Job ID = 2008386 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,865,399 reads read : 10,865,399 reads written : 10,865,399 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637592.sra.cache’: No such file or directory 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: 00:03:34 10865399 reads; of these: 10865399 (100.00%) were unpaired; of these: 2329196 (21.44%) aligned 0 times 6892511 (63.44%) aligned exactly 1 time 1643692 (15.13%) aligned >1 times 78.56% overall alignment rate Time searching: 00:03:34 Overall time: 00:03:34 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] 4449292 / 8536203 = 0.5212 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, 05 Jul 2019 18:59:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.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, 05 Jul 2019 18:59:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:59:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:59:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.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, 05 Jul 2019 18:59:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:59:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:00:02: 1000000 INFO @ Fri, 05 Jul 2019 19:00:02: 1000000 INFO @ Fri, 05 Jul 2019 19:00:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.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, 05 Jul 2019 19:00:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:00:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:00:10: 2000000 INFO @ Fri, 05 Jul 2019 19:00:11: 2000000 INFO @ Fri, 05 Jul 2019 19:00:18: 3000000 INFO @ Fri, 05 Jul 2019 19:00:19: 1000000 INFO @ Fri, 05 Jul 2019 19:00:21: 3000000 INFO @ Fri, 05 Jul 2019 19:00:27: 4000000 INFO @ Fri, 05 Jul 2019 19:00:27: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 19:00:27: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 19:00:27: #1 total tags in treatment: 4086911 INFO @ Fri, 05 Jul 2019 19:00:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:00:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:00:27: #1 tags after filtering in treatment: 4086911 INFO @ Fri, 05 Jul 2019 19:00:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:00:27: #1 finished! INFO @ Fri, 05 Jul 2019 19:00:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:00:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:00:28: #2 number of paired peaks: 108 WARNING @ Fri, 05 Jul 2019 19:00:28: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Fri, 05 Jul 2019 19:00:28: start model_add_line... INFO @ Fri, 05 Jul 2019 19:00:28: start X-correlation... INFO @ Fri, 05 Jul 2019 19:00:28: end of X-cor INFO @ Fri, 05 Jul 2019 19:00:28: #2 finished! INFO @ Fri, 05 Jul 2019 19:00:28: #2 predicted fragment length is 92 bps INFO @ Fri, 05 Jul 2019 19:00:28: #2 alternative fragment length(s) may be 3,71,92 bps INFO @ Fri, 05 Jul 2019 19:00:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.10_model.r WARNING @ Fri, 05 Jul 2019 19:00:28: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 19:00:28: #2 You may need to consider one of the other alternative d(s): 3,71,92 WARNING @ Fri, 05 Jul 2019 19:00:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 19:00:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:00:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:00:28: 2000000 INFO @ Fri, 05 Jul 2019 19:00:30: 4000000 INFO @ Fri, 05 Jul 2019 19:00:31: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 19:00:31: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 19:00:31: #1 total tags in treatment: 4086911 INFO @ Fri, 05 Jul 2019 19:00:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:00:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:00:31: #1 tags after filtering in treatment: 4086911 INFO @ Fri, 05 Jul 2019 19:00:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:00:31: #1 finished! INFO @ Fri, 05 Jul 2019 19:00:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:00:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:00:31: #2 number of paired peaks: 108 WARNING @ Fri, 05 Jul 2019 19:00:31: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Fri, 05 Jul 2019 19:00:31: start model_add_line... INFO @ Fri, 05 Jul 2019 19:00:31: start X-correlation... INFO @ Fri, 05 Jul 2019 19:00:31: end of X-cor INFO @ Fri, 05 Jul 2019 19:00:31: #2 finished! INFO @ Fri, 05 Jul 2019 19:00:31: #2 predicted fragment length is 92 bps INFO @ Fri, 05 Jul 2019 19:00:31: #2 alternative fragment length(s) may be 3,71,92 bps INFO @ Fri, 05 Jul 2019 19:00:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.05_model.r INFO @ Fri, 05 Jul 2019 19:00:37: 3000000 INFO @ Fri, 05 Jul 2019 19:00:39: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:00:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:00:46: 4000000 INFO @ Fri, 05 Jul 2019 19:00:47: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 19:00:47: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 19:00:47: #1 total tags in treatment: 4086911 INFO @ Fri, 05 Jul 2019 19:00:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:00:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:00:47: #1 tags after filtering in treatment: 4086911 INFO @ Fri, 05 Jul 2019 19:00:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:00:47: #1 finished! INFO @ Fri, 05 Jul 2019 19:00:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:00:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:00:47: #2 number of paired peaks: 108 WARNING @ Fri, 05 Jul 2019 19:00:47: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Fri, 05 Jul 2019 19:00:47: start model_add_line... INFO @ Fri, 05 Jul 2019 19:00:47: start X-correlation... INFO @ Fri, 05 Jul 2019 19:00:47: end of X-cor INFO @ Fri, 05 Jul 2019 19:00:47: #2 finished! INFO @ Fri, 05 Jul 2019 19:00:47: #2 predicted fragment length is 92 bps INFO @ Fri, 05 Jul 2019 19:00:47: #2 alternative fragment length(s) may be 3,71,92 bps INFO @ Fri, 05 Jul 2019 19:00:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.20_model.r WARNING @ Fri, 05 Jul 2019 19:01:19: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 19:01:19: #2 You may need to consider one of the other alternative d(s): 3,71,92 WARNING @ Fri, 05 Jul 2019 19:01:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 19:01:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:01:19: #3 Pre-compute pvalue-qvalue table... WARNING @ Fri, 05 Jul 2019 19:01:19: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 19:01:19: #2 You may need to consider one of the other alternative d(s): 3,71,92 WARNING @ Fri, 05 Jul 2019 19:01:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 19:01:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:01:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:01:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:01:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.10_summits.bed INFO @ Fri, 05 Jul 2019 19:01:19: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (3830 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:01:31: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:01:31: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 19:01:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:01:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:01:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:01:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.20_summits.bed INFO @ Fri, 05 Jul 2019 19:01:35: Done! INFO @ Fri, 05 Jul 2019 19:01:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:01:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX593999/ERX593999.05_summits.bed INFO @ Fri, 05 Jul 2019 19:01:35: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (1935 records, 4 fields): 7 millis pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (5534 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling