Job ID = 2589535 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,482,158 reads read : 6,482,158 reads written : 6,482,158 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR701511.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:02 6482158 reads; of these: 6482158 (100.00%) were unpaired; of these: 1175260 (18.13%) aligned 0 times 4429295 (68.33%) aligned exactly 1 time 877603 (13.54%) aligned >1 times 81.87% overall alignment rate Time searching: 00:01:03 Overall time: 00:01:03 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 326210 / 5306898 = 0.0615 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 17:55:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 17:55:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:55:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:55:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 17:55:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:55:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:55:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 17:55:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:55:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:55:39: 1000000 INFO @ Mon, 12 Aug 2019 17:55:41: 1000000 INFO @ Mon, 12 Aug 2019 17:55:43: 1000000 INFO @ Mon, 12 Aug 2019 17:55:45: 2000000 INFO @ Mon, 12 Aug 2019 17:55:48: 2000000 INFO @ Mon, 12 Aug 2019 17:55:51: 2000000 INFO @ Mon, 12 Aug 2019 17:55:52: 3000000 INFO @ Mon, 12 Aug 2019 17:55:55: 3000000 INFO @ Mon, 12 Aug 2019 17:55:58: 4000000 INFO @ Mon, 12 Aug 2019 17:55:59: 3000000 INFO @ Mon, 12 Aug 2019 17:56:01: 4000000 INFO @ Mon, 12 Aug 2019 17:56:04: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:56:04: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:56:04: #1 total tags in treatment: 4980688 INFO @ Mon, 12 Aug 2019 17:56:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:56:04: #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 17:56:04: #1 tags after filtering in treatment: 4980688 INFO @ Mon, 12 Aug 2019 17:56:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:56:04: #1 finished! INFO @ Mon, 12 Aug 2019 17:56:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:56:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:56:05: #2 number of paired peaks: 416 WARNING @ Mon, 12 Aug 2019 17:56:05: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Mon, 12 Aug 2019 17:56:05: start model_add_line... INFO @ Mon, 12 Aug 2019 17:56:05: start X-correlation... INFO @ Mon, 12 Aug 2019 17:56:05: end of X-cor INFO @ Mon, 12 Aug 2019 17:56:05: #2 finished! INFO @ Mon, 12 Aug 2019 17:56:05: #2 predicted fragment length is 35 bps INFO @ Mon, 12 Aug 2019 17:56:05: #2 alternative fragment length(s) may be 3,35,528,569 bps INFO @ Mon, 12 Aug 2019 17:56:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.05_model.r WARNING @ Mon, 12 Aug 2019 17:56:05: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:56:05: #2 You may need to consider one of the other alternative d(s): 3,35,528,569 WARNING @ Mon, 12 Aug 2019 17:56:05: #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 17:56:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:56:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:56:07: 4000000 INFO @ Mon, 12 Aug 2019 17:56:08: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:56:08: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:56:08: #1 total tags in treatment: 4980688 INFO @ Mon, 12 Aug 2019 17:56:08: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:56:08: #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 17:56:08: #1 tags after filtering in treatment: 4980688 INFO @ Mon, 12 Aug 2019 17:56:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:56:08: #1 finished! INFO @ Mon, 12 Aug 2019 17:56:08: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:56:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:56:09: #2 number of paired peaks: 416 WARNING @ Mon, 12 Aug 2019 17:56:09: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Mon, 12 Aug 2019 17:56:09: start model_add_line... INFO @ Mon, 12 Aug 2019 17:56:09: start X-correlation... INFO @ Mon, 12 Aug 2019 17:56:09: end of X-cor INFO @ Mon, 12 Aug 2019 17:56:09: #2 finished! INFO @ Mon, 12 Aug 2019 17:56:09: #2 predicted fragment length is 35 bps INFO @ Mon, 12 Aug 2019 17:56:09: #2 alternative fragment length(s) may be 3,35,528,569 bps INFO @ Mon, 12 Aug 2019 17:56:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.10_model.r WARNING @ Mon, 12 Aug 2019 17:56:09: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:56:09: #2 You may need to consider one of the other alternative d(s): 3,35,528,569 WARNING @ Mon, 12 Aug 2019 17:56:09: #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 17:56:09: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:56:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:56:14: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:56:14: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:56:14: #1 total tags in treatment: 4980688 INFO @ Mon, 12 Aug 2019 17:56:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:56:14: #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 17:56:14: #1 tags after filtering in treatment: 4980688 INFO @ Mon, 12 Aug 2019 17:56:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:56:14: #1 finished! INFO @ Mon, 12 Aug 2019 17:56:14: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:56:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:56:15: #2 number of paired peaks: 416 WARNING @ Mon, 12 Aug 2019 17:56:15: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Mon, 12 Aug 2019 17:56:15: start model_add_line... INFO @ Mon, 12 Aug 2019 17:56:15: start X-correlation... INFO @ Mon, 12 Aug 2019 17:56:15: end of X-cor INFO @ Mon, 12 Aug 2019 17:56:15: #2 finished! INFO @ Mon, 12 Aug 2019 17:56:15: #2 predicted fragment length is 35 bps INFO @ Mon, 12 Aug 2019 17:56:15: #2 alternative fragment length(s) may be 3,35,528,569 bps INFO @ Mon, 12 Aug 2019 17:56:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.20_model.r WARNING @ Mon, 12 Aug 2019 17:56:15: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:56:15: #2 You may need to consider one of the other alternative d(s): 3,35,528,569 WARNING @ Mon, 12 Aug 2019 17:56:15: #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 17:56:15: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:56:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:56:20: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:56:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:56:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:56:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:56:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.05_summits.bed INFO @ Mon, 12 Aug 2019 17:56:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (512 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:56:29: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:56:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:56:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:56:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.10_summits.bed INFO @ Mon, 12 Aug 2019 17:56:31: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (229 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:56:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:56:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:56:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233455/SRX233455.20_summits.bed INFO @ Mon, 12 Aug 2019 17:56:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (71 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。