Job ID = 2590037 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,924,428 reads read : 25,924,428 reads written : 25,924,428 rm: cannot remove ‘[DSE]RR*’: 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: 00:06:16 25924428 reads; of these: 25924428 (100.00%) were unpaired; of these: 927159 (3.58%) aligned 0 times 20625372 (79.56%) aligned exactly 1 time 4371897 (16.86%) aligned >1 times 96.42% overall alignment rate Time searching: 00:06:16 Overall time: 00:06:16 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] 8858594 / 24997269 = 0.3544 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 @ Mon, 12 Aug 2019 19:34:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.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 @ Mon, 12 Aug 2019 19:34:41: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:34:41: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:34:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.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 @ Mon, 12 Aug 2019 19:34:42: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:34:42: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:34:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.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 @ Mon, 12 Aug 2019 19:34:43: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:34:43: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:34:48: 1000000 INFO @ Mon, 12 Aug 2019 19:34:50: 1000000 INFO @ Mon, 12 Aug 2019 19:34:51: 1000000 INFO @ Mon, 12 Aug 2019 19:34:55: 2000000 INFO @ Mon, 12 Aug 2019 19:34:58: 2000000 INFO @ Mon, 12 Aug 2019 19:34:59: 2000000 INFO @ Mon, 12 Aug 2019 19:35:02: 3000000 INFO @ Mon, 12 Aug 2019 19:35:05: 3000000 INFO @ Mon, 12 Aug 2019 19:35:06: 3000000 INFO @ Mon, 12 Aug 2019 19:35:09: 4000000 INFO @ Mon, 12 Aug 2019 19:35:13: 4000000 INFO @ Mon, 12 Aug 2019 19:35:14: 4000000 INFO @ Mon, 12 Aug 2019 19:35:16: 5000000 INFO @ Mon, 12 Aug 2019 19:35:20: 5000000 INFO @ Mon, 12 Aug 2019 19:35:21: 5000000 INFO @ Mon, 12 Aug 2019 19:35:23: 6000000 INFO @ Mon, 12 Aug 2019 19:35:28: 6000000 INFO @ Mon, 12 Aug 2019 19:35:29: 6000000 INFO @ Mon, 12 Aug 2019 19:35:30: 7000000 INFO @ Mon, 12 Aug 2019 19:35:35: 7000000 INFO @ Mon, 12 Aug 2019 19:35:36: 7000000 INFO @ Mon, 12 Aug 2019 19:35:37: 8000000 INFO @ Mon, 12 Aug 2019 19:35:43: 8000000 INFO @ Mon, 12 Aug 2019 19:35:44: 8000000 INFO @ Mon, 12 Aug 2019 19:35:44: 9000000 INFO @ Mon, 12 Aug 2019 19:35:51: 9000000 INFO @ Mon, 12 Aug 2019 19:35:51: 10000000 INFO @ Mon, 12 Aug 2019 19:35:51: 9000000 INFO @ Mon, 12 Aug 2019 19:35:58: 11000000 INFO @ Mon, 12 Aug 2019 19:35:58: 10000000 INFO @ Mon, 12 Aug 2019 19:35:59: 10000000 INFO @ Mon, 12 Aug 2019 19:36:05: 12000000 INFO @ Mon, 12 Aug 2019 19:36:06: 11000000 INFO @ Mon, 12 Aug 2019 19:36:06: 11000000 INFO @ Mon, 12 Aug 2019 19:36:12: 13000000 INFO @ Mon, 12 Aug 2019 19:36:13: 12000000 INFO @ Mon, 12 Aug 2019 19:36:14: 12000000 INFO @ Mon, 12 Aug 2019 19:36:18: 14000000 INFO @ Mon, 12 Aug 2019 19:36:21: 13000000 INFO @ Mon, 12 Aug 2019 19:36:21: 13000000 INFO @ Mon, 12 Aug 2019 19:36:25: 15000000 INFO @ Mon, 12 Aug 2019 19:36:28: 14000000 INFO @ Mon, 12 Aug 2019 19:36:29: 14000000 INFO @ Mon, 12 Aug 2019 19:36:32: 16000000 INFO @ Mon, 12 Aug 2019 19:36:33: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:36:33: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:36:33: #1 total tags in treatment: 16138675 INFO @ Mon, 12 Aug 2019 19:36:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:36:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:36:34: #1 tags after filtering in treatment: 16138675 INFO @ Mon, 12 Aug 2019 19:36:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:36:34: #1 finished! INFO @ Mon, 12 Aug 2019 19:36:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:36:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:36:35: #2 number of paired peaks: 302 WARNING @ Mon, 12 Aug 2019 19:36:35: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Mon, 12 Aug 2019 19:36:35: start model_add_line... INFO @ Mon, 12 Aug 2019 19:36:35: start X-correlation... INFO @ Mon, 12 Aug 2019 19:36:35: end of X-cor INFO @ Mon, 12 Aug 2019 19:36:35: #2 finished! INFO @ Mon, 12 Aug 2019 19:36:35: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 19:36:35: #2 alternative fragment length(s) may be 1,43,579 bps INFO @ Mon, 12 Aug 2019 19:36:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.05_model.r WARNING @ Mon, 12 Aug 2019 19:36:35: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:36:35: #2 You may need to consider one of the other alternative d(s): 1,43,579 WARNING @ Mon, 12 Aug 2019 19:36:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:36:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:36:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:36:36: 15000000 INFO @ Mon, 12 Aug 2019 19:36:36: 15000000 INFO @ Mon, 12 Aug 2019 19:36:43: 16000000 INFO @ Mon, 12 Aug 2019 19:36:44: 16000000 INFO @ Mon, 12 Aug 2019 19:36:44: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:36:44: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:36:44: #1 total tags in treatment: 16138675 INFO @ Mon, 12 Aug 2019 19:36:44: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:36:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:36:45: #1 tags after filtering in treatment: 16138675 INFO @ Mon, 12 Aug 2019 19:36:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:36:45: #1 finished! INFO @ Mon, 12 Aug 2019 19:36:45: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:36:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:36:45: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:36:45: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:36:45: #1 total tags in treatment: 16138675 INFO @ Mon, 12 Aug 2019 19:36:45: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:36:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:36:45: #1 tags after filtering in treatment: 16138675 INFO @ Mon, 12 Aug 2019 19:36:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:36:45: #1 finished! INFO @ Mon, 12 Aug 2019 19:36:45: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:36:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:36:46: #2 number of paired peaks: 302 WARNING @ Mon, 12 Aug 2019 19:36:46: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Mon, 12 Aug 2019 19:36:46: start model_add_line... INFO @ Mon, 12 Aug 2019 19:36:46: start X-correlation... INFO @ Mon, 12 Aug 2019 19:36:46: end of X-cor INFO @ Mon, 12 Aug 2019 19:36:46: #2 finished! INFO @ Mon, 12 Aug 2019 19:36:46: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 19:36:46: #2 alternative fragment length(s) may be 1,43,579 bps INFO @ Mon, 12 Aug 2019 19:36:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.10_model.r WARNING @ Mon, 12 Aug 2019 19:36:46: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:36:46: #2 You may need to consider one of the other alternative d(s): 1,43,579 WARNING @ Mon, 12 Aug 2019 19:36:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:36:46: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:36:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:36:47: #2 number of paired peaks: 302 WARNING @ Mon, 12 Aug 2019 19:36:47: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Mon, 12 Aug 2019 19:36:47: start model_add_line... INFO @ Mon, 12 Aug 2019 19:36:47: start X-correlation... INFO @ Mon, 12 Aug 2019 19:36:47: end of X-cor INFO @ Mon, 12 Aug 2019 19:36:47: #2 finished! INFO @ Mon, 12 Aug 2019 19:36:47: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 19:36:47: #2 alternative fragment length(s) may be 1,43,579 bps INFO @ Mon, 12 Aug 2019 19:36:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.20_model.r WARNING @ Mon, 12 Aug 2019 19:36:47: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:36:47: #2 You may need to consider one of the other alternative d(s): 1,43,579 WARNING @ Mon, 12 Aug 2019 19:36:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:36:47: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:36:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:37:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:37:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:37:24: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:37:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:37:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:37:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.05_summits.bed INFO @ Mon, 12 Aug 2019 19:37:29: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:37:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:37:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:37:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.10_summits.bed INFO @ Mon, 12 Aug 2019 19:37:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:37:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:37:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:37:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494881/SRX494881.20_summits.bed INFO @ Mon, 12 Aug 2019 19:37:41: Done! pass1 - making usageList (0 chroms): 2 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。