Job ID = 1293185 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 49,034,372 reads read : 49,034,372 reads written : 49,034,372 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: 00:12:35 49034372 reads; of these: 49034372 (100.00%) were unpaired; of these: 10668258 (21.76%) aligned 0 times 26645495 (54.34%) aligned exactly 1 time 11720619 (23.90%) aligned >1 times 78.24% overall alignment rate Time searching: 00:12:35 Overall time: 00:12:35 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] 10771545 / 38366114 = 0.2808 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 22:57:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.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 22:57:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:57:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:57:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.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 22:57:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:57:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:57:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.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 22:57:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:57:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:57:38: 1000000 INFO @ Sun, 02 Jun 2019 22:57:39: 1000000 INFO @ Sun, 02 Jun 2019 22:57:39: 1000000 INFO @ Sun, 02 Jun 2019 22:57:45: 2000000 INFO @ Sun, 02 Jun 2019 22:57:47: 2000000 INFO @ Sun, 02 Jun 2019 22:57:47: 2000000 INFO @ Sun, 02 Jun 2019 22:57:52: 3000000 INFO @ Sun, 02 Jun 2019 22:57:55: 3000000 INFO @ Sun, 02 Jun 2019 22:57:56: 3000000 INFO @ Sun, 02 Jun 2019 22:58:00: 4000000 INFO @ Sun, 02 Jun 2019 22:58:04: 4000000 INFO @ Sun, 02 Jun 2019 22:58:04: 4000000 INFO @ Sun, 02 Jun 2019 22:58:07: 5000000 INFO @ Sun, 02 Jun 2019 22:58:12: 5000000 INFO @ Sun, 02 Jun 2019 22:58:13: 5000000 INFO @ Sun, 02 Jun 2019 22:58:14: 6000000 INFO @ Sun, 02 Jun 2019 22:58:20: 6000000 INFO @ Sun, 02 Jun 2019 22:58:21: 6000000 INFO @ Sun, 02 Jun 2019 22:58:21: 7000000 INFO @ Sun, 02 Jun 2019 22:58:28: 7000000 INFO @ Sun, 02 Jun 2019 22:58:29: 8000000 INFO @ Sun, 02 Jun 2019 22:58:29: 7000000 INFO @ Sun, 02 Jun 2019 22:58:36: 8000000 INFO @ Sun, 02 Jun 2019 22:58:36: 9000000 INFO @ Sun, 02 Jun 2019 22:58:38: 8000000 INFO @ Sun, 02 Jun 2019 22:58:43: 10000000 INFO @ Sun, 02 Jun 2019 22:58:44: 9000000 INFO @ Sun, 02 Jun 2019 22:58:46: 9000000 INFO @ Sun, 02 Jun 2019 22:58:51: 11000000 INFO @ Sun, 02 Jun 2019 22:58:52: 10000000 INFO @ Sun, 02 Jun 2019 22:58:54: 10000000 INFO @ Sun, 02 Jun 2019 22:58:58: 12000000 INFO @ Sun, 02 Jun 2019 22:59:00: 11000000 INFO @ Sun, 02 Jun 2019 22:59:02: 11000000 INFO @ Sun, 02 Jun 2019 22:59:05: 13000000 INFO @ Sun, 02 Jun 2019 22:59:08: 12000000 INFO @ Sun, 02 Jun 2019 22:59:11: 12000000 INFO @ Sun, 02 Jun 2019 22:59:12: 14000000 INFO @ Sun, 02 Jun 2019 22:59:16: 13000000 INFO @ Sun, 02 Jun 2019 22:59:19: 13000000 INFO @ Sun, 02 Jun 2019 22:59:20: 15000000 INFO @ Sun, 02 Jun 2019 22:59:24: 14000000 INFO @ Sun, 02 Jun 2019 22:59:27: 16000000 INFO @ Sun, 02 Jun 2019 22:59:27: 14000000 INFO @ Sun, 02 Jun 2019 22:59:32: 15000000 INFO @ Sun, 02 Jun 2019 22:59:34: 17000000 INFO @ Sun, 02 Jun 2019 22:59:35: 15000000 INFO @ Sun, 02 Jun 2019 22:59:40: 16000000 INFO @ Sun, 02 Jun 2019 22:59:41: 18000000 INFO @ Sun, 02 Jun 2019 22:59:43: 16000000 INFO @ Sun, 02 Jun 2019 22:59:48: 17000000 INFO @ Sun, 02 Jun 2019 22:59:48: 19000000 INFO @ Sun, 02 Jun 2019 22:59:52: 17000000 INFO @ Sun, 02 Jun 2019 22:59:56: 20000000 INFO @ Sun, 02 Jun 2019 22:59:56: 18000000 INFO @ Sun, 02 Jun 2019 23:00:00: 18000000 INFO @ Sun, 02 Jun 2019 23:00:03: 21000000 INFO @ Sun, 02 Jun 2019 23:00:04: 19000000 INFO @ Sun, 02 Jun 2019 23:00:08: 19000000 INFO @ Sun, 02 Jun 2019 23:00:10: 22000000 INFO @ Sun, 02 Jun 2019 23:00:13: 20000000 INFO @ Sun, 02 Jun 2019 23:00:16: 20000000 INFO @ Sun, 02 Jun 2019 23:00:17: 23000000 INFO @ Sun, 02 Jun 2019 23:00:21: 21000000 INFO @ Sun, 02 Jun 2019 23:00:25: 21000000 INFO @ Sun, 02 Jun 2019 23:00:25: 24000000 INFO @ Sun, 02 Jun 2019 23:00:29: 22000000 INFO @ Sun, 02 Jun 2019 23:00:32: 25000000 INFO @ Sun, 02 Jun 2019 23:00:33: 22000000 INFO @ Sun, 02 Jun 2019 23:00:37: 23000000 INFO @ Sun, 02 Jun 2019 23:00:39: 26000000 INFO @ Sun, 02 Jun 2019 23:00:41: 23000000 INFO @ Sun, 02 Jun 2019 23:00:45: 24000000 INFO @ Sun, 02 Jun 2019 23:00:46: 27000000 INFO @ Sun, 02 Jun 2019 23:00:49: 24000000 INFO @ Sun, 02 Jun 2019 23:00:51: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 23:00:51: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 23:00:51: #1 total tags in treatment: 27594569 INFO @ Sun, 02 Jun 2019 23:00:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:00:51: #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 23:00:51: #1 tags after filtering in treatment: 27594569 INFO @ Sun, 02 Jun 2019 23:00:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:00:51: #1 finished! INFO @ Sun, 02 Jun 2019 23:00:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:00:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:00:53: 25000000 INFO @ Sun, 02 Jun 2019 23:00:54: #2 number of paired peaks: 319 WARNING @ Sun, 02 Jun 2019 23:00:54: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Sun, 02 Jun 2019 23:00:54: start model_add_line... INFO @ Sun, 02 Jun 2019 23:00:54: start X-correlation... INFO @ Sun, 02 Jun 2019 23:00:54: end of X-cor INFO @ Sun, 02 Jun 2019 23:00:54: #2 finished! INFO @ Sun, 02 Jun 2019 23:00:54: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 23:00:54: #2 alternative fragment length(s) may be 1,22,561 bps INFO @ Sun, 02 Jun 2019 23:00:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.05_model.r WARNING @ Sun, 02 Jun 2019 23:00:54: #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 23:00:54: #2 You may need to consider one of the other alternative d(s): 1,22,561 WARNING @ Sun, 02 Jun 2019 23:00:54: #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 23:00:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:00:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:00:57: 25000000 INFO @ Sun, 02 Jun 2019 23:01:01: 26000000 INFO @ Sun, 02 Jun 2019 23:01:05: 26000000 INFO @ Sun, 02 Jun 2019 23:01:09: 27000000 INFO @ Sun, 02 Jun 2019 23:01:13: 27000000 INFO @ Sun, 02 Jun 2019 23:01:14: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 23:01:14: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 23:01:14: #1 total tags in treatment: 27594569 INFO @ Sun, 02 Jun 2019 23:01:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:01:14: #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 23:01:15: #1 tags after filtering in treatment: 27594569 INFO @ Sun, 02 Jun 2019 23:01:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:01:15: #1 finished! INFO @ Sun, 02 Jun 2019 23:01:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:01:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:01:17: #2 number of paired peaks: 319 WARNING @ Sun, 02 Jun 2019 23:01:17: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Sun, 02 Jun 2019 23:01:17: start model_add_line... INFO @ Sun, 02 Jun 2019 23:01:17: start X-correlation... INFO @ Sun, 02 Jun 2019 23:01:17: end of X-cor INFO @ Sun, 02 Jun 2019 23:01:17: #2 finished! INFO @ Sun, 02 Jun 2019 23:01:17: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 23:01:17: #2 alternative fragment length(s) may be 1,22,561 bps INFO @ Sun, 02 Jun 2019 23:01:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.10_model.r WARNING @ Sun, 02 Jun 2019 23:01:17: #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 23:01:17: #2 You may need to consider one of the other alternative d(s): 1,22,561 WARNING @ Sun, 02 Jun 2019 23:01:17: #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 23:01:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:01:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:01:18: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 23:01:18: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 23:01:18: #1 total tags in treatment: 27594569 INFO @ Sun, 02 Jun 2019 23:01:18: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:01:18: #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 23:01:19: #1 tags after filtering in treatment: 27594569 INFO @ Sun, 02 Jun 2019 23:01:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:01:19: #1 finished! INFO @ Sun, 02 Jun 2019 23:01:19: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:01:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:01:21: #2 number of paired peaks: 319 WARNING @ Sun, 02 Jun 2019 23:01:21: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Sun, 02 Jun 2019 23:01:21: start model_add_line... INFO @ Sun, 02 Jun 2019 23:01:21: start X-correlation... INFO @ Sun, 02 Jun 2019 23:01:21: end of X-cor INFO @ Sun, 02 Jun 2019 23:01:21: #2 finished! INFO @ Sun, 02 Jun 2019 23:01:21: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 23:01:21: #2 alternative fragment length(s) may be 1,22,561 bps INFO @ Sun, 02 Jun 2019 23:01:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.20_model.r WARNING @ Sun, 02 Jun 2019 23:01:21: #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 23:01:21: #2 You may need to consider one of the other alternative d(s): 1,22,561 WARNING @ Sun, 02 Jun 2019 23:01:21: #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 23:01:21: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:01:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:01:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:02:09: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:02:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:02:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:02:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.05_summits.bed INFO @ Sun, 02 Jun 2019 23:02:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:02:14: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:02:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:02:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:02:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.10_summits.bed INFO @ Sun, 02 Jun 2019 23:02:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:02:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:02:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:02:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402744/SRX5402744.20_summits.bed INFO @ Sun, 02 Jun 2019 23:02:37: 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。