Job ID = 9161999 sra ファイルのダウンロード中... Completed: 907552K bytes transferred in 11 seconds (622477K 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 20314069 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423731/SRR2931020.sra Written 20314069 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: 00:13:36 20314069 reads; of these: 20314069 (100.00%) were paired; of these: 3804714 (18.73%) aligned concordantly 0 times 14860056 (73.15%) aligned concordantly exactly 1 time 1649299 (8.12%) aligned concordantly >1 times ---- 3804714 pairs aligned concordantly 0 times; of these: 16680 (0.44%) aligned discordantly 1 time ---- 3788034 pairs aligned 0 times concordantly or discordantly; of these: 7576068 mates make up the pairs; of these: 7106064 (93.80%) aligned 0 times 422861 (5.58%) aligned exactly 1 time 47143 (0.62%) aligned >1 times 82.51% overall alignment rate Time searching: 00:13:36 Overall time: 00:13:36 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_sort_core] merging from 16 files... [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] 15065287 / 16517137 = 0.9121 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 05:31:32: # Command line: callpeak -t SRX1423731.bam -f BAM -g 12100000 -n SRX1423731.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423731.05 # format = BAM # ChIP-seq file = ['SRX1423731.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 05:31:32: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:31:32: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:31:32: # Command line: callpeak -t SRX1423731.bam -f BAM -g 12100000 -n SRX1423731.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423731.10 # format = BAM # ChIP-seq file = ['SRX1423731.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 05:31:32: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:31:32: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:31:32: # Command line: callpeak -t SRX1423731.bam -f BAM -g 12100000 -n SRX1423731.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423731.20 # format = BAM # ChIP-seq file = ['SRX1423731.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 05:31:32: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:31:32: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:31:37: 1000000 INFO @ Wed, 28 Jun 2017 05:31:37: 1000000 INFO @ Wed, 28 Jun 2017 05:31:37: 1000000 INFO @ Wed, 28 Jun 2017 05:31:43: 2000000 INFO @ Wed, 28 Jun 2017 05:31:43: 2000000 INFO @ Wed, 28 Jun 2017 05:31:43: 2000000 INFO @ Wed, 28 Jun 2017 05:31:48: 3000000 INFO @ Wed, 28 Jun 2017 05:31:48: 3000000 INFO @ Wed, 28 Jun 2017 05:31:49: 3000000 INFO @ Wed, 28 Jun 2017 05:31:50: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:31:50: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:31:50: #1 total tags in treatment: 1451839 INFO @ Wed, 28 Jun 2017 05:31:50: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:31:50: #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 05:31:50: #1 tags after filtering in treatment: 1320439 INFO @ Wed, 28 Jun 2017 05:31:50: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 28 Jun 2017 05:31:50: #1 finished! INFO @ Wed, 28 Jun 2017 05:31:50: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:31:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:31:50: #2 number of paired peaks: 152 WARNING @ Wed, 28 Jun 2017 05:31:50: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Wed, 28 Jun 2017 05:31:50: start model_add_line... INFO @ Wed, 28 Jun 2017 05:31:50: start X-correlation... INFO @ Wed, 28 Jun 2017 05:31:50: end of X-cor INFO @ Wed, 28 Jun 2017 05:31:50: #2 finished! INFO @ Wed, 28 Jun 2017 05:31:50: #2 predicted fragment length is 204 bps INFO @ Wed, 28 Jun 2017 05:31:50: #2 alternative fragment length(s) may be 3,125,129,153,171,179,204,242 bps INFO @ Wed, 28 Jun 2017 05:31:50: #2.2 Generate R script for model : SRX1423731.05_model.r INFO @ Wed, 28 Jun 2017 05:31:50: #3 Call peaks... INFO @ Wed, 28 Jun 2017 05:31:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 05:31:51: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:31:51: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:31:51: #1 total tags in treatment: 1451839 INFO @ Wed, 28 Jun 2017 05:31:51: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:31:51: #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 05:31:51: #1 tags after filtering in treatment: 1320439 INFO @ Wed, 28 Jun 2017 05:31:51: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 28 Jun 2017 05:31:51: #1 finished! INFO @ Wed, 28 Jun 2017 05:31:51: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:31:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:31:51: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:31:51: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:31:51: #1 total tags in treatment: 1451839 INFO @ Wed, 28 Jun 2017 05:31:51: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:31:51: #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 05:31:51: #2 number of paired peaks: 152 WARNING @ Wed, 28 Jun 2017 05:31:51: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Wed, 28 Jun 2017 05:31:51: start model_add_line... INFO @ Wed, 28 Jun 2017 05:31:51: start X-correlation... INFO @ Wed, 28 Jun 2017 05:31:51: end of X-cor INFO @ Wed, 28 Jun 2017 05:31:51: #2 finished! INFO @ Wed, 28 Jun 2017 05:31:51: #2 predicted fragment length is 204 bps INFO @ Wed, 28 Jun 2017 05:31:51: #2 alternative fragment length(s) may be 3,125,129,153,171,179,204,242 bps INFO @ Wed, 28 Jun 2017 05:31:51: #2.2 Generate R script for model : SRX1423731.20_model.r INFO @ Wed, 28 Jun 2017 05:31:51: #1 tags after filtering in treatment: 1320439 INFO @ Wed, 28 Jun 2017 05:31:51: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 28 Jun 2017 05:31:51: #1 finished! INFO @ Wed, 28 Jun 2017 05:31:51: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:31:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:31:51: #3 Call peaks... INFO @ Wed, 28 Jun 2017 05:31:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 05:31:51: #2 number of paired peaks: 152 WARNING @ Wed, 28 Jun 2017 05:31:51: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Wed, 28 Jun 2017 05:31:51: start model_add_line... INFO @ Wed, 28 Jun 2017 05:31:51: start X-correlation... INFO @ Wed, 28 Jun 2017 05:31:51: end of X-cor INFO @ Wed, 28 Jun 2017 05:31:51: #2 finished! INFO @ Wed, 28 Jun 2017 05:31:51: #2 predicted fragment length is 204 bps INFO @ Wed, 28 Jun 2017 05:31:51: #2 alternative fragment length(s) may be 3,125,129,153,171,179,204,242 bps INFO @ Wed, 28 Jun 2017 05:31:51: #2.2 Generate R script for model : SRX1423731.10_model.r INFO @ Wed, 28 Jun 2017 05:31:51: #3 Call peaks... INFO @ Wed, 28 Jun 2017 05:31:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 05:31:55: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 05:31:55: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 05:31:56: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 05:31:57: #4 Write output xls file... SRX1423731.05_peaks.xls INFO @ Wed, 28 Jun 2017 05:31:57: #4 Write peak in narrowPeak format file... SRX1423731.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 05:31:57: #4 Write summits bed file... SRX1423731.05_summits.bed INFO @ Wed, 28 Jun 2017 05:31:57: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (623 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 05:31:57: #4 Write output xls file... SRX1423731.20_peaks.xls INFO @ Wed, 28 Jun 2017 05:31:57: #4 Write peak in narrowPeak format file... SRX1423731.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 05:31:57: #4 Write summits bed file... SRX1423731.20_summits.bed INFO @ Wed, 28 Jun 2017 05:31:57: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (144 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 05:31:57: #4 Write output xls file... SRX1423731.10_peaks.xls INFO @ Wed, 28 Jun 2017 05:31:57: #4 Write peak in narrowPeak format file... SRX1423731.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 05:31:57: #4 Write summits bed file... SRX1423731.10_summits.bed INFO @ Wed, 28 Jun 2017 05:31:57: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (274 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。