Job ID = 1292594 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,509,609 reads read : 21,509,609 reads written : 21,509,609 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: 00:04:38 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 256455 (1.19%) aligned 0 times 17820692 (82.85%) aligned exactly 1 time 3432462 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:04:38 Overall time: 00:04:38 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3666843 / 21253154 = 0.1725 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 20:03:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.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 20:03:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:03:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:03:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.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 20:03:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:03:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:03:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.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 20:03:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:03:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:03:47: 1000000 INFO @ Sun, 02 Jun 2019 20:03:47: 1000000 INFO @ Sun, 02 Jun 2019 20:03:48: 1000000 INFO @ Sun, 02 Jun 2019 20:03:54: 2000000 INFO @ Sun, 02 Jun 2019 20:03:55: 2000000 INFO @ Sun, 02 Jun 2019 20:03:56: 2000000 INFO @ Sun, 02 Jun 2019 20:04:02: 3000000 INFO @ Sun, 02 Jun 2019 20:04:03: 3000000 INFO @ Sun, 02 Jun 2019 20:04:04: 3000000 INFO @ Sun, 02 Jun 2019 20:04:10: 4000000 INFO @ Sun, 02 Jun 2019 20:04:10: 4000000 INFO @ Sun, 02 Jun 2019 20:04:12: 4000000 INFO @ Sun, 02 Jun 2019 20:04:17: 5000000 INFO @ Sun, 02 Jun 2019 20:04:18: 5000000 INFO @ Sun, 02 Jun 2019 20:04:19: 5000000 INFO @ Sun, 02 Jun 2019 20:04:25: 6000000 INFO @ Sun, 02 Jun 2019 20:04:25: 6000000 INFO @ Sun, 02 Jun 2019 20:04:27: 6000000 INFO @ Sun, 02 Jun 2019 20:04:32: 7000000 INFO @ Sun, 02 Jun 2019 20:04:32: 7000000 INFO @ Sun, 02 Jun 2019 20:04:34: 7000000 INFO @ Sun, 02 Jun 2019 20:04:40: 8000000 INFO @ Sun, 02 Jun 2019 20:04:40: 8000000 INFO @ Sun, 02 Jun 2019 20:04:42: 8000000 INFO @ Sun, 02 Jun 2019 20:04:47: 9000000 INFO @ Sun, 02 Jun 2019 20:04:47: 9000000 INFO @ Sun, 02 Jun 2019 20:04:49: 9000000 INFO @ Sun, 02 Jun 2019 20:04:55: 10000000 INFO @ Sun, 02 Jun 2019 20:04:55: 10000000 INFO @ Sun, 02 Jun 2019 20:04:57: 10000000 INFO @ Sun, 02 Jun 2019 20:05:03: 11000000 INFO @ Sun, 02 Jun 2019 20:05:03: 11000000 INFO @ Sun, 02 Jun 2019 20:05:05: 11000000 INFO @ Sun, 02 Jun 2019 20:05:11: 12000000 INFO @ Sun, 02 Jun 2019 20:05:11: 12000000 INFO @ Sun, 02 Jun 2019 20:05:12: 12000000 INFO @ Sun, 02 Jun 2019 20:05:19: 13000000 INFO @ Sun, 02 Jun 2019 20:05:19: 13000000 INFO @ Sun, 02 Jun 2019 20:05:20: 13000000 INFO @ Sun, 02 Jun 2019 20:05:26: 14000000 INFO @ Sun, 02 Jun 2019 20:05:27: 14000000 INFO @ Sun, 02 Jun 2019 20:05:28: 14000000 INFO @ Sun, 02 Jun 2019 20:05:34: 15000000 INFO @ Sun, 02 Jun 2019 20:05:35: 15000000 INFO @ Sun, 02 Jun 2019 20:05:36: 15000000 INFO @ Sun, 02 Jun 2019 20:05:42: 16000000 INFO @ Sun, 02 Jun 2019 20:05:43: 16000000 INFO @ Sun, 02 Jun 2019 20:05:43: 16000000 INFO @ Sun, 02 Jun 2019 20:05:49: 17000000 INFO @ Sun, 02 Jun 2019 20:05:50: 17000000 INFO @ Sun, 02 Jun 2019 20:05:51: 17000000 INFO @ Sun, 02 Jun 2019 20:05:54: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:05:54: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:05:54: #1 total tags in treatment: 17586311 INFO @ Sun, 02 Jun 2019 20:05:54: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:05:54: #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 20:05:54: #1 tags after filtering in treatment: 17586311 INFO @ Sun, 02 Jun 2019 20:05:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:05:54: #1 finished! INFO @ Sun, 02 Jun 2019 20:05:54: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:05:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:05:55: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:05:55: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:05:55: #1 total tags in treatment: 17586311 INFO @ Sun, 02 Jun 2019 20:05:55: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:05:55: #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 20:05:55: #1 tags after filtering in treatment: 17586311 INFO @ Sun, 02 Jun 2019 20:05:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:05:55: #1 finished! INFO @ Sun, 02 Jun 2019 20:05:55: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:05:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:05:56: #2 number of paired peaks: 207 WARNING @ Sun, 02 Jun 2019 20:05:56: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sun, 02 Jun 2019 20:05:56: start model_add_line... INFO @ Sun, 02 Jun 2019 20:05:56: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:05:56: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:05:56: #1 total tags in treatment: 17586311 INFO @ Sun, 02 Jun 2019 20:05:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:05:56: #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 20:05:56: start X-correlation... INFO @ Sun, 02 Jun 2019 20:05:56: end of X-cor INFO @ Sun, 02 Jun 2019 20:05:56: #2 finished! INFO @ Sun, 02 Jun 2019 20:05:56: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 20:05:56: #2 alternative fragment length(s) may be 1,36,567,592,598 bps INFO @ Sun, 02 Jun 2019 20:05:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.20_model.r WARNING @ Sun, 02 Jun 2019 20:05:56: #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 20:05:56: #2 You may need to consider one of the other alternative d(s): 1,36,567,592,598 WARNING @ Sun, 02 Jun 2019 20:05:56: #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 20:05:56: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:05:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:05:56: #1 tags after filtering in treatment: 17586311 INFO @ Sun, 02 Jun 2019 20:05:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:05:56: #1 finished! INFO @ Sun, 02 Jun 2019 20:05:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:05:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:05:57: #2 number of paired peaks: 207 WARNING @ Sun, 02 Jun 2019 20:05:57: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sun, 02 Jun 2019 20:05:57: start model_add_line... INFO @ Sun, 02 Jun 2019 20:05:57: start X-correlation... INFO @ Sun, 02 Jun 2019 20:05:57: end of X-cor INFO @ Sun, 02 Jun 2019 20:05:57: #2 finished! INFO @ Sun, 02 Jun 2019 20:05:57: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 20:05:57: #2 alternative fragment length(s) may be 1,36,567,592,598 bps INFO @ Sun, 02 Jun 2019 20:05:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.05_model.r WARNING @ Sun, 02 Jun 2019 20:05:57: #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 20:05:57: #2 You may need to consider one of the other alternative d(s): 1,36,567,592,598 WARNING @ Sun, 02 Jun 2019 20:05:57: #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 20:05:57: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:05:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:05:57: #2 number of paired peaks: 207 WARNING @ Sun, 02 Jun 2019 20:05:57: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sun, 02 Jun 2019 20:05:57: start model_add_line... INFO @ Sun, 02 Jun 2019 20:05:58: start X-correlation... INFO @ Sun, 02 Jun 2019 20:05:58: end of X-cor INFO @ Sun, 02 Jun 2019 20:05:58: #2 finished! INFO @ Sun, 02 Jun 2019 20:05:58: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 20:05:58: #2 alternative fragment length(s) may be 1,36,567,592,598 bps INFO @ Sun, 02 Jun 2019 20:05:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.10_model.r WARNING @ Sun, 02 Jun 2019 20:05:58: #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 20:05:58: #2 You may need to consider one of the other alternative d(s): 1,36,567,592,598 WARNING @ Sun, 02 Jun 2019 20:05:58: #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 20:05:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:05:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:06:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:06:37: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:06:37: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:06:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:06:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:06:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.20_summits.bed INFO @ Sun, 02 Jun 2019 20:06:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:06:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:06:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:06:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.10_summits.bed INFO @ Sun, 02 Jun 2019 20:06:55: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:06:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:06:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:06:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494845/SRX494845.05_summits.bed INFO @ Sun, 02 Jun 2019 20:06:55: 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。