Job ID = 11634719 sra ファイルのダウンロード中... Completed: 614961K bytes transferred in 9 seconds (511161K 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 34210977 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4957454/SRR8136468.sra Written 34210977 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4957454/SRR8136468.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: 00:06:15 34210977 reads; of these: 34210977 (100.00%) were unpaired; of these: 2890232 (8.45%) aligned 0 times 21388340 (62.52%) aligned exactly 1 time 9932405 (29.03%) aligned >1 times 91.55% overall alignment rate Time searching: 00:06:15 Overall time: 00:06:15 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 16 files... [bam_rmdupse_core] 28976583 / 31320745 = 0.9252 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 @ Fri, 15 Feb 2019 10:53:37: # Command line: callpeak -t SRX4957454.bam -f BAM -g 12100000 -n SRX4957454.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4957454.10 # format = BAM # ChIP-seq file = ['SRX4957454.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 @ Fri, 15 Feb 2019 10:53:37: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:53:37: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:53:37: # Command line: callpeak -t SRX4957454.bam -f BAM -g 12100000 -n SRX4957454.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4957454.20 # format = BAM # ChIP-seq file = ['SRX4957454.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 @ Fri, 15 Feb 2019 10:53:37: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:53:37: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:53:37: # Command line: callpeak -t SRX4957454.bam -f BAM -g 12100000 -n SRX4957454.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4957454.05 # format = BAM # ChIP-seq file = ['SRX4957454.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 @ Fri, 15 Feb 2019 10:53:37: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:53:37: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:53:44: 1000000 INFO @ Fri, 15 Feb 2019 10:53:44: 1000000 INFO @ Fri, 15 Feb 2019 10:53:44: 1000000 INFO @ Fri, 15 Feb 2019 10:53:50: 2000000 INFO @ Fri, 15 Feb 2019 10:53:51: 2000000 INFO @ Fri, 15 Feb 2019 10:53:51: 2000000 INFO @ Fri, 15 Feb 2019 10:53:53: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:53:53: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:53:53: #1 total tags in treatment: 2344162 INFO @ Fri, 15 Feb 2019 10:53:53: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:53:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:53:53: #1 tags after filtering in treatment: 2344162 INFO @ Fri, 15 Feb 2019 10:53:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:53:53: #1 finished! INFO @ Fri, 15 Feb 2019 10:53:53: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:53:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:53:53: #2 number of paired peaks: 320 WARNING @ Fri, 15 Feb 2019 10:53:53: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Fri, 15 Feb 2019 10:53:53: start model_add_line... INFO @ Fri, 15 Feb 2019 10:53:53: start X-correlation... INFO @ Fri, 15 Feb 2019 10:53:53: end of X-cor INFO @ Fri, 15 Feb 2019 10:53:53: #2 finished! INFO @ Fri, 15 Feb 2019 10:53:53: #2 predicted fragment length is 349 bps INFO @ Fri, 15 Feb 2019 10:53:53: #2 alternative fragment length(s) may be 349 bps INFO @ Fri, 15 Feb 2019 10:53:53: #2.2 Generate R script for model : SRX4957454.05_model.r INFO @ Fri, 15 Feb 2019 10:53:53: #3 Call peaks... INFO @ Fri, 15 Feb 2019 10:53:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 10:53:53: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:53:53: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:53:53: #1 total tags in treatment: 2344162 INFO @ Fri, 15 Feb 2019 10:53:53: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:53:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:53:53: #1 tags after filtering in treatment: 2344162 INFO @ Fri, 15 Feb 2019 10:53:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:53:53: #1 finished! INFO @ Fri, 15 Feb 2019 10:53:53: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:53:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:53:53: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:53:53: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:53:53: #1 total tags in treatment: 2344162 INFO @ Fri, 15 Feb 2019 10:53:53: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:53:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:53:53: #2 number of paired peaks: 320 WARNING @ Fri, 15 Feb 2019 10:53:53: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Fri, 15 Feb 2019 10:53:53: start model_add_line... INFO @ Fri, 15 Feb 2019 10:53:53: #1 tags after filtering in treatment: 2344162 INFO @ Fri, 15 Feb 2019 10:53:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:53:53: #1 finished! INFO @ Fri, 15 Feb 2019 10:53:53: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:53:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:53:53: start X-correlation... INFO @ Fri, 15 Feb 2019 10:53:53: end of X-cor INFO @ Fri, 15 Feb 2019 10:53:53: #2 finished! INFO @ Fri, 15 Feb 2019 10:53:53: #2 predicted fragment length is 349 bps INFO @ Fri, 15 Feb 2019 10:53:53: #2 alternative fragment length(s) may be 349 bps INFO @ Fri, 15 Feb 2019 10:53:53: #2.2 Generate R script for model : SRX4957454.20_model.r INFO @ Fri, 15 Feb 2019 10:53:53: #3 Call peaks... INFO @ Fri, 15 Feb 2019 10:53:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 10:53:54: #2 number of paired peaks: 320 WARNING @ Fri, 15 Feb 2019 10:53:54: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Fri, 15 Feb 2019 10:53:54: start model_add_line... INFO @ Fri, 15 Feb 2019 10:53:54: start X-correlation... INFO @ Fri, 15 Feb 2019 10:53:54: end of X-cor INFO @ Fri, 15 Feb 2019 10:53:54: #2 finished! INFO @ Fri, 15 Feb 2019 10:53:54: #2 predicted fragment length is 349 bps INFO @ Fri, 15 Feb 2019 10:53:54: #2 alternative fragment length(s) may be 349 bps INFO @ Fri, 15 Feb 2019 10:53:54: #2.2 Generate R script for model : SRX4957454.10_model.r INFO @ Fri, 15 Feb 2019 10:53:54: #3 Call peaks... INFO @ Fri, 15 Feb 2019 10:53:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 10:54:09: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 10:54:09: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 10:54:09: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 10:54:12: #4 Write output xls file... SRX4957454.20_peaks.xls INFO @ Fri, 15 Feb 2019 10:54:12: #4 Write peak in narrowPeak format file... SRX4957454.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 10:54:12: #4 Write output xls file... SRX4957454.05_peaks.xls INFO @ Fri, 15 Feb 2019 10:54:12: #4 Write summits bed file... SRX4957454.20_summits.bed INFO @ Fri, 15 Feb 2019 10:54:12: Done! INFO @ Fri, 15 Feb 2019 10:54:12: #4 Write peak in narrowPeak format file... SRX4957454.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 10:54:12: #4 Write summits bed file... SRX4957454.05_summits.bed INFO @ Fri, 15 Feb 2019 10:54:12: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (643 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (16 chroms): 16 millis pass2 - checking and writing primary data (991 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 10:54:12: #4 Write output xls file... SRX4957454.10_peaks.xls INFO @ Fri, 15 Feb 2019 10:54:12: #4 Write peak in narrowPeak format file... SRX4957454.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 10:54:12: #4 Write summits bed file... SRX4957454.10_summits.bed INFO @ Fri, 15 Feb 2019 10:54:12: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (794 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。