Job ID = 1292400 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,861,156 reads read : 6,861,156 reads written : 6,861,156 spots read : 5,956,085 reads read : 5,956,085 reads written : 5,956,085 rm: cannot remove ‘fastqDump_tmp*’: 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: 00:02:29 12817241 reads; of these: 12817241 (100.00%) were unpaired; of these: 105269 (0.82%) aligned 0 times 10658932 (83.16%) aligned exactly 1 time 2053040 (16.02%) aligned >1 times 99.18% overall alignment rate Time searching: 00:02:30 Overall time: 00:02:30 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] 1211824 / 12711972 = 0.0953 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 @ Sun, 02 Jun 2019 18:21:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.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 @ Sun, 02 Jun 2019 18:21:02: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:21:02: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:21:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.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 @ Sun, 02 Jun 2019 18:21:02: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:21:02: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:21:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.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 @ Sun, 02 Jun 2019 18:21:02: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:21:02: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:21:09: 1000000 INFO @ Sun, 02 Jun 2019 18:21:10: 1000000 INFO @ Sun, 02 Jun 2019 18:21:10: 1000000 INFO @ Sun, 02 Jun 2019 18:21:15: 2000000 INFO @ Sun, 02 Jun 2019 18:21:17: 2000000 INFO @ Sun, 02 Jun 2019 18:21:17: 2000000 INFO @ Sun, 02 Jun 2019 18:21:22: 3000000 INFO @ Sun, 02 Jun 2019 18:21:24: 3000000 INFO @ Sun, 02 Jun 2019 18:21:24: 3000000 INFO @ Sun, 02 Jun 2019 18:21:28: 4000000 INFO @ Sun, 02 Jun 2019 18:21:31: 4000000 INFO @ Sun, 02 Jun 2019 18:21:31: 4000000 INFO @ Sun, 02 Jun 2019 18:21:35: 5000000 INFO @ Sun, 02 Jun 2019 18:21:38: 5000000 INFO @ Sun, 02 Jun 2019 18:21:39: 5000000 INFO @ Sun, 02 Jun 2019 18:21:42: 6000000 INFO @ Sun, 02 Jun 2019 18:21:45: 6000000 INFO @ Sun, 02 Jun 2019 18:21:46: 6000000 INFO @ Sun, 02 Jun 2019 18:21:48: 7000000 INFO @ Sun, 02 Jun 2019 18:21:52: 7000000 INFO @ Sun, 02 Jun 2019 18:21:54: 7000000 INFO @ Sun, 02 Jun 2019 18:21:54: 8000000 INFO @ Sun, 02 Jun 2019 18:21:59: 8000000 INFO @ Sun, 02 Jun 2019 18:22:00: 9000000 INFO @ Sun, 02 Jun 2019 18:22:01: 8000000 INFO @ Sun, 02 Jun 2019 18:22:06: 9000000 INFO @ Sun, 02 Jun 2019 18:22:07: 10000000 INFO @ Sun, 02 Jun 2019 18:22:08: 9000000 INFO @ Sun, 02 Jun 2019 18:22:13: 11000000 INFO @ Sun, 02 Jun 2019 18:22:13: 10000000 INFO @ Sun, 02 Jun 2019 18:22:15: 10000000 INFO @ Sun, 02 Jun 2019 18:22:16: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 18:22:16: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 18:22:16: #1 total tags in treatment: 11500148 INFO @ Sun, 02 Jun 2019 18:22:16: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:22:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:22:16: #1 tags after filtering in treatment: 11500148 INFO @ Sun, 02 Jun 2019 18:22:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:22:16: #1 finished! INFO @ Sun, 02 Jun 2019 18:22:16: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:22:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:22:17: #2 number of paired peaks: 330 WARNING @ Sun, 02 Jun 2019 18:22:17: Fewer paired peaks (330) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 330 pairs to build model! INFO @ Sun, 02 Jun 2019 18:22:17: start model_add_line... INFO @ Sun, 02 Jun 2019 18:22:17: start X-correlation... INFO @ Sun, 02 Jun 2019 18:22:17: end of X-cor INFO @ Sun, 02 Jun 2019 18:22:17: #2 finished! INFO @ Sun, 02 Jun 2019 18:22:17: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 18:22:17: #2 alternative fragment length(s) may be 1,26,539,549,578 bps INFO @ Sun, 02 Jun 2019 18:22:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.10_model.r WARNING @ Sun, 02 Jun 2019 18:22:17: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:22:17: #2 You may need to consider one of the other alternative d(s): 1,26,539,549,578 WARNING @ Sun, 02 Jun 2019 18:22:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:22:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:22:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:22:20: 11000000 INFO @ Sun, 02 Jun 2019 18:22:23: 11000000 INFO @ Sun, 02 Jun 2019 18:22:24: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 18:22:24: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 18:22:24: #1 total tags in treatment: 11500148 INFO @ Sun, 02 Jun 2019 18:22:24: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:22:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:22:24: #1 tags after filtering in treatment: 11500148 INFO @ Sun, 02 Jun 2019 18:22:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:22:24: #1 finished! INFO @ Sun, 02 Jun 2019 18:22:24: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:22:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:22:25: #2 number of paired peaks: 330 WARNING @ Sun, 02 Jun 2019 18:22:25: Fewer paired peaks (330) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 330 pairs to build model! INFO @ Sun, 02 Jun 2019 18:22:25: start model_add_line... INFO @ Sun, 02 Jun 2019 18:22:25: start X-correlation... INFO @ Sun, 02 Jun 2019 18:22:25: end of X-cor INFO @ Sun, 02 Jun 2019 18:22:25: #2 finished! INFO @ Sun, 02 Jun 2019 18:22:25: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 18:22:25: #2 alternative fragment length(s) may be 1,26,539,549,578 bps INFO @ Sun, 02 Jun 2019 18:22:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.20_model.r WARNING @ Sun, 02 Jun 2019 18:22:25: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:22:25: #2 You may need to consider one of the other alternative d(s): 1,26,539,549,578 WARNING @ Sun, 02 Jun 2019 18:22:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:22:25: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:22:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:22:27: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 18:22:27: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 18:22:27: #1 total tags in treatment: 11500148 INFO @ Sun, 02 Jun 2019 18:22:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:22:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:22:27: #1 tags after filtering in treatment: 11500148 INFO @ Sun, 02 Jun 2019 18:22:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:22:27: #1 finished! INFO @ Sun, 02 Jun 2019 18:22:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:22:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:22:28: #2 number of paired peaks: 330 WARNING @ Sun, 02 Jun 2019 18:22:28: Fewer paired peaks (330) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 330 pairs to build model! INFO @ Sun, 02 Jun 2019 18:22:28: start model_add_line... INFO @ Sun, 02 Jun 2019 18:22:28: start X-correlation... INFO @ Sun, 02 Jun 2019 18:22:28: end of X-cor INFO @ Sun, 02 Jun 2019 18:22:28: #2 finished! INFO @ Sun, 02 Jun 2019 18:22:28: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 18:22:28: #2 alternative fragment length(s) may be 1,26,539,549,578 bps INFO @ Sun, 02 Jun 2019 18:22:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.05_model.r WARNING @ Sun, 02 Jun 2019 18:22:28: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:22:28: #2 You may need to consider one of the other alternative d(s): 1,26,539,549,578 WARNING @ Sun, 02 Jun 2019 18:22:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:22:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:22:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:22:46: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:22:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:22:56: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:22:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:22:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:22:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.10_summits.bed INFO @ Sun, 02 Jun 2019 18:22:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:23:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:23:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:23:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.20_summits.bed INFO @ Sun, 02 Jun 2019 18:23:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:23:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:23:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:23:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX395532/SRX395532.05_summits.bed INFO @ Sun, 02 Jun 2019 18:23:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。