Job ID = 2589525 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,490,240 reads read : 7,490,240 reads written : 7,490,240 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR701501.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: 00:01:22 7490240 reads; of these: 7490240 (100.00%) were unpaired; of these: 948919 (12.67%) aligned 0 times 5428677 (72.48%) aligned exactly 1 time 1112644 (14.85%) aligned >1 times 87.33% overall alignment rate Time searching: 00:01:22 Overall time: 00:01:22 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] 464024 / 6541321 = 0.0709 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 17:55:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.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 17:55:03: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:55:03: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:55:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.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 17:55:04: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:55:04: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:55:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.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 17:55:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:55:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:55:11: 1000000 INFO @ Mon, 12 Aug 2019 17:55:12: 1000000 INFO @ Mon, 12 Aug 2019 17:55:15: 1000000 INFO @ Mon, 12 Aug 2019 17:55:19: 2000000 INFO @ Mon, 12 Aug 2019 17:55:20: 2000000 INFO @ Mon, 12 Aug 2019 17:55:23: 2000000 INFO @ Mon, 12 Aug 2019 17:55:27: 3000000 INFO @ Mon, 12 Aug 2019 17:55:28: 3000000 INFO @ Mon, 12 Aug 2019 17:55:32: 3000000 INFO @ Mon, 12 Aug 2019 17:55:34: 4000000 INFO @ Mon, 12 Aug 2019 17:55:35: 4000000 INFO @ Mon, 12 Aug 2019 17:55:41: 4000000 INFO @ Mon, 12 Aug 2019 17:55:42: 5000000 INFO @ Mon, 12 Aug 2019 17:55:43: 5000000 INFO @ Mon, 12 Aug 2019 17:55:50: 6000000 INFO @ Mon, 12 Aug 2019 17:55:50: 5000000 INFO @ Mon, 12 Aug 2019 17:55:50: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:55:50: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:55:50: #1 total tags in treatment: 6077297 INFO @ Mon, 12 Aug 2019 17:55:50: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:55:50: #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 17:55:50: #1 tags after filtering in treatment: 6077297 INFO @ Mon, 12 Aug 2019 17:55:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:55:50: #1 finished! INFO @ Mon, 12 Aug 2019 17:55:50: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:55:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:55:51: 6000000 INFO @ Mon, 12 Aug 2019 17:55:51: #2 number of paired peaks: 403 WARNING @ Mon, 12 Aug 2019 17:55:51: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Mon, 12 Aug 2019 17:55:51: start model_add_line... INFO @ Mon, 12 Aug 2019 17:55:51: start X-correlation... INFO @ Mon, 12 Aug 2019 17:55:51: end of X-cor INFO @ Mon, 12 Aug 2019 17:55:51: #2 finished! INFO @ Mon, 12 Aug 2019 17:55:51: #2 predicted fragment length is 29 bps INFO @ Mon, 12 Aug 2019 17:55:51: #2 alternative fragment length(s) may be 2,29,550 bps INFO @ Mon, 12 Aug 2019 17:55:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.05_model.r WARNING @ Mon, 12 Aug 2019 17:55:51: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:55:51: #2 You may need to consider one of the other alternative d(s): 2,29,550 WARNING @ Mon, 12 Aug 2019 17:55:51: #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 17:55:51: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:55:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:55:51: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:55:51: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:55:51: #1 total tags in treatment: 6077297 INFO @ Mon, 12 Aug 2019 17:55:51: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:55:51: #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 17:55:51: #1 tags after filtering in treatment: 6077297 INFO @ Mon, 12 Aug 2019 17:55:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:55:51: #1 finished! INFO @ Mon, 12 Aug 2019 17:55:51: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:55:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:55:52: #2 number of paired peaks: 403 WARNING @ Mon, 12 Aug 2019 17:55:52: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Mon, 12 Aug 2019 17:55:52: start model_add_line... INFO @ Mon, 12 Aug 2019 17:55:52: start X-correlation... INFO @ Mon, 12 Aug 2019 17:55:52: end of X-cor INFO @ Mon, 12 Aug 2019 17:55:52: #2 finished! INFO @ Mon, 12 Aug 2019 17:55:52: #2 predicted fragment length is 29 bps INFO @ Mon, 12 Aug 2019 17:55:52: #2 alternative fragment length(s) may be 2,29,550 bps INFO @ Mon, 12 Aug 2019 17:55:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.10_model.r WARNING @ Mon, 12 Aug 2019 17:55:52: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:55:52: #2 You may need to consider one of the other alternative d(s): 2,29,550 WARNING @ Mon, 12 Aug 2019 17:55:52: #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 17:55:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:55:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:55:58: 6000000 INFO @ Mon, 12 Aug 2019 17:55:59: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:55:59: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:55:59: #1 total tags in treatment: 6077297 INFO @ Mon, 12 Aug 2019 17:55:59: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:55:59: #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 17:55:59: #1 tags after filtering in treatment: 6077297 INFO @ Mon, 12 Aug 2019 17:55:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:55:59: #1 finished! INFO @ Mon, 12 Aug 2019 17:55:59: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:55:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:56:00: #2 number of paired peaks: 403 WARNING @ Mon, 12 Aug 2019 17:56:00: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Mon, 12 Aug 2019 17:56:00: start model_add_line... INFO @ Mon, 12 Aug 2019 17:56:00: start X-correlation... INFO @ Mon, 12 Aug 2019 17:56:00: end of X-cor INFO @ Mon, 12 Aug 2019 17:56:00: #2 finished! INFO @ Mon, 12 Aug 2019 17:56:00: #2 predicted fragment length is 29 bps INFO @ Mon, 12 Aug 2019 17:56:00: #2 alternative fragment length(s) may be 2,29,550 bps INFO @ Mon, 12 Aug 2019 17:56:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.20_model.r WARNING @ Mon, 12 Aug 2019 17:56:00: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:56:00: #2 You may need to consider one of the other alternative d(s): 2,29,550 WARNING @ Mon, 12 Aug 2019 17:56:00: #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 17:56:00: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:56:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:56:08: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:56:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:56:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:56:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:56:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.05_summits.bed INFO @ Mon, 12 Aug 2019 17:56:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (574 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:56:17: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:56:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:56:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:56:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.10_summits.bed INFO @ Mon, 12 Aug 2019 17:56:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (296 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:56:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:56:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:56:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233446/SRX233446.20_summits.bed INFO @ Mon, 12 Aug 2019 17:56:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (74 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。