Job ID = 1291863 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,816,963 reads read : 14,816,963 reads written : 14,816,963 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:02:41 14816963 reads; of these: 14816963 (100.00%) were unpaired; of these: 41566 (0.28%) aligned 0 times 12300120 (83.01%) aligned exactly 1 time 2475277 (16.71%) aligned >1 times 99.72% overall alignment rate Time searching: 00:02:41 Overall time: 00:02:41 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] 1634090 / 14775397 = 0.1106 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 16:52:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.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 16:52:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:52:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:52:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.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 16:52:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:52:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:52:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.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 16:52:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:52:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:52:39: 1000000 INFO @ Sun, 02 Jun 2019 16:52:39: 1000000 INFO @ Sun, 02 Jun 2019 16:52:41: 1000000 INFO @ Sun, 02 Jun 2019 16:52:46: 2000000 INFO @ Sun, 02 Jun 2019 16:52:47: 2000000 INFO @ Sun, 02 Jun 2019 16:52:50: 2000000 INFO @ Sun, 02 Jun 2019 16:52:52: 3000000 INFO @ Sun, 02 Jun 2019 16:52:53: 3000000 INFO @ Sun, 02 Jun 2019 16:52:59: 3000000 INFO @ Sun, 02 Jun 2019 16:52:59: 4000000 INFO @ Sun, 02 Jun 2019 16:53:00: 4000000 INFO @ Sun, 02 Jun 2019 16:53:06: 5000000 INFO @ Sun, 02 Jun 2019 16:53:07: 5000000 INFO @ Sun, 02 Jun 2019 16:53:07: 4000000 INFO @ Sun, 02 Jun 2019 16:53:12: 6000000 INFO @ Sun, 02 Jun 2019 16:53:14: 6000000 INFO @ Sun, 02 Jun 2019 16:53:16: 5000000 INFO @ Sun, 02 Jun 2019 16:53:19: 7000000 INFO @ Sun, 02 Jun 2019 16:53:21: 7000000 INFO @ Sun, 02 Jun 2019 16:53:24: 6000000 INFO @ Sun, 02 Jun 2019 16:53:25: 8000000 INFO @ Sun, 02 Jun 2019 16:53:28: 8000000 INFO @ Sun, 02 Jun 2019 16:53:32: 7000000 INFO @ Sun, 02 Jun 2019 16:53:32: 9000000 INFO @ Sun, 02 Jun 2019 16:53:35: 9000000 INFO @ Sun, 02 Jun 2019 16:53:38: 10000000 INFO @ Sun, 02 Jun 2019 16:53:40: 8000000 INFO @ Sun, 02 Jun 2019 16:53:42: 10000000 INFO @ Sun, 02 Jun 2019 16:53:45: 11000000 INFO @ Sun, 02 Jun 2019 16:53:47: 9000000 INFO @ Sun, 02 Jun 2019 16:53:48: 11000000 INFO @ Sun, 02 Jun 2019 16:53:51: 12000000 INFO @ Sun, 02 Jun 2019 16:53:55: 10000000 INFO @ Sun, 02 Jun 2019 16:53:55: 12000000 INFO @ Sun, 02 Jun 2019 16:53:58: 13000000 INFO @ Sun, 02 Jun 2019 16:53:59: #1 tag size is determined as 28 bps INFO @ Sun, 02 Jun 2019 16:53:59: #1 tag size = 28 INFO @ Sun, 02 Jun 2019 16:53:59: #1 total tags in treatment: 13141307 INFO @ Sun, 02 Jun 2019 16:53:59: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:53:59: #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 16:53:59: #1 tags after filtering in treatment: 13141307 INFO @ Sun, 02 Jun 2019 16:53:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:53:59: #1 finished! INFO @ Sun, 02 Jun 2019 16:53:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:53:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:54:00: #2 number of paired peaks: 334 WARNING @ Sun, 02 Jun 2019 16:54:00: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Sun, 02 Jun 2019 16:54:00: start model_add_line... INFO @ Sun, 02 Jun 2019 16:54:00: start X-correlation... INFO @ Sun, 02 Jun 2019 16:54:00: end of X-cor INFO @ Sun, 02 Jun 2019 16:54:00: #2 finished! INFO @ Sun, 02 Jun 2019 16:54:00: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:54:00: #2 alternative fragment length(s) may be 1,22,546 bps INFO @ Sun, 02 Jun 2019 16:54:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.05_model.r WARNING @ Sun, 02 Jun 2019 16:54:00: #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 16:54:00: #2 You may need to consider one of the other alternative d(s): 1,22,546 WARNING @ Sun, 02 Jun 2019 16:54:00: #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 16:54:00: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:54:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:54:02: 13000000 INFO @ Sun, 02 Jun 2019 16:54:03: #1 tag size is determined as 28 bps INFO @ Sun, 02 Jun 2019 16:54:03: #1 tag size = 28 INFO @ Sun, 02 Jun 2019 16:54:03: #1 total tags in treatment: 13141307 INFO @ Sun, 02 Jun 2019 16:54:03: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:54:03: #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 16:54:03: 11000000 INFO @ Sun, 02 Jun 2019 16:54:03: #1 tags after filtering in treatment: 13141307 INFO @ Sun, 02 Jun 2019 16:54:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:54:03: #1 finished! INFO @ Sun, 02 Jun 2019 16:54:03: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:54:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:54:04: #2 number of paired peaks: 334 WARNING @ Sun, 02 Jun 2019 16:54:04: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Sun, 02 Jun 2019 16:54:04: start model_add_line... INFO @ Sun, 02 Jun 2019 16:54:04: start X-correlation... INFO @ Sun, 02 Jun 2019 16:54:04: end of X-cor INFO @ Sun, 02 Jun 2019 16:54:04: #2 finished! INFO @ Sun, 02 Jun 2019 16:54:04: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:54:04: #2 alternative fragment length(s) may be 1,22,546 bps INFO @ Sun, 02 Jun 2019 16:54:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.20_model.r WARNING @ Sun, 02 Jun 2019 16:54:04: #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 16:54:04: #2 You may need to consider one of the other alternative d(s): 1,22,546 WARNING @ Sun, 02 Jun 2019 16:54:04: #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 16:54:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:54:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:54:11: 12000000 INFO @ Sun, 02 Jun 2019 16:54:18: 13000000 INFO @ Sun, 02 Jun 2019 16:54:19: #1 tag size is determined as 28 bps INFO @ Sun, 02 Jun 2019 16:54:19: #1 tag size = 28 INFO @ Sun, 02 Jun 2019 16:54:19: #1 total tags in treatment: 13141307 INFO @ Sun, 02 Jun 2019 16:54:19: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:54:19: #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 16:54:20: #1 tags after filtering in treatment: 13141307 INFO @ Sun, 02 Jun 2019 16:54:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:54:20: #1 finished! INFO @ Sun, 02 Jun 2019 16:54:20: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:54:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:54:21: #2 number of paired peaks: 334 WARNING @ Sun, 02 Jun 2019 16:54:21: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Sun, 02 Jun 2019 16:54:21: start model_add_line... INFO @ Sun, 02 Jun 2019 16:54:21: start X-correlation... INFO @ Sun, 02 Jun 2019 16:54:21: end of X-cor INFO @ Sun, 02 Jun 2019 16:54:21: #2 finished! INFO @ Sun, 02 Jun 2019 16:54:21: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:54:21: #2 alternative fragment length(s) may be 1,22,546 bps INFO @ Sun, 02 Jun 2019 16:54:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.10_model.r WARNING @ Sun, 02 Jun 2019 16:54:21: #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 16:54:21: #2 You may need to consider one of the other alternative d(s): 1,22,546 WARNING @ Sun, 02 Jun 2019 16:54:21: #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 16:54:21: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:54:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:54:32: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:54:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:54:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:54:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:54:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.05_summits.bed INFO @ Sun, 02 Jun 2019 16:54:47: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:54:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:54:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:54:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.20_summits.bed INFO @ Sun, 02 Jun 2019 16:54:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:54:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:55:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:55:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:55:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257698/SRX257698.10_summits.bed INFO @ Sun, 02 Jun 2019 16:55:08: 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。