Job ID = 2589980 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,236,000 reads read : 14,236,000 reads written : 14,236,000 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1163632.sra.cache’: 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: 00:03:19 14236000 reads; of these: 14236000 (100.00%) were unpaired; of these: 1509333 (10.60%) aligned 0 times 10939090 (76.84%) aligned exactly 1 time 1787577 (12.56%) aligned >1 times 89.40% overall alignment rate Time searching: 00:03:19 Overall time: 00:03:19 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 8 files... [bam_rmdupse_core] 1919374 / 12726667 = 0.1508 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 19:01:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.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 19:01:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:01:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:01:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.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 19:01:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:01:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:02:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.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 19:02:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:02:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:02:08: 1000000 INFO @ Mon, 12 Aug 2019 19:02:08: 1000000 INFO @ Mon, 12 Aug 2019 19:02:09: 1000000 INFO @ Mon, 12 Aug 2019 19:02:16: 2000000 INFO @ Mon, 12 Aug 2019 19:02:17: 2000000 INFO @ Mon, 12 Aug 2019 19:02:17: 2000000 INFO @ Mon, 12 Aug 2019 19:02:25: 3000000 INFO @ Mon, 12 Aug 2019 19:02:25: 3000000 INFO @ Mon, 12 Aug 2019 19:02:26: 3000000 INFO @ Mon, 12 Aug 2019 19:02:33: 4000000 INFO @ Mon, 12 Aug 2019 19:02:34: 4000000 INFO @ Mon, 12 Aug 2019 19:02:35: 4000000 INFO @ Mon, 12 Aug 2019 19:02:42: 5000000 INFO @ Mon, 12 Aug 2019 19:02:43: 5000000 INFO @ Mon, 12 Aug 2019 19:02:44: 5000000 INFO @ Mon, 12 Aug 2019 19:02:50: 6000000 INFO @ Mon, 12 Aug 2019 19:02:52: 6000000 INFO @ Mon, 12 Aug 2019 19:02:53: 6000000 INFO @ Mon, 12 Aug 2019 19:02:59: 7000000 INFO @ Mon, 12 Aug 2019 19:03:01: 7000000 INFO @ Mon, 12 Aug 2019 19:03:01: 7000000 INFO @ Mon, 12 Aug 2019 19:03:07: 8000000 INFO @ Mon, 12 Aug 2019 19:03:10: 8000000 INFO @ Mon, 12 Aug 2019 19:03:10: 8000000 INFO @ Mon, 12 Aug 2019 19:03:16: 9000000 INFO @ Mon, 12 Aug 2019 19:03:19: 9000000 INFO @ Mon, 12 Aug 2019 19:03:19: 9000000 INFO @ Mon, 12 Aug 2019 19:03:24: 10000000 INFO @ Mon, 12 Aug 2019 19:03:27: 10000000 INFO @ Mon, 12 Aug 2019 19:03:28: 10000000 INFO @ Mon, 12 Aug 2019 19:03:31: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:03:31: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:03:31: #1 total tags in treatment: 10807293 INFO @ Mon, 12 Aug 2019 19:03:31: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:03:31: #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 19:03:31: #1 tags after filtering in treatment: 10807293 INFO @ Mon, 12 Aug 2019 19:03:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:03:31: #1 finished! INFO @ Mon, 12 Aug 2019 19:03:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:03:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:03:32: #2 number of paired peaks: 259 WARNING @ Mon, 12 Aug 2019 19:03:32: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Mon, 12 Aug 2019 19:03:32: start model_add_line... INFO @ Mon, 12 Aug 2019 19:03:32: start X-correlation... INFO @ Mon, 12 Aug 2019 19:03:32: end of X-cor INFO @ Mon, 12 Aug 2019 19:03:32: #2 finished! INFO @ Mon, 12 Aug 2019 19:03:32: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 19:03:32: #2 alternative fragment length(s) may be 3,48,514,543 bps INFO @ Mon, 12 Aug 2019 19:03:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.05_model.r WARNING @ Mon, 12 Aug 2019 19:03:32: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:03:32: #2 You may need to consider one of the other alternative d(s): 3,48,514,543 WARNING @ Mon, 12 Aug 2019 19:03:32: #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 19:03:32: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:03:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:03:34: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:03:34: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:03:34: #1 total tags in treatment: 10807293 INFO @ Mon, 12 Aug 2019 19:03:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:03:34: #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 19:03:35: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:03:35: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:03:35: #1 total tags in treatment: 10807293 INFO @ Mon, 12 Aug 2019 19:03:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:03:35: #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 19:03:35: #1 tags after filtering in treatment: 10807293 INFO @ Mon, 12 Aug 2019 19:03:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:03:35: #1 finished! INFO @ Mon, 12 Aug 2019 19:03:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:03:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:03:35: #1 tags after filtering in treatment: 10807293 INFO @ Mon, 12 Aug 2019 19:03:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:03:35: #1 finished! INFO @ Mon, 12 Aug 2019 19:03:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:03:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:03:36: #2 number of paired peaks: 259 WARNING @ Mon, 12 Aug 2019 19:03:36: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Mon, 12 Aug 2019 19:03:36: start model_add_line... INFO @ Mon, 12 Aug 2019 19:03:36: start X-correlation... INFO @ Mon, 12 Aug 2019 19:03:36: end of X-cor INFO @ Mon, 12 Aug 2019 19:03:36: #2 finished! INFO @ Mon, 12 Aug 2019 19:03:36: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 19:03:36: #2 alternative fragment length(s) may be 3,48,514,543 bps INFO @ Mon, 12 Aug 2019 19:03:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.20_model.r WARNING @ Mon, 12 Aug 2019 19:03:36: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:03:36: #2 You may need to consider one of the other alternative d(s): 3,48,514,543 WARNING @ Mon, 12 Aug 2019 19:03:36: #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 19:03:36: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:03:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:03:36: #2 number of paired peaks: 259 WARNING @ Mon, 12 Aug 2019 19:03:36: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Mon, 12 Aug 2019 19:03:36: start model_add_line... INFO @ Mon, 12 Aug 2019 19:03:36: start X-correlation... INFO @ Mon, 12 Aug 2019 19:03:36: end of X-cor INFO @ Mon, 12 Aug 2019 19:03:36: #2 finished! INFO @ Mon, 12 Aug 2019 19:03:36: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 19:03:36: #2 alternative fragment length(s) may be 3,48,514,543 bps INFO @ Mon, 12 Aug 2019 19:03:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.10_model.r WARNING @ Mon, 12 Aug 2019 19:03:36: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:03:36: #2 You may need to consider one of the other alternative d(s): 3,48,514,543 WARNING @ Mon, 12 Aug 2019 19:03:36: #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 19:03:36: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:03:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:04:00: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:04:04: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:04:04: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:04:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:04:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:04:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.05_summits.bed INFO @ Mon, 12 Aug 2019 19:04:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (602 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:04:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:04:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:04:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.10_summits.bed INFO @ Mon, 12 Aug 2019 19:04:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (402 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:04:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:04:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:04:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466566/SRX466566.20_summits.bed INFO @ Mon, 12 Aug 2019 19:04:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (157 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。