Job ID = 11162638 sra ファイルのダウンロード中... Completed: 39046K bytes transferred in 3 seconds (84139K 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 1142853 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3709390/SRR6736442.sra Written 1142853 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3709390/SRR6736442.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: 00:00:54 1142853 reads; of these: 1142853 (100.00%) were paired; of these: 332454 (29.09%) aligned concordantly 0 times 470944 (41.21%) aligned concordantly exactly 1 time 339455 (29.70%) aligned concordantly >1 times ---- 332454 pairs aligned concordantly 0 times; of these: 521 (0.16%) aligned discordantly 1 time ---- 331933 pairs aligned 0 times concordantly or discordantly; of these: 663866 mates make up the pairs; of these: 376633 (56.73%) aligned 0 times 161980 (24.40%) aligned exactly 1 time 125253 (18.87%) aligned >1 times 83.52% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 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] 255859 / 810729 = 0.3156 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, 05 Sep 2018 10:40:29: # Command line: callpeak -t SRX3709390.bam -f BAM -g 12100000 -n SRX3709390.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3709390.05 # format = BAM # ChIP-seq file = ['SRX3709390.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, 05 Sep 2018 10:40:29: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:40:29: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:40:29: # Command line: callpeak -t SRX3709390.bam -f BAM -g 12100000 -n SRX3709390.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3709390.20 # format = BAM # ChIP-seq file = ['SRX3709390.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, 05 Sep 2018 10:40:29: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:40:29: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:40:29: # Command line: callpeak -t SRX3709390.bam -f BAM -g 12100000 -n SRX3709390.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3709390.10 # format = BAM # ChIP-seq file = ['SRX3709390.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, 05 Sep 2018 10:40:29: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:40:29: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:40:35: 1000000 INFO @ Wed, 05 Sep 2018 10:40:36: 1000000 INFO @ Wed, 05 Sep 2018 10:40:36: 1000000 INFO @ Wed, 05 Sep 2018 10:40:37: #1 tag size is determined as 40 bps INFO @ Wed, 05 Sep 2018 10:40:37: #1 tag size = 40 INFO @ Wed, 05 Sep 2018 10:40:37: #1 total tags in treatment: 554556 INFO @ Wed, 05 Sep 2018 10:40:37: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:40:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:40:37: #1 tags after filtering in treatment: 360459 INFO @ Wed, 05 Sep 2018 10:40:37: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 05 Sep 2018 10:40:37: #1 finished! INFO @ Wed, 05 Sep 2018 10:40:37: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:40:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:40:37: #2 number of paired peaks: 417 WARNING @ Wed, 05 Sep 2018 10:40:37: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Wed, 05 Sep 2018 10:40:37: start model_add_line... INFO @ Wed, 05 Sep 2018 10:40:37: start X-correlation... INFO @ Wed, 05 Sep 2018 10:40:37: end of X-cor INFO @ Wed, 05 Sep 2018 10:40:37: #2 finished! INFO @ Wed, 05 Sep 2018 10:40:37: #2 predicted fragment length is 125 bps INFO @ Wed, 05 Sep 2018 10:40:37: #2 alternative fragment length(s) may be 125 bps INFO @ Wed, 05 Sep 2018 10:40:37: #2.2 Generate R script for model : SRX3709390.20_model.r INFO @ Wed, 05 Sep 2018 10:40:37: #3 Call peaks... INFO @ Wed, 05 Sep 2018 10:40:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 05 Sep 2018 10:40:38: #1 tag size is determined as 40 bps INFO @ Wed, 05 Sep 2018 10:40:38: #1 tag size = 40 INFO @ Wed, 05 Sep 2018 10:40:38: #1 total tags in treatment: 554556 INFO @ Wed, 05 Sep 2018 10:40:38: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:40:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:40:38: #1 tag size is determined as 40 bps INFO @ Wed, 05 Sep 2018 10:40:38: #1 tag size = 40 INFO @ Wed, 05 Sep 2018 10:40:38: #1 total tags in treatment: 554556 INFO @ Wed, 05 Sep 2018 10:40:38: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:40:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:40:38: #1 tags after filtering in treatment: 360459 INFO @ Wed, 05 Sep 2018 10:40:38: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 05 Sep 2018 10:40:38: #1 finished! INFO @ Wed, 05 Sep 2018 10:40:38: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:40:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:40:38: #1 tags after filtering in treatment: 360459 INFO @ Wed, 05 Sep 2018 10:40:38: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 05 Sep 2018 10:40:38: #1 finished! INFO @ Wed, 05 Sep 2018 10:40:38: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:40:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:40:38: #2 number of paired peaks: 417 WARNING @ Wed, 05 Sep 2018 10:40:38: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Wed, 05 Sep 2018 10:40:38: start model_add_line... INFO @ Wed, 05 Sep 2018 10:40:38: start X-correlation... INFO @ Wed, 05 Sep 2018 10:40:38: #2 number of paired peaks: 417 WARNING @ Wed, 05 Sep 2018 10:40:38: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Wed, 05 Sep 2018 10:40:38: start model_add_line... INFO @ Wed, 05 Sep 2018 10:40:38: end of X-cor INFO @ Wed, 05 Sep 2018 10:40:38: #2 finished! INFO @ Wed, 05 Sep 2018 10:40:38: #2 predicted fragment length is 125 bps INFO @ Wed, 05 Sep 2018 10:40:38: #2 alternative fragment length(s) may be 125 bps INFO @ Wed, 05 Sep 2018 10:40:38: #2.2 Generate R script for model : SRX3709390.05_model.r INFO @ Wed, 05 Sep 2018 10:40:38: start X-correlation... INFO @ Wed, 05 Sep 2018 10:40:38: end of X-cor INFO @ Wed, 05 Sep 2018 10:40:38: #2 finished! INFO @ Wed, 05 Sep 2018 10:40:38: #2 predicted fragment length is 125 bps INFO @ Wed, 05 Sep 2018 10:40:38: #2 alternative fragment length(s) may be 125 bps INFO @ Wed, 05 Sep 2018 10:40:38: #2.2 Generate R script for model : SRX3709390.10_model.r INFO @ Wed, 05 Sep 2018 10:40:38: #3 Call peaks... INFO @ Wed, 05 Sep 2018 10:40:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 05 Sep 2018 10:40:38: #3 Call peaks... INFO @ Wed, 05 Sep 2018 10:40:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 05 Sep 2018 10:40:38: #3 Call peaks for each chromosome... INFO @ Wed, 05 Sep 2018 10:40:39: #4 Write output xls file... SRX3709390.20_peaks.xls INFO @ Wed, 05 Sep 2018 10:40:39: #4 Write peak in narrowPeak format file... SRX3709390.20_peaks.narrowPeak INFO @ Wed, 05 Sep 2018 10:40:39: #4 Write summits bed file... SRX3709390.20_summits.bed INFO @ Wed, 05 Sep 2018 10:40:39: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (307 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 05 Sep 2018 10:40:39: #3 Call peaks for each chromosome... INFO @ Wed, 05 Sep 2018 10:40:39: #3 Call peaks for each chromosome... INFO @ Wed, 05 Sep 2018 10:40:40: #4 Write output xls file... SRX3709390.05_peaks.xls INFO @ Wed, 05 Sep 2018 10:40:40: #4 Write peak in narrowPeak format file... SRX3709390.05_peaks.narrowPeak INFO @ Wed, 05 Sep 2018 10:40:40: #4 Write summits bed file... SRX3709390.05_summits.bed INFO @ Wed, 05 Sep 2018 10:40:40: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (628 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 05 Sep 2018 10:40:40: #4 Write output xls file... SRX3709390.10_peaks.xls INFO @ Wed, 05 Sep 2018 10:40:40: #4 Write peak in narrowPeak format file... SRX3709390.10_peaks.narrowPeak INFO @ Wed, 05 Sep 2018 10:40:40: #4 Write summits bed file... SRX3709390.10_summits.bed INFO @ Wed, 05 Sep 2018 10:40:40: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (491 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。