Job ID = 1293213 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 44,731,113 reads read : 44,731,113 reads written : 44,731,113 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: 00:09:18 44731113 reads; of these: 44731113 (100.00%) were unpaired; of these: 11048939 (24.70%) aligned 0 times 27954967 (62.50%) aligned exactly 1 time 5727207 (12.80%) aligned >1 times 75.30% overall alignment rate Time searching: 00:09:18 Overall time: 00:09:18 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 16 files... [bam_rmdupse_core] 5720108 / 33682174 = 0.1698 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 22:56:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.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 22:56:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.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 22:56:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:56:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:56:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:56:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:56:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.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 22:56:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:56:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:56:54: 1000000 INFO @ Sun, 02 Jun 2019 22:56:55: 1000000 INFO @ Sun, 02 Jun 2019 22:56:56: 1000000 INFO @ Sun, 02 Jun 2019 22:57:03: 2000000 INFO @ Sun, 02 Jun 2019 22:57:06: 2000000 INFO @ Sun, 02 Jun 2019 22:57:06: 2000000 INFO @ Sun, 02 Jun 2019 22:57:12: 3000000 INFO @ Sun, 02 Jun 2019 22:57:17: 3000000 INFO @ Sun, 02 Jun 2019 22:57:17: 3000000 INFO @ Sun, 02 Jun 2019 22:57:20: 4000000 INFO @ Sun, 02 Jun 2019 22:57:28: 4000000 INFO @ Sun, 02 Jun 2019 22:57:28: 4000000 INFO @ Sun, 02 Jun 2019 22:57:29: 5000000 INFO @ Sun, 02 Jun 2019 22:57:38: 6000000 INFO @ Sun, 02 Jun 2019 22:57:38: 5000000 INFO @ Sun, 02 Jun 2019 22:57:38: 5000000 INFO @ Sun, 02 Jun 2019 22:57:46: 7000000 INFO @ Sun, 02 Jun 2019 22:57:48: 6000000 INFO @ Sun, 02 Jun 2019 22:57:48: 6000000 INFO @ Sun, 02 Jun 2019 22:57:55: 8000000 INFO @ Sun, 02 Jun 2019 22:57:59: 7000000 INFO @ Sun, 02 Jun 2019 22:57:59: 7000000 INFO @ Sun, 02 Jun 2019 22:58:04: 9000000 INFO @ Sun, 02 Jun 2019 22:58:10: 8000000 INFO @ Sun, 02 Jun 2019 22:58:10: 8000000 INFO @ Sun, 02 Jun 2019 22:58:13: 10000000 INFO @ Sun, 02 Jun 2019 22:58:20: 9000000 INFO @ Sun, 02 Jun 2019 22:58:20: 9000000 INFO @ Sun, 02 Jun 2019 22:58:21: 11000000 INFO @ Sun, 02 Jun 2019 22:58:30: 12000000 INFO @ Sun, 02 Jun 2019 22:58:31: 10000000 INFO @ Sun, 02 Jun 2019 22:58:31: 10000000 INFO @ Sun, 02 Jun 2019 22:58:39: 13000000 INFO @ Sun, 02 Jun 2019 22:58:42: 11000000 INFO @ Sun, 02 Jun 2019 22:58:42: 11000000 INFO @ Sun, 02 Jun 2019 22:58:50: 14000000 INFO @ Sun, 02 Jun 2019 22:58:53: 12000000 INFO @ Sun, 02 Jun 2019 22:58:54: 12000000 INFO @ Sun, 02 Jun 2019 22:59:01: 15000000 INFO @ Sun, 02 Jun 2019 22:59:05: 13000000 INFO @ Sun, 02 Jun 2019 22:59:06: 13000000 INFO @ Sun, 02 Jun 2019 22:59:10: 16000000 INFO @ Sun, 02 Jun 2019 22:59:16: 14000000 INFO @ Sun, 02 Jun 2019 22:59:18: 14000000 INFO @ Sun, 02 Jun 2019 22:59:19: 17000000 INFO @ Sun, 02 Jun 2019 22:59:26: 15000000 INFO @ Sun, 02 Jun 2019 22:59:28: 18000000 INFO @ Sun, 02 Jun 2019 22:59:29: 15000000 INFO @ Sun, 02 Jun 2019 22:59:36: 19000000 INFO @ Sun, 02 Jun 2019 22:59:37: 16000000 INFO @ Sun, 02 Jun 2019 22:59:41: 16000000 INFO @ Sun, 02 Jun 2019 22:59:45: 20000000 INFO @ Sun, 02 Jun 2019 22:59:47: 17000000 INFO @ Sun, 02 Jun 2019 22:59:51: 17000000 INFO @ Sun, 02 Jun 2019 22:59:54: 21000000 INFO @ Sun, 02 Jun 2019 22:59:57: 18000000 INFO @ Sun, 02 Jun 2019 23:00:01: 18000000 INFO @ Sun, 02 Jun 2019 23:00:04: 22000000 INFO @ Sun, 02 Jun 2019 23:00:07: 19000000 INFO @ Sun, 02 Jun 2019 23:00:12: 19000000 INFO @ Sun, 02 Jun 2019 23:00:12: 23000000 INFO @ Sun, 02 Jun 2019 23:00:18: 20000000 INFO @ Sun, 02 Jun 2019 23:00:21: 24000000 INFO @ Sun, 02 Jun 2019 23:00:22: 20000000 INFO @ Sun, 02 Jun 2019 23:00:28: 21000000 INFO @ Sun, 02 Jun 2019 23:00:30: 25000000 INFO @ Sun, 02 Jun 2019 23:00:32: 21000000 INFO @ Sun, 02 Jun 2019 23:00:38: 22000000 INFO @ Sun, 02 Jun 2019 23:00:39: 26000000 INFO @ Sun, 02 Jun 2019 23:00:42: 22000000 INFO @ Sun, 02 Jun 2019 23:00:48: 27000000 INFO @ Sun, 02 Jun 2019 23:00:49: 23000000 INFO @ Sun, 02 Jun 2019 23:00:53: 23000000 INFO @ Sun, 02 Jun 2019 23:00:56: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 23:00:56: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 23:00:56: #1 total tags in treatment: 27962066 INFO @ Sun, 02 Jun 2019 23:00:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:00:56: #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 23:00:57: #1 tags after filtering in treatment: 27962066 INFO @ Sun, 02 Jun 2019 23:00:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:00:57: #1 finished! INFO @ Sun, 02 Jun 2019 23:00:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:00:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:00:59: 24000000 INFO @ Sun, 02 Jun 2019 23:00:59: #2 number of paired peaks: 123 WARNING @ Sun, 02 Jun 2019 23:00:59: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sun, 02 Jun 2019 23:00:59: start model_add_line... INFO @ Sun, 02 Jun 2019 23:01:00: start X-correlation... INFO @ Sun, 02 Jun 2019 23:01:00: end of X-cor INFO @ Sun, 02 Jun 2019 23:01:00: #2 finished! INFO @ Sun, 02 Jun 2019 23:01:00: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 23:01:00: #2 alternative fragment length(s) may be 1,49,104,123,536,554 bps INFO @ Sun, 02 Jun 2019 23:01:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.10_model.r WARNING @ Sun, 02 Jun 2019 23:01:00: #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 23:01:00: #2 You may need to consider one of the other alternative d(s): 1,49,104,123,536,554 WARNING @ Sun, 02 Jun 2019 23:01:00: #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 23:01:00: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:01:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:01:03: 24000000 INFO @ Sun, 02 Jun 2019 23:01:10: 25000000 INFO @ Sun, 02 Jun 2019 23:01:14: 25000000 INFO @ Sun, 02 Jun 2019 23:01:21: 26000000 INFO @ Sun, 02 Jun 2019 23:01:25: 26000000 INFO @ Sun, 02 Jun 2019 23:01:31: 27000000 INFO @ Sun, 02 Jun 2019 23:01:35: 27000000 INFO @ Sun, 02 Jun 2019 23:01:41: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 23:01:41: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 23:01:41: #1 total tags in treatment: 27962066 INFO @ Sun, 02 Jun 2019 23:01:41: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:01:41: #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 23:01:41: #1 tags after filtering in treatment: 27962066 INFO @ Sun, 02 Jun 2019 23:01:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:01:41: #1 finished! INFO @ Sun, 02 Jun 2019 23:01:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:01:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:01:44: #2 number of paired peaks: 123 WARNING @ Sun, 02 Jun 2019 23:01:44: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sun, 02 Jun 2019 23:01:44: start model_add_line... INFO @ Sun, 02 Jun 2019 23:01:44: start X-correlation... INFO @ Sun, 02 Jun 2019 23:01:44: end of X-cor INFO @ Sun, 02 Jun 2019 23:01:44: #2 finished! INFO @ Sun, 02 Jun 2019 23:01:44: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 23:01:44: #2 alternative fragment length(s) may be 1,49,104,123,536,554 bps INFO @ Sun, 02 Jun 2019 23:01:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.20_model.r WARNING @ Sun, 02 Jun 2019 23:01:44: #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 23:01:44: #2 You may need to consider one of the other alternative d(s): 1,49,104,123,536,554 WARNING @ Sun, 02 Jun 2019 23:01:44: #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 23:01:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:01:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:01:45: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 23:01:45: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 23:01:45: #1 total tags in treatment: 27962066 INFO @ Sun, 02 Jun 2019 23:01:45: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:01:45: #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 23:01:45: #1 tags after filtering in treatment: 27962066 INFO @ Sun, 02 Jun 2019 23:01:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:01:45: #1 finished! INFO @ Sun, 02 Jun 2019 23:01:45: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:01:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:01:48: #2 number of paired peaks: 123 WARNING @ Sun, 02 Jun 2019 23:01:48: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sun, 02 Jun 2019 23:01:48: start model_add_line... INFO @ Sun, 02 Jun 2019 23:01:48: start X-correlation... INFO @ Sun, 02 Jun 2019 23:01:48: end of X-cor INFO @ Sun, 02 Jun 2019 23:01:48: #2 finished! INFO @ Sun, 02 Jun 2019 23:01:48: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 23:01:48: #2 alternative fragment length(s) may be 1,49,104,123,536,554 bps INFO @ Sun, 02 Jun 2019 23:01:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.05_model.r WARNING @ Sun, 02 Jun 2019 23:01:48: #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 23:01:48: #2 You may need to consider one of the other alternative d(s): 1,49,104,123,536,554 WARNING @ Sun, 02 Jun 2019 23:01:48: #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 23:01:48: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:01:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:01:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:02:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:02:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:02:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.10_summits.bed INFO @ Sun, 02 Jun 2019 23:02:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:02:38: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:02:42: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:03:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:03:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:03:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.20_summits.bed INFO @ Sun, 02 Jun 2019 23:03:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:03:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:03:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:03:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402763/SRX5402763.05_summits.bed INFO @ Sun, 02 Jun 2019 23:03:06: 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。