Job ID = 11192633 sra ファイルのダウンロード中... Completed: 475517K bytes transferred in 7 seconds (542192K 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 8737450 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1491895/SRR3033156.sra Written 8737450 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1491895/SRR3033156.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: 00:09:02 8737450 reads; of these: 8737450 (100.00%) were paired; of these: 624715 (7.15%) aligned concordantly 0 times 6873032 (78.66%) aligned concordantly exactly 1 time 1239703 (14.19%) aligned concordantly >1 times ---- 624715 pairs aligned concordantly 0 times; of these: 26636 (4.26%) aligned discordantly 1 time ---- 598079 pairs aligned 0 times concordantly or discordantly; of these: 1196158 mates make up the pairs; of these: 867972 (72.56%) aligned 0 times 252089 (21.07%) aligned exactly 1 time 76097 (6.36%) aligned >1 times 95.03% overall alignment rate Time searching: 00:09:02 Overall time: 00:09:02 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 8 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] 8056355 / 8133091 = 0.9906 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 @ Sat, 15 Sep 2018 09:50:29: # Command line: callpeak -t SRX1491895.bam -f BAM -g 12100000 -n SRX1491895.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1491895.10 # format = BAM # ChIP-seq file = ['SRX1491895.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 @ Sat, 15 Sep 2018 09:50:29: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:50:29: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:50:29: # Command line: callpeak -t SRX1491895.bam -f BAM -g 12100000 -n SRX1491895.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1491895.05 # format = BAM # ChIP-seq file = ['SRX1491895.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 @ Sat, 15 Sep 2018 09:50:29: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:50:29: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:50:29: # Command line: callpeak -t SRX1491895.bam -f BAM -g 12100000 -n SRX1491895.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1491895.20 # format = BAM # ChIP-seq file = ['SRX1491895.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 @ Sat, 15 Sep 2018 09:50:29: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:50:29: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:50:32: #1 tag size is determined as 36 bps INFO @ Sat, 15 Sep 2018 09:50:32: #1 tag size = 36 INFO @ Sat, 15 Sep 2018 09:50:32: #1 total tags in treatment: 80050 INFO @ Sat, 15 Sep 2018 09:50:32: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:50:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:50:32: #1 tag size is determined as 36 bps INFO @ Sat, 15 Sep 2018 09:50:32: #1 tag size = 36 INFO @ Sat, 15 Sep 2018 09:50:32: #1 total tags in treatment: 80050 INFO @ Sat, 15 Sep 2018 09:50:32: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:50:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:50:32: #1 tags after filtering in treatment: 71551 INFO @ Sat, 15 Sep 2018 09:50:32: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 15 Sep 2018 09:50:32: #1 finished! INFO @ Sat, 15 Sep 2018 09:50:32: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:50:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:50:32: #1 tags after filtering in treatment: 71551 INFO @ Sat, 15 Sep 2018 09:50:32: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 15 Sep 2018 09:50:32: #1 finished! INFO @ Sat, 15 Sep 2018 09:50:32: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:50:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:50:32: #2 number of paired peaks: 324 WARNING @ Sat, 15 Sep 2018 09:50:32: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Sat, 15 Sep 2018 09:50:32: start model_add_line... INFO @ Sat, 15 Sep 2018 09:50:32: #2 number of paired peaks: 324 WARNING @ Sat, 15 Sep 2018 09:50:32: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Sat, 15 Sep 2018 09:50:32: start model_add_line... INFO @ Sat, 15 Sep 2018 09:50:32: start X-correlation... INFO @ Sat, 15 Sep 2018 09:50:32: start X-correlation... INFO @ Sat, 15 Sep 2018 09:50:32: #1 tag size is determined as 36 bps INFO @ Sat, 15 Sep 2018 09:50:32: #1 tag size = 36 INFO @ Sat, 15 Sep 2018 09:50:32: #1 total tags in treatment: 80050 INFO @ Sat, 15 Sep 2018 09:50:32: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:50:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:50:32: end of X-cor INFO @ Sat, 15 Sep 2018 09:50:32: end of X-cor INFO @ Sat, 15 Sep 2018 09:50:32: #2 finished! INFO @ Sat, 15 Sep 2018 09:50:32: #2 finished! INFO @ Sat, 15 Sep 2018 09:50:32: #2 predicted fragment length is 96 bps INFO @ Sat, 15 Sep 2018 09:50:32: #2 predicted fragment length is 96 bps INFO @ Sat, 15 Sep 2018 09:50:32: #2 alternative fragment length(s) may be 57,96,136,249,267,448,559 bps INFO @ Sat, 15 Sep 2018 09:50:32: #2 alternative fragment length(s) may be 57,96,136,249,267,448,559 bps INFO @ Sat, 15 Sep 2018 09:50:32: #2.2 Generate R script for model : SRX1491895.10_model.r INFO @ Sat, 15 Sep 2018 09:50:32: #2.2 Generate R script for model : SRX1491895.05_model.r INFO @ Sat, 15 Sep 2018 09:50:32: #1 tags after filtering in treatment: 71551 INFO @ Sat, 15 Sep 2018 09:50:32: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 15 Sep 2018 09:50:32: #1 finished! INFO @ Sat, 15 Sep 2018 09:50:32: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:50:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:50:32: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:50:32: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:50:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:50:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:50:32: #2 number of paired peaks: 324 WARNING @ Sat, 15 Sep 2018 09:50:32: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Sat, 15 Sep 2018 09:50:32: start model_add_line... INFO @ Sat, 15 Sep 2018 09:50:32: start X-correlation... INFO @ Sat, 15 Sep 2018 09:50:32: end of X-cor INFO @ Sat, 15 Sep 2018 09:50:32: #2 finished! INFO @ Sat, 15 Sep 2018 09:50:32: #2 predicted fragment length is 96 bps INFO @ Sat, 15 Sep 2018 09:50:32: #2 alternative fragment length(s) may be 57,96,136,249,267,448,559 bps INFO @ Sat, 15 Sep 2018 09:50:32: #2.2 Generate R script for model : SRX1491895.20_model.r INFO @ Sat, 15 Sep 2018 09:50:32: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:50:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:50:32: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:50:32: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:50:32: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:50:32: #4 Write output xls file... SRX1491895.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:50:32: #4 Write peak in narrowPeak format file... SRX1491895.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:50:32: #4 Write summits bed file... SRX1491895.10_summits.bed INFO @ Sat, 15 Sep 2018 09:50:32: Done! INFO @ Sat, 15 Sep 2018 09:50:32: #4 Write output xls file... SRX1491895.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:50:32: #4 Write peak in narrowPeak format file... SRX1491895.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:50:32: #4 Write summits bed file... SRX1491895.05_summits.bed INFO @ Sat, 15 Sep 2018 09:50:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (37 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:50:32: #4 Write output xls file... SRX1491895.20_peaks.xls pass1 - making usageList (16 chroms): 0 millis INFO @ Sat, 15 Sep 2018 09:50:32: #4 Write peak in narrowPeak format file... SRX1491895.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:50:32: #4 Write summits bed file... SRX1491895.20_summits.bed pass2 - checking and writing primary data (60 records, 4 fields): 2 millis INFO @ Sat, 15 Sep 2018 09:50:32: Done! CompletedMACS2peakCalling pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (20 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。