Job ID = 2590207 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,137,366 reads read : 16,137,366 reads written : 16,137,366 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: 00:02:36 16137366 reads; of these: 16137366 (100.00%) were unpaired; of these: 923605 (5.72%) aligned 0 times 12431825 (77.04%) aligned exactly 1 time 2781936 (17.24%) aligned >1 times 94.28% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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_rmdupse_core] 1283499 / 15213761 = 0.0844 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 20:11:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.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 20:11:58: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:11:58: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:11:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.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 20:11:58: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:11:58: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:11:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.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 20:11:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:11:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:12:05: 1000000 INFO @ Mon, 12 Aug 2019 20:12:06: 1000000 INFO @ Mon, 12 Aug 2019 20:12:08: 1000000 INFO @ Mon, 12 Aug 2019 20:12:13: 2000000 INFO @ Mon, 12 Aug 2019 20:12:13: 2000000 INFO @ Mon, 12 Aug 2019 20:12:16: 2000000 INFO @ Mon, 12 Aug 2019 20:12:20: 3000000 INFO @ Mon, 12 Aug 2019 20:12:20: 3000000 INFO @ Mon, 12 Aug 2019 20:12:24: 3000000 INFO @ Mon, 12 Aug 2019 20:12:27: 4000000 INFO @ Mon, 12 Aug 2019 20:12:28: 4000000 INFO @ Mon, 12 Aug 2019 20:12:33: 4000000 INFO @ Mon, 12 Aug 2019 20:12:35: 5000000 INFO @ Mon, 12 Aug 2019 20:12:35: 5000000 INFO @ Mon, 12 Aug 2019 20:12:41: 5000000 INFO @ Mon, 12 Aug 2019 20:12:42: 6000000 INFO @ Mon, 12 Aug 2019 20:12:42: 6000000 INFO @ Mon, 12 Aug 2019 20:12:49: 6000000 INFO @ Mon, 12 Aug 2019 20:12:49: 7000000 INFO @ Mon, 12 Aug 2019 20:12:50: 7000000 INFO @ Mon, 12 Aug 2019 20:12:56: 8000000 INFO @ Mon, 12 Aug 2019 20:12:57: 8000000 INFO @ Mon, 12 Aug 2019 20:12:57: 7000000 INFO @ Mon, 12 Aug 2019 20:13:04: 9000000 INFO @ Mon, 12 Aug 2019 20:13:04: 9000000 INFO @ Mon, 12 Aug 2019 20:13:05: 8000000 INFO @ Mon, 12 Aug 2019 20:13:11: 10000000 INFO @ Mon, 12 Aug 2019 20:13:11: 10000000 INFO @ Mon, 12 Aug 2019 20:13:13: 9000000 INFO @ Mon, 12 Aug 2019 20:13:18: 11000000 INFO @ Mon, 12 Aug 2019 20:13:18: 11000000 INFO @ Mon, 12 Aug 2019 20:13:21: 10000000 INFO @ Mon, 12 Aug 2019 20:13:25: 12000000 INFO @ Mon, 12 Aug 2019 20:13:26: 12000000 INFO @ Mon, 12 Aug 2019 20:13:29: 11000000 INFO @ Mon, 12 Aug 2019 20:13:32: 13000000 INFO @ Mon, 12 Aug 2019 20:13:33: 13000000 INFO @ Mon, 12 Aug 2019 20:13:38: 12000000 INFO @ Mon, 12 Aug 2019 20:13:39: #1 tag size is determined as 28 bps INFO @ Mon, 12 Aug 2019 20:13:39: #1 tag size = 28 INFO @ Mon, 12 Aug 2019 20:13:39: #1 total tags in treatment: 13930262 INFO @ Mon, 12 Aug 2019 20:13:39: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:13:39: #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 20:13:39: #1 tags after filtering in treatment: 13930262 INFO @ Mon, 12 Aug 2019 20:13:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:13:39: #1 finished! INFO @ Mon, 12 Aug 2019 20:13:39: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:13:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:13:40: #1 tag size is determined as 28 bps INFO @ Mon, 12 Aug 2019 20:13:40: #1 tag size = 28 INFO @ Mon, 12 Aug 2019 20:13:40: #1 total tags in treatment: 13930262 INFO @ Mon, 12 Aug 2019 20:13:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:13:40: #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 20:13:40: #1 tags after filtering in treatment: 13930262 INFO @ Mon, 12 Aug 2019 20:13:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:13:40: #1 finished! INFO @ Mon, 12 Aug 2019 20:13:40: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:13:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:13:40: #2 number of paired peaks: 320 WARNING @ Mon, 12 Aug 2019 20:13:40: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Mon, 12 Aug 2019 20:13:40: start model_add_line... INFO @ Mon, 12 Aug 2019 20:13:41: start X-correlation... INFO @ Mon, 12 Aug 2019 20:13:41: end of X-cor INFO @ Mon, 12 Aug 2019 20:13:41: #2 finished! INFO @ Mon, 12 Aug 2019 20:13:41: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 20:13:41: #2 alternative fragment length(s) may be 1,29,69,548,551,583 bps INFO @ Mon, 12 Aug 2019 20:13:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.05_model.r WARNING @ Mon, 12 Aug 2019 20:13:41: #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 20:13:41: #2 You may need to consider one of the other alternative d(s): 1,29,69,548,551,583 WARNING @ Mon, 12 Aug 2019 20:13:41: #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 20:13:41: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:13:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:13:41: #2 number of paired peaks: 320 WARNING @ Mon, 12 Aug 2019 20:13:41: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Mon, 12 Aug 2019 20:13:41: start model_add_line... INFO @ Mon, 12 Aug 2019 20:13:41: start X-correlation... INFO @ Mon, 12 Aug 2019 20:13:41: end of X-cor INFO @ Mon, 12 Aug 2019 20:13:41: #2 finished! INFO @ Mon, 12 Aug 2019 20:13:41: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 20:13:41: #2 alternative fragment length(s) may be 1,29,69,548,551,583 bps INFO @ Mon, 12 Aug 2019 20:13:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.10_model.r WARNING @ Mon, 12 Aug 2019 20:13:41: #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 20:13:41: #2 You may need to consider one of the other alternative d(s): 1,29,69,548,551,583 WARNING @ Mon, 12 Aug 2019 20:13:41: #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 20:13:41: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:13:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:13:45: 13000000 INFO @ Mon, 12 Aug 2019 20:13:52: #1 tag size is determined as 28 bps INFO @ Mon, 12 Aug 2019 20:13:52: #1 tag size = 28 INFO @ Mon, 12 Aug 2019 20:13:52: #1 total tags in treatment: 13930262 INFO @ Mon, 12 Aug 2019 20:13:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:13:52: #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 20:13:53: #1 tags after filtering in treatment: 13930262 INFO @ Mon, 12 Aug 2019 20:13:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:13:53: #1 finished! INFO @ Mon, 12 Aug 2019 20:13:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:13:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:13:54: #2 number of paired peaks: 320 WARNING @ Mon, 12 Aug 2019 20:13:54: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Mon, 12 Aug 2019 20:13:54: start model_add_line... INFO @ Mon, 12 Aug 2019 20:13:54: start X-correlation... INFO @ Mon, 12 Aug 2019 20:13:54: end of X-cor INFO @ Mon, 12 Aug 2019 20:13:54: #2 finished! INFO @ Mon, 12 Aug 2019 20:13:54: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 20:13:54: #2 alternative fragment length(s) may be 1,29,69,548,551,583 bps INFO @ Mon, 12 Aug 2019 20:13:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.20_model.r WARNING @ Mon, 12 Aug 2019 20:13:54: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:13:54: #2 You may need to consider one of the other alternative d(s): 1,29,69,548,551,583 WARNING @ Mon, 12 Aug 2019 20:13:54: #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 20:13:54: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:13:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:14:13: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:14:13: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:14:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:14:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:14:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:14:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.05_summits.bed INFO @ Mon, 12 Aug 2019 20:14:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:14:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:14:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:14:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.10_summits.bed INFO @ Mon, 12 Aug 2019 20:14:29: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:14:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:14:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:14:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529214/SRX529214.20_summits.bed INFO @ Mon, 12 Aug 2019 20:14:42: 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。