Job ID = 1293122 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,974,752 reads read : 25,974,752 reads written : 25,974,752 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: 00:06:29 25974752 reads; of these: 25974752 (100.00%) were unpaired; of these: 2609906 (10.05%) aligned 0 times 17719369 (68.22%) aligned exactly 1 time 5645477 (21.73%) aligned >1 times 89.95% overall alignment rate Time searching: 00:06:29 Overall time: 00:06:29 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 12 files... [bam_rmdupse_core] 6139601 / 23364846 = 0.2628 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 22:19:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.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 22:19:00: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:19:00: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:19:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.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 22:19:00: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:19:00: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:19:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.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 22:19:00: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:19:00: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:19:08: 1000000 INFO @ Sun, 02 Jun 2019 22:19:09: 1000000 INFO @ Sun, 02 Jun 2019 22:19:12: 1000000 INFO @ Sun, 02 Jun 2019 22:19:16: 2000000 INFO @ Sun, 02 Jun 2019 22:19:18: 2000000 INFO @ Sun, 02 Jun 2019 22:19:23: 2000000 INFO @ Sun, 02 Jun 2019 22:19:25: 3000000 INFO @ Sun, 02 Jun 2019 22:19:27: 3000000 INFO @ Sun, 02 Jun 2019 22:19:33: 4000000 INFO @ Sun, 02 Jun 2019 22:19:35: 3000000 INFO @ Sun, 02 Jun 2019 22:19:37: 4000000 INFO @ Sun, 02 Jun 2019 22:19:41: 5000000 INFO @ Sun, 02 Jun 2019 22:19:46: 5000000 INFO @ Sun, 02 Jun 2019 22:19:47: 4000000 INFO @ Sun, 02 Jun 2019 22:19:50: 6000000 INFO @ Sun, 02 Jun 2019 22:19:55: 6000000 INFO @ Sun, 02 Jun 2019 22:19:58: 7000000 INFO @ Sun, 02 Jun 2019 22:19:58: 5000000 INFO @ Sun, 02 Jun 2019 22:20:05: 7000000 INFO @ Sun, 02 Jun 2019 22:20:07: 8000000 INFO @ Sun, 02 Jun 2019 22:20:10: 6000000 INFO @ Sun, 02 Jun 2019 22:20:14: 8000000 INFO @ Sun, 02 Jun 2019 22:20:15: 9000000 INFO @ Sun, 02 Jun 2019 22:20:22: 7000000 INFO @ Sun, 02 Jun 2019 22:20:23: 9000000 INFO @ Sun, 02 Jun 2019 22:20:23: 10000000 INFO @ Sun, 02 Jun 2019 22:20:32: 11000000 INFO @ Sun, 02 Jun 2019 22:20:32: 10000000 INFO @ Sun, 02 Jun 2019 22:20:33: 8000000 INFO @ Sun, 02 Jun 2019 22:20:40: 12000000 INFO @ Sun, 02 Jun 2019 22:20:41: 11000000 INFO @ Sun, 02 Jun 2019 22:20:45: 9000000 INFO @ Sun, 02 Jun 2019 22:20:48: 13000000 INFO @ Sun, 02 Jun 2019 22:20:51: 12000000 INFO @ Sun, 02 Jun 2019 22:20:56: 14000000 INFO @ Sun, 02 Jun 2019 22:20:57: 10000000 INFO @ Sun, 02 Jun 2019 22:21:00: 13000000 INFO @ Sun, 02 Jun 2019 22:21:05: 15000000 INFO @ Sun, 02 Jun 2019 22:21:08: 11000000 INFO @ Sun, 02 Jun 2019 22:21:09: 14000000 INFO @ Sun, 02 Jun 2019 22:21:13: 16000000 INFO @ Sun, 02 Jun 2019 22:21:18: 15000000 INFO @ Sun, 02 Jun 2019 22:21:20: 12000000 INFO @ Sun, 02 Jun 2019 22:21:22: 17000000 INFO @ Sun, 02 Jun 2019 22:21:24: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:21:24: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:21:24: #1 total tags in treatment: 17225245 INFO @ Sun, 02 Jun 2019 22:21:24: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:21:24: #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 22:21:24: #1 tags after filtering in treatment: 17225245 INFO @ Sun, 02 Jun 2019 22:21:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:21:24: #1 finished! INFO @ Sun, 02 Jun 2019 22:21:24: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:21:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:21:26: #2 number of paired peaks: 396 WARNING @ Sun, 02 Jun 2019 22:21:26: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Sun, 02 Jun 2019 22:21:26: start model_add_line... INFO @ Sun, 02 Jun 2019 22:21:26: start X-correlation... INFO @ Sun, 02 Jun 2019 22:21:26: end of X-cor INFO @ Sun, 02 Jun 2019 22:21:26: #2 finished! INFO @ Sun, 02 Jun 2019 22:21:26: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:21:26: #2 alternative fragment length(s) may be 1,10,37 bps INFO @ Sun, 02 Jun 2019 22:21:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.05_model.r WARNING @ Sun, 02 Jun 2019 22:21:26: #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 22:21:26: #2 You may need to consider one of the other alternative d(s): 1,10,37 WARNING @ Sun, 02 Jun 2019 22:21:26: #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 22:21:26: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:21:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:21:27: 16000000 INFO @ Sun, 02 Jun 2019 22:21:32: 13000000 INFO @ Sun, 02 Jun 2019 22:21:36: 17000000 INFO @ Sun, 02 Jun 2019 22:21:38: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:21:38: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:21:38: #1 total tags in treatment: 17225245 INFO @ Sun, 02 Jun 2019 22:21:38: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:21:38: #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 22:21:39: #1 tags after filtering in treatment: 17225245 INFO @ Sun, 02 Jun 2019 22:21:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:21:39: #1 finished! INFO @ Sun, 02 Jun 2019 22:21:39: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:21:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:21:40: #2 number of paired peaks: 396 WARNING @ Sun, 02 Jun 2019 22:21:40: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Sun, 02 Jun 2019 22:21:40: start model_add_line... INFO @ Sun, 02 Jun 2019 22:21:40: start X-correlation... INFO @ Sun, 02 Jun 2019 22:21:40: end of X-cor INFO @ Sun, 02 Jun 2019 22:21:40: #2 finished! INFO @ Sun, 02 Jun 2019 22:21:40: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:21:40: #2 alternative fragment length(s) may be 1,10,37 bps INFO @ Sun, 02 Jun 2019 22:21:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.10_model.r WARNING @ Sun, 02 Jun 2019 22:21:40: #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 22:21:40: #2 You may need to consider one of the other alternative d(s): 1,10,37 WARNING @ Sun, 02 Jun 2019 22:21:40: #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 22:21:40: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:21:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:21:43: 14000000 INFO @ Sun, 02 Jun 2019 22:21:55: 15000000 INFO @ Sun, 02 Jun 2019 22:22:04: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:22:06: 16000000 INFO @ Sun, 02 Jun 2019 22:22:17: 17000000 INFO @ Sun, 02 Jun 2019 22:22:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:22:20: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:22:20: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:22:20: #1 total tags in treatment: 17225245 INFO @ Sun, 02 Jun 2019 22:22:20: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:22:20: #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 22:22:20: #1 tags after filtering in treatment: 17225245 INFO @ Sun, 02 Jun 2019 22:22:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:22:20: #1 finished! INFO @ Sun, 02 Jun 2019 22:22:20: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:22:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:22:22: #2 number of paired peaks: 396 WARNING @ Sun, 02 Jun 2019 22:22:22: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Sun, 02 Jun 2019 22:22:22: start model_add_line... INFO @ Sun, 02 Jun 2019 22:22:22: start X-correlation... INFO @ Sun, 02 Jun 2019 22:22:22: end of X-cor INFO @ Sun, 02 Jun 2019 22:22:22: #2 finished! INFO @ Sun, 02 Jun 2019 22:22:22: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:22:22: #2 alternative fragment length(s) may be 1,10,37 bps INFO @ Sun, 02 Jun 2019 22:22:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.20_model.r WARNING @ Sun, 02 Jun 2019 22:22:22: #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 22:22:22: #2 You may need to consider one of the other alternative d(s): 1,10,37 WARNING @ Sun, 02 Jun 2019 22:22:22: #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 22:22:22: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:22:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:22:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:22:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:22:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.05_summits.bed INFO @ Sun, 02 Jun 2019 22:22:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:22:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:22:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:22:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.10_summits.bed INFO @ Sun, 02 Jun 2019 22:22:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:23:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:23:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:23:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:23:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402698/SRX5402698.20_summits.bed INFO @ Sun, 02 Jun 2019 22:23:18: 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。