Job ID = 2590273 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,743,774 reads read : 5,743,774 reads written : 5,743,774 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR504795.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: 00:01:51 5743774 reads; of these: 5743774 (100.00%) were unpaired; of these: 275142 (4.79%) aligned 0 times 3821697 (66.54%) aligned exactly 1 time 1646935 (28.67%) aligned >1 times 95.21% overall alignment rate Time searching: 00:01:51 Overall time: 00:01:51 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 552130 / 5468632 = 0.1010 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 @ Mon, 12 Aug 2019 20:24:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 12 Aug 2019 20:24:47: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:24:47: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:24:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 12 Aug 2019 20:24:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:24:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:24:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 12 Aug 2019 20:24:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:24:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:24:55: 1000000 INFO @ Mon, 12 Aug 2019 20:24:56: 1000000 INFO @ Mon, 12 Aug 2019 20:24:56: 1000000 INFO @ Mon, 12 Aug 2019 20:25:02: 2000000 INFO @ Mon, 12 Aug 2019 20:25:03: 2000000 INFO @ Mon, 12 Aug 2019 20:25:03: 2000000 INFO @ Mon, 12 Aug 2019 20:25:10: 3000000 INFO @ Mon, 12 Aug 2019 20:25:11: 3000000 INFO @ Mon, 12 Aug 2019 20:25:11: 3000000 INFO @ Mon, 12 Aug 2019 20:25:18: 4000000 INFO @ Mon, 12 Aug 2019 20:25:18: 4000000 INFO @ Mon, 12 Aug 2019 20:25:19: 4000000 INFO @ Mon, 12 Aug 2019 20:25:25: #1 tag size is determined as 30 bps INFO @ Mon, 12 Aug 2019 20:25:25: #1 tag size = 30 INFO @ Mon, 12 Aug 2019 20:25:25: #1 total tags in treatment: 4916502 INFO @ Mon, 12 Aug 2019 20:25:25: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:25:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:25:25: #1 tags after filtering in treatment: 4916502 INFO @ Mon, 12 Aug 2019 20:25:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:25:25: #1 finished! INFO @ Mon, 12 Aug 2019 20:25:25: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:25:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:25:25: #1 tag size is determined as 30 bps INFO @ Mon, 12 Aug 2019 20:25:25: #1 tag size = 30 INFO @ Mon, 12 Aug 2019 20:25:25: #1 total tags in treatment: 4916502 INFO @ Mon, 12 Aug 2019 20:25:25: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:25:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:25:25: #1 tags after filtering in treatment: 4916502 INFO @ Mon, 12 Aug 2019 20:25:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:25:25: #1 finished! INFO @ Mon, 12 Aug 2019 20:25:25: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:25:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:25:25: #2 number of paired peaks: 931 WARNING @ Mon, 12 Aug 2019 20:25:25: Fewer paired peaks (931) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 931 pairs to build model! INFO @ Mon, 12 Aug 2019 20:25:25: start model_add_line... INFO @ Mon, 12 Aug 2019 20:25:25: start X-correlation... INFO @ Mon, 12 Aug 2019 20:25:25: end of X-cor INFO @ Mon, 12 Aug 2019 20:25:25: #2 finished! INFO @ Mon, 12 Aug 2019 20:25:25: #2 predicted fragment length is 32 bps INFO @ Mon, 12 Aug 2019 20:25:25: #2 alternative fragment length(s) may be 32 bps INFO @ Mon, 12 Aug 2019 20:25:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.05_model.r WARNING @ Mon, 12 Aug 2019 20:25:25: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:25:25: #2 You may need to consider one of the other alternative d(s): 32 WARNING @ Mon, 12 Aug 2019 20:25:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:25:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:25:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:25:25: #2 number of paired peaks: 931 WARNING @ Mon, 12 Aug 2019 20:25:25: Fewer paired peaks (931) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 931 pairs to build model! INFO @ Mon, 12 Aug 2019 20:25:25: start model_add_line... INFO @ Mon, 12 Aug 2019 20:25:25: start X-correlation... INFO @ Mon, 12 Aug 2019 20:25:25: end of X-cor INFO @ Mon, 12 Aug 2019 20:25:25: #2 finished! INFO @ Mon, 12 Aug 2019 20:25:25: #2 predicted fragment length is 32 bps INFO @ Mon, 12 Aug 2019 20:25:25: #2 alternative fragment length(s) may be 32 bps INFO @ Mon, 12 Aug 2019 20:25:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.20_model.r WARNING @ Mon, 12 Aug 2019 20:25:25: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:25:25: #2 You may need to consider one of the other alternative d(s): 32 WARNING @ Mon, 12 Aug 2019 20:25:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:25:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:25:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:25:26: #1 tag size is determined as 30 bps INFO @ Mon, 12 Aug 2019 20:25:26: #1 tag size = 30 INFO @ Mon, 12 Aug 2019 20:25:26: #1 total tags in treatment: 4916502 INFO @ Mon, 12 Aug 2019 20:25:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:25:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:25:26: #1 tags after filtering in treatment: 4916502 INFO @ Mon, 12 Aug 2019 20:25:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:25:26: #1 finished! INFO @ Mon, 12 Aug 2019 20:25:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:25:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:25:26: #2 number of paired peaks: 931 WARNING @ Mon, 12 Aug 2019 20:25:26: Fewer paired peaks (931) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 931 pairs to build model! INFO @ Mon, 12 Aug 2019 20:25:26: start model_add_line... INFO @ Mon, 12 Aug 2019 20:25:27: start X-correlation... INFO @ Mon, 12 Aug 2019 20:25:27: end of X-cor INFO @ Mon, 12 Aug 2019 20:25:27: #2 finished! INFO @ Mon, 12 Aug 2019 20:25:27: #2 predicted fragment length is 32 bps INFO @ Mon, 12 Aug 2019 20:25:27: #2 alternative fragment length(s) may be 32 bps INFO @ Mon, 12 Aug 2019 20:25:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.10_model.r WARNING @ Mon, 12 Aug 2019 20:25:27: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:25:27: #2 You may need to consider one of the other alternative d(s): 32 WARNING @ Mon, 12 Aug 2019 20:25:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:25:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:25:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:25:40: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:25:40: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:25:41: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:25:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:25:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:25:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.05_summits.bed INFO @ Mon, 12 Aug 2019 20:25:47: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1853 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:25:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:25:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:25:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.20_summits.bed INFO @ Mon, 12 Aug 2019 20:25:48: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (658 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:25:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:25:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:25:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX151961/SRX151961.10_summits.bed INFO @ Mon, 12 Aug 2019 20:25:48: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1143 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。