Job ID = 11193050 sra ファイルのダウンロード中... Completed: 149795K bytes transferred in 4 seconds (247280K 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 8183284 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4233888/SRR7360661.sra Written 8183284 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4233888/SRR7360661.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: 00:01:10 8183284 reads; of these: 8183284 (100.00%) were unpaired; of these: 2762595 (33.76%) aligned 0 times 4464457 (54.56%) aligned exactly 1 time 956232 (11.69%) aligned >1 times 66.24% overall alignment rate Time searching: 00:01:10 Overall time: 00:01:10 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] 3650566 / 5420689 = 0.6735 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 10:52:33: # Command line: callpeak -t SRX4233888.bam -f BAM -g 12100000 -n SRX4233888.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4233888.10 # format = BAM # ChIP-seq file = ['SRX4233888.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 10:52:33: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:52:33: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:52:33: # Command line: callpeak -t SRX4233888.bam -f BAM -g 12100000 -n SRX4233888.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4233888.20 # format = BAM # ChIP-seq file = ['SRX4233888.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 10:52:33: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:52:33: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:52:33: # Command line: callpeak -t SRX4233888.bam -f BAM -g 12100000 -n SRX4233888.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4233888.05 # format = BAM # ChIP-seq file = ['SRX4233888.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 10:52:33: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:52:33: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:52:40: 1000000 INFO @ Sat, 15 Sep 2018 10:52:41: 1000000 INFO @ Sat, 15 Sep 2018 10:52:41: 1000000 INFO @ Sat, 15 Sep 2018 10:52:46: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 10:52:46: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 10:52:46: #1 total tags in treatment: 1770123 INFO @ Sat, 15 Sep 2018 10:52:46: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:52:46: #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 10:52:46: #1 tags after filtering in treatment: 1770123 INFO @ Sat, 15 Sep 2018 10:52:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:52:46: #1 finished! INFO @ Sat, 15 Sep 2018 10:52:46: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:52:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:52:46: #2 number of paired peaks: 395 WARNING @ Sat, 15 Sep 2018 10:52:46: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Sat, 15 Sep 2018 10:52:46: start model_add_line... INFO @ Sat, 15 Sep 2018 10:52:46: start X-correlation... INFO @ Sat, 15 Sep 2018 10:52:46: end of X-cor INFO @ Sat, 15 Sep 2018 10:52:46: #2 finished! INFO @ Sat, 15 Sep 2018 10:52:46: #2 predicted fragment length is 248 bps INFO @ Sat, 15 Sep 2018 10:52:46: #2 alternative fragment length(s) may be 3,222,242,246,248 bps INFO @ Sat, 15 Sep 2018 10:52:46: #2.2 Generate R script for model : SRX4233888.10_model.r INFO @ Sat, 15 Sep 2018 10:52:46: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:52:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:52:46: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 10:52:46: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 10:52:46: #1 total tags in treatment: 1770123 INFO @ Sat, 15 Sep 2018 10:52:46: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:52:46: #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 10:52:46: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 10:52:46: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 10:52:46: #1 total tags in treatment: 1770123 INFO @ Sat, 15 Sep 2018 10:52:46: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:52:46: #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 10:52:46: #1 tags after filtering in treatment: 1770123 INFO @ Sat, 15 Sep 2018 10:52:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:52:46: #1 finished! INFO @ Sat, 15 Sep 2018 10:52:46: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:52:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:52:46: #1 tags after filtering in treatment: 1770123 INFO @ Sat, 15 Sep 2018 10:52:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:52:46: #1 finished! INFO @ Sat, 15 Sep 2018 10:52:46: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:52:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:52:47: #2 number of paired peaks: 395 WARNING @ Sat, 15 Sep 2018 10:52:47: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Sat, 15 Sep 2018 10:52:47: start model_add_line... INFO @ Sat, 15 Sep 2018 10:52:47: #2 number of paired peaks: 395 WARNING @ Sat, 15 Sep 2018 10:52:47: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Sat, 15 Sep 2018 10:52:47: start model_add_line... INFO @ Sat, 15 Sep 2018 10:52:47: start X-correlation... INFO @ Sat, 15 Sep 2018 10:52:47: end of X-cor INFO @ Sat, 15 Sep 2018 10:52:47: #2 finished! INFO @ Sat, 15 Sep 2018 10:52:47: #2 predicted fragment length is 248 bps INFO @ Sat, 15 Sep 2018 10:52:47: #2 alternative fragment length(s) may be 3,222,242,246,248 bps INFO @ Sat, 15 Sep 2018 10:52:47: #2.2 Generate R script for model : SRX4233888.20_model.r INFO @ Sat, 15 Sep 2018 10:52:47: start X-correlation... INFO @ Sat, 15 Sep 2018 10:52:47: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:52:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:52:47: end of X-cor INFO @ Sat, 15 Sep 2018 10:52:47: #2 finished! INFO @ Sat, 15 Sep 2018 10:52:47: #2 predicted fragment length is 248 bps INFO @ Sat, 15 Sep 2018 10:52:47: #2 alternative fragment length(s) may be 3,222,242,246,248 bps INFO @ Sat, 15 Sep 2018 10:52:47: #2.2 Generate R script for model : SRX4233888.05_model.r INFO @ Sat, 15 Sep 2018 10:52:47: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:52:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:52:55: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:52:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:52:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:52:57: #4 Write output xls file... SRX4233888.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:52:57: #4 Write peak in narrowPeak format file... SRX4233888.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:52:57: #4 Write summits bed file... SRX4233888.10_summits.bed INFO @ Sat, 15 Sep 2018 10:52:57: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (528 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:52:58: #4 Write output xls file... SRX4233888.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:52:58: #4 Write peak in narrowPeak format file... SRX4233888.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:52:58: #4 Write summits bed file... SRX4233888.20_summits.bed INFO @ Sat, 15 Sep 2018 10:52:58: Done! INFO @ Sat, 15 Sep 2018 10:52:58: #4 Write output xls file... SRX4233888.05_peaks.xls pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (292 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:52:58: #4 Write peak in narrowPeak format file... SRX4233888.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:52:58: #4 Write summits bed file... SRX4233888.05_summits.bed INFO @ Sat, 15 Sep 2018 10:52:58: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (848 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。