Wed, 28 Jun 2017 08:03:33: #2 finished! INFO @ Wed, 28 Jun 2017 08:03:33: #2 predicted fragment length is 179 bps INFO @ Wed, 28 Jun 2017 08:03:33: #2 alternative fragment length(s) may be 147,179,203,231,300,551,571,590 bps INFO @ Wed, 28 Jun 2017 08:03:33: #2.2 Generate R script for model : SRX360915.05_model.r INFO @ Wed, 28 Jun 2017 08:03:33: end of X-cor INFO @ Wed, 28 Jun 2017 08:03:33: #2 finished! INFO @ Wed, 28 Jun 2017 08:03:33: #2 predicted fragment length is 179 bps INFO @ Wed, 28 Jun 2017 08:03:33: #2 alternative fragment length(s) may be 147,179,203,231,300,551,571,590 bps INFO @ Wed, 28 Jun 2017 08:03:33: #2.2 Generate R script for model : SRX360915.20_model.r INFO @ Wed, 28 Jun 2017 08:03:33: #3 Call peaks... INFO @ Wed, 28 Jun 2017 08:03:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 08:03:33: #3 Call peaks... INFO @ Wed, 28 Jun 2017 08:03:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 08:03:33: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 08:03:33: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 08:03:33: #4 Write output xls file... SRX360915.05_peaks.xls INFO @ Wed, 28 Jun 2017 08:03:33: #4 Write peak in narrowPeak format file... SRX360915.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 08:03:33: #4 Write summits bed file... SRX360915.05_summits.bed INFO @ Wed, 28 Jun 2017 08:03:33: Done! INFO @ Wed, 28 Jun 2017 08:03:33: #4 Write output xls file... SRX360915.20_peaks.xls INFO @ Wed, 28 Jun 2017 08:03:33: #4 Write peak in narrowPeak format file... SRX360915.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 08:03:33: #4 Write summits bed file... SRX360915.20_summits.bed INFO @ Wed, 28 Jun 2017 08:03:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (43 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。