Job ID = 11245247 sra ファイルのダウンロード中... Completed: 50453K bytes transferred in 3 seconds (110455K 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 2001506 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4733457/SRR7896012.sra Written 2001506 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4733457/SRR7896012.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: 00:00:19 2001506 reads; of these: 2001506 (100.00%) were unpaired; of these: 108485 (5.42%) aligned 0 times 1173875 (58.65%) aligned exactly 1 time 719146 (35.93%) aligned >1 times 94.58% overall alignment rate Time searching: 00:00:19 Overall time: 00:00:19 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] 881917 / 1893021 = 0.4659 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 00:03:44: # Command line: callpeak -t SRX4733457.bam -f BAM -g 12100000 -n SRX4733457.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4733457.10 # format = BAM # ChIP-seq file = ['SRX4733457.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 00:03:44: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:03:44: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:03:44: # Command line: callpeak -t SRX4733457.bam -f BAM -g 12100000 -n SRX4733457.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4733457.20 # format = BAM # ChIP-seq file = ['SRX4733457.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 00:03:44: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:03:44: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:03:44: # Command line: callpeak -t SRX4733457.bam -f BAM -g 12100000 -n SRX4733457.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4733457.05 # format = BAM # ChIP-seq file = ['SRX4733457.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 00:03:44: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:03:44: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:03:51: 1000000 INFO @ Wed, 10 Oct 2018 00:03:51: #1 tag size is determined as 51 bps INFO @ Wed, 10 Oct 2018 00:03:51: #1 tag size = 51 INFO @ Wed, 10 Oct 2018 00:03:51: #1 total tags in treatment: 1011104 INFO @ Wed, 10 Oct 2018 00:03:51: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:03:51: #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 00:03:51: #1 tags after filtering in treatment: 1011104 INFO @ Wed, 10 Oct 2018 00:03:51: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:03:51: #1 finished! INFO @ Wed, 10 Oct 2018 00:03:51: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:03:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:03:51: #2 number of paired peaks: 197 WARNING @ Wed, 10 Oct 2018 00:03:51: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Wed, 10 Oct 2018 00:03:51: start model_add_line... INFO @ Wed, 10 Oct 2018 00:03:51: start X-correlation... INFO @ Wed, 10 Oct 2018 00:03:51: end of X-cor INFO @ Wed, 10 Oct 2018 00:03:51: #2 finished! INFO @ Wed, 10 Oct 2018 00:03:51: #2 predicted fragment length is 188 bps INFO @ Wed, 10 Oct 2018 00:03:51: #2 alternative fragment length(s) may be 3,188,579 bps INFO @ Wed, 10 Oct 2018 00:03:51: #2.2 Generate R script for model : SRX4733457.05_model.r INFO @ Wed, 10 Oct 2018 00:03:51: #3 Call peaks... INFO @ Wed, 10 Oct 2018 00:03:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 10 Oct 2018 00:03:52: 1000000 INFO @ Wed, 10 Oct 2018 00:03:52: 1000000 INFO @ Wed, 10 Oct 2018 00:03:52: #1 tag size is determined as 51 bps INFO @ Wed, 10 Oct 2018 00:03:52: #1 tag size = 51 INFO @ Wed, 10 Oct 2018 00:03:52: #1 total tags in treatment: 1011104 INFO @ Wed, 10 Oct 2018 00:03:52: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:03:52: #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 00:03:52: #1 tag size is determined as 51 bps INFO @ Wed, 10 Oct 2018 00:03:52: #1 tag size = 51 INFO @ Wed, 10 Oct 2018 00:03:52: #1 total tags in treatment: 1011104 INFO @ Wed, 10 Oct 2018 00:03:52: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:03:52: #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 00:03:52: #1 tags after filtering in treatment: 1011104 INFO @ Wed, 10 Oct 2018 00:03:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:03:52: #1 finished! INFO @ Wed, 10 Oct 2018 00:03:52: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:03:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:03:52: #1 tags after filtering in treatment: 1011104 INFO @ Wed, 10 Oct 2018 00:03:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:03:52: #1 finished! INFO @ Wed, 10 Oct 2018 00:03:52: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:03:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:03:52: #2 number of paired peaks: 197 WARNING @ Wed, 10 Oct 2018 00:03:52: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Wed, 10 Oct 2018 00:03:52: start model_add_line... INFO @ Wed, 10 Oct 2018 00:03:52: start X-correlation... INFO @ Wed, 10 Oct 2018 00:03:52: #2 number of paired peaks: 197 WARNING @ Wed, 10 Oct 2018 00:03:52: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Wed, 10 Oct 2018 00:03:52: start model_add_line... INFO @ Wed, 10 Oct 2018 00:03:52: end of X-cor INFO @ Wed, 10 Oct 2018 00:03:52: #2 finished! INFO @ Wed, 10 Oct 2018 00:03:52: #2 predicted fragment length is 188 bps INFO @ Wed, 10 Oct 2018 00:03:52: #2 alternative fragment length(s) may be 3,188,579 bps INFO @ Wed, 10 Oct 2018 00:03:52: #2.2 Generate R script for model : SRX4733457.20_model.r INFO @ Wed, 10 Oct 2018 00:03:52: start X-correlation... INFO @ Wed, 10 Oct 2018 00:03:52: #3 Call peaks... INFO @ Wed, 10 Oct 2018 00:03:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 10 Oct 2018 00:03:52: end of X-cor INFO @ Wed, 10 Oct 2018 00:03:52: #2 finished! INFO @ Wed, 10 Oct 2018 00:03:52: #2 predicted fragment length is 188 bps INFO @ Wed, 10 Oct 2018 00:03:52: #2 alternative fragment length(s) may be 3,188,579 bps INFO @ Wed, 10 Oct 2018 00:03:52: #2.2 Generate R script for model : SRX4733457.10_model.r INFO @ Wed, 10 Oct 2018 00:03:52: #3 Call peaks... INFO @ Wed, 10 Oct 2018 00:03:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 10 Oct 2018 00:03:55: #3 Call peaks for each chromosome... INFO @ Wed, 10 Oct 2018 00:03:55: #3 Call peaks for each chromosome... INFO @ Wed, 10 Oct 2018 00:03:55: #3 Call peaks for each chromosome... INFO @ Wed, 10 Oct 2018 00:03:56: #4 Write output xls file... SRX4733457.05_peaks.xls INFO @ Wed, 10 Oct 2018 00:03:56: #4 Write peak in narrowPeak format file... SRX4733457.05_peaks.narrowPeak INFO @ Wed, 10 Oct 2018 00:03:56: #4 Write summits bed file... SRX4733457.05_summits.bed INFO @ Wed, 10 Oct 2018 00:03:56: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (39 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 10 Oct 2018 00:03:56: #4 Write output xls file... SRX4733457.20_peaks.xls INFO @ Wed, 10 Oct 2018 00:03:56: #4 Write peak in narrowPeak format file... SRX4733457.20_peaks.narrowPeak INFO @ Wed, 10 Oct 2018 00:03:56: #4 Write summits bed file... SRX4733457.20_summits.bed INFO @ Wed, 10 Oct 2018 00:03:56: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (6 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 10 Oct 2018 00:03:56: #4 Write output xls file... SRX4733457.10_peaks.xls INFO @ Wed, 10 Oct 2018 00:03:56: #4 Write peak in narrowPeak format file... SRX4733457.10_peaks.narrowPeak INFO @ Wed, 10 Oct 2018 00:03:56: #4 Write summits bed file... SRX4733457.10_summits.bed INFO @ Wed, 10 Oct 2018 00:03:56: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (19 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。