Job ID = 11245255 sra ファイルのダウンロード中... Completed: 250551K bytes transferred in 5 seconds (365650K 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: SINGLE fastq に変換中... Read 5969101 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4733465/SRR7896020.sra Written 5969101 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4733465/SRR7896020.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: 00:01:42 5969101 reads; of these: 5969101 (100.00%) were unpaired; of these: 570248 (9.55%) aligned 0 times 3159798 (52.94%) aligned exactly 1 time 2239055 (37.51%) aligned >1 times 90.45% overall alignment rate Time searching: 00:01:42 Overall time: 00:01:42 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_rmdupse_core] 3066955 / 5398853 = 0.5681 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, 10 Oct 2018 00:07:12: # Command line: callpeak -t SRX4733465.bam -f BAM -g 12100000 -n SRX4733465.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4733465.05 # format = BAM # ChIP-seq file = ['SRX4733465.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, 10 Oct 2018 00:07:12: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:07:12: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:07:12: # Command line: callpeak -t SRX4733465.bam -f BAM -g 12100000 -n SRX4733465.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4733465.20 # format = BAM # ChIP-seq file = ['SRX4733465.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, 10 Oct 2018 00:07:12: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:07:12: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:07:12: # Command line: callpeak -t SRX4733465.bam -f BAM -g 12100000 -n SRX4733465.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4733465.10 # format = BAM # ChIP-seq file = ['SRX4733465.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, 10 Oct 2018 00:07:12: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:07:12: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:07:20: 1000000 INFO @ Wed, 10 Oct 2018 00:07:20: 1000000 INFO @ Wed, 10 Oct 2018 00:07:20: 1000000 INFO @ Wed, 10 Oct 2018 00:07:28: 2000000 INFO @ Wed, 10 Oct 2018 00:07:28: 2000000 INFO @ Wed, 10 Oct 2018 00:07:28: 2000000 INFO @ Wed, 10 Oct 2018 00:07:30: #1 tag size is determined as 101 bps INFO @ Wed, 10 Oct 2018 00:07:30: #1 tag size = 101 INFO @ Wed, 10 Oct 2018 00:07:30: #1 total tags in treatment: 2331898 INFO @ Wed, 10 Oct 2018 00:07:30: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:07:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:07:30: #1 tags after filtering in treatment: 2331898 INFO @ Wed, 10 Oct 2018 00:07:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:07:30: #1 finished! INFO @ Wed, 10 Oct 2018 00:07:30: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:07:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:07:30: #2 number of paired peaks: 190 WARNING @ Wed, 10 Oct 2018 00:07:30: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Wed, 10 Oct 2018 00:07:30: start model_add_line... INFO @ Wed, 10 Oct 2018 00:07:30: start X-correlation... INFO @ Wed, 10 Oct 2018 00:07:30: end of X-cor INFO @ Wed, 10 Oct 2018 00:07:30: #2 finished! INFO @ Wed, 10 Oct 2018 00:07:30: #2 predicted fragment length is 242 bps INFO @ Wed, 10 Oct 2018 00:07:30: #2 alternative fragment length(s) may be 2,227,242 bps INFO @ Wed, 10 Oct 2018 00:07:30: #2.2 Generate R script for model : SRX4733465.05_model.r INFO @ Wed, 10 Oct 2018 00:07:30: #3 Call peaks... INFO @ Wed, 10 Oct 2018 00:07:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 10 Oct 2018 00:07:31: #1 tag size is determined as 101 bps INFO @ Wed, 10 Oct 2018 00:07:31: #1 tag size = 101 INFO @ Wed, 10 Oct 2018 00:07:31: #1 total tags in treatment: 2331898 INFO @ Wed, 10 Oct 2018 00:07:31: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:07:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:07:31: #1 tags after filtering in treatment: 2331898 INFO @ Wed, 10 Oct 2018 00:07:31: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:07:31: #1 finished! INFO @ Wed, 10 Oct 2018 00:07:31: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:07:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:07:31: #2 number of paired peaks: 190 WARNING @ Wed, 10 Oct 2018 00:07:31: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Wed, 10 Oct 2018 00:07:31: start model_add_line... INFO @ Wed, 10 Oct 2018 00:07:31: #1 tag size is determined as 101 bps INFO @ Wed, 10 Oct 2018 00:07:31: #1 tag size = 101 INFO @ Wed, 10 Oct 2018 00:07:31: #1 total tags in treatment: 2331898 INFO @ Wed, 10 Oct 2018 00:07:31: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:07:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:07:31: start X-correlation... INFO @ Wed, 10 Oct 2018 00:07:31: end of X-cor INFO @ Wed, 10 Oct 2018 00:07:31: #2 finished! INFO @ Wed, 10 Oct 2018 00:07:31: #2 predicted fragment length is 242 bps INFO @ Wed, 10 Oct 2018 00:07:31: #2 alternative fragment length(s) may be 2,227,242 bps INFO @ Wed, 10 Oct 2018 00:07:31: #2.2 Generate R script for model : SRX4733465.20_model.r INFO @ Wed, 10 Oct 2018 00:07:31: #3 Call peaks... INFO @ Wed, 10 Oct 2018 00:07:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 10 Oct 2018 00:07:31: #1 tags after filtering in treatment: 2331898 INFO @ Wed, 10 Oct 2018 00:07:31: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:07:31: #1 finished! INFO @ Wed, 10 Oct 2018 00:07:31: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:07:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:07:31: #2 number of paired peaks: 190 WARNING @ Wed, 10 Oct 2018 00:07:31: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Wed, 10 Oct 2018 00:07:31: start model_add_line... INFO @ Wed, 10 Oct 2018 00:07:31: start X-correlation... INFO @ Wed, 10 Oct 2018 00:07:31: end of X-cor INFO @ Wed, 10 Oct 2018 00:07:31: #2 finished! INFO @ Wed, 10 Oct 2018 00:07:31: #2 predicted fragment length is 242 bps INFO @ Wed, 10 Oct 2018 00:07:31: #2 alternative fragment length(s) may be 2,227,242 bps INFO @ Wed, 10 Oct 2018 00:07:31: #2.2 Generate R script for model : SRX4733465.10_model.r INFO @ Wed, 10 Oct 2018 00:07:31: #3 Call peaks... INFO @ Wed, 10 Oct 2018 00:07:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 10 Oct 2018 00:07:37: #3 Call peaks for each chromosome... INFO @ Wed, 10 Oct 2018 00:07:37: #3 Call peaks for each chromosome... INFO @ Wed, 10 Oct 2018 00:07:37: #3 Call peaks for each chromosome... INFO @ Wed, 10 Oct 2018 00:07:39: #4 Write output xls file... SRX4733465.20_peaks.xls INFO @ Wed, 10 Oct 2018 00:07:39: #4 Write peak in narrowPeak format file... SRX4733465.20_peaks.narrowPeak INFO @ Wed, 10 Oct 2018 00:07:39: #4 Write summits bed file... SRX4733465.20_summits.bed INFO @ Wed, 10 Oct 2018 00:07:39: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (8 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 10 Oct 2018 00:07:39: #4 Write output xls file... SRX4733465.05_peaks.xls INFO @ Wed, 10 Oct 2018 00:07:39: #4 Write peak in narrowPeak format file... SRX4733465.05_peaks.narrowPeak INFO @ Wed, 10 Oct 2018 00:07:39: #4 Write summits bed file... SRX4733465.05_summits.bed INFO @ Wed, 10 Oct 2018 00:07:39: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (26 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 10 Oct 2018 00:07:39: #4 Write output xls file... SRX4733465.10_peaks.xls INFO @ Wed, 10 Oct 2018 00:07:39: #4 Write peak in narrowPeak format file... SRX4733465.10_peaks.narrowPeak INFO @ Wed, 10 Oct 2018 00:07:39: #4 Write summits bed file... SRX4733465.10_summits.bed INFO @ Wed, 10 Oct 2018 00:07:39: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (16 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。