Job ID = 2589510 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,862,966 reads read : 8,862,966 reads written : 8,862,966 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR660147.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: 00:01:27 8862966 reads; of these: 8862966 (100.00%) were unpaired; of these: 244534 (2.76%) aligned 0 times 7345992 (82.88%) aligned exactly 1 time 1272440 (14.36%) aligned >1 times 97.24% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 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] 1214792 / 8618432 = 0.1410 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 17:53:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.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 17:53:26: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:53:26: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:53:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.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 17:53:27: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:53:27: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:53:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.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 17:53:28: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:53:28: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:53:33: 1000000 INFO @ Mon, 12 Aug 2019 17:53:35: 1000000 INFO @ Mon, 12 Aug 2019 17:53:35: 1000000 INFO @ Mon, 12 Aug 2019 17:53:40: 2000000 INFO @ Mon, 12 Aug 2019 17:53:43: 2000000 INFO @ Mon, 12 Aug 2019 17:53:43: 2000000 INFO @ Mon, 12 Aug 2019 17:53:46: 3000000 INFO @ Mon, 12 Aug 2019 17:53:50: 3000000 INFO @ Mon, 12 Aug 2019 17:53:52: 3000000 INFO @ Mon, 12 Aug 2019 17:53:53: 4000000 INFO @ Mon, 12 Aug 2019 17:53:57: 4000000 INFO @ Mon, 12 Aug 2019 17:53:59: 5000000 INFO @ Mon, 12 Aug 2019 17:54:00: 4000000 INFO @ Mon, 12 Aug 2019 17:54:04: 5000000 INFO @ Mon, 12 Aug 2019 17:54:06: 6000000 INFO @ Mon, 12 Aug 2019 17:54:09: 5000000 INFO @ Mon, 12 Aug 2019 17:54:11: 6000000 INFO @ Mon, 12 Aug 2019 17:54:12: 7000000 INFO @ Mon, 12 Aug 2019 17:54:15: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:54:15: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:54:15: #1 total tags in treatment: 7403640 INFO @ Mon, 12 Aug 2019 17:54:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:54:15: #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 17:54:15: #1 tags after filtering in treatment: 7403640 INFO @ Mon, 12 Aug 2019 17:54:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:54:15: #1 finished! INFO @ Mon, 12 Aug 2019 17:54:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:54:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:54:16: #2 number of paired peaks: 402 WARNING @ Mon, 12 Aug 2019 17:54:16: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Mon, 12 Aug 2019 17:54:16: start model_add_line... INFO @ Mon, 12 Aug 2019 17:54:16: start X-correlation... INFO @ Mon, 12 Aug 2019 17:54:16: end of X-cor INFO @ Mon, 12 Aug 2019 17:54:16: #2 finished! INFO @ Mon, 12 Aug 2019 17:54:16: #2 predicted fragment length is 32 bps INFO @ Mon, 12 Aug 2019 17:54:16: #2 alternative fragment length(s) may be 2,32,575 bps INFO @ Mon, 12 Aug 2019 17:54:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.05_model.r WARNING @ Mon, 12 Aug 2019 17:54:16: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:54:16: #2 You may need to consider one of the other alternative d(s): 2,32,575 WARNING @ Mon, 12 Aug 2019 17:54:16: #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 17:54:16: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:54:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:54:17: 6000000 INFO @ Mon, 12 Aug 2019 17:54:18: 7000000 INFO @ Mon, 12 Aug 2019 17:54:21: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:54:21: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:54:21: #1 total tags in treatment: 7403640 INFO @ Mon, 12 Aug 2019 17:54:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:54:21: #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 17:54:21: #1 tags after filtering in treatment: 7403640 INFO @ Mon, 12 Aug 2019 17:54:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:54:21: #1 finished! INFO @ Mon, 12 Aug 2019 17:54:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:54:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:54:22: #2 number of paired peaks: 402 WARNING @ Mon, 12 Aug 2019 17:54:22: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Mon, 12 Aug 2019 17:54:22: start model_add_line... INFO @ Mon, 12 Aug 2019 17:54:22: start X-correlation... INFO @ Mon, 12 Aug 2019 17:54:22: end of X-cor INFO @ Mon, 12 Aug 2019 17:54:22: #2 finished! INFO @ Mon, 12 Aug 2019 17:54:22: #2 predicted fragment length is 32 bps INFO @ Mon, 12 Aug 2019 17:54:22: #2 alternative fragment length(s) may be 2,32,575 bps INFO @ Mon, 12 Aug 2019 17:54:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.20_model.r WARNING @ Mon, 12 Aug 2019 17:54:22: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:54:22: #2 You may need to consider one of the other alternative d(s): 2,32,575 WARNING @ Mon, 12 Aug 2019 17:54:22: #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 17:54:22: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:54:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:54:25: 7000000 INFO @ Mon, 12 Aug 2019 17:54:29: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:54:29: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:54:29: #1 total tags in treatment: 7403640 INFO @ Mon, 12 Aug 2019 17:54:29: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:54:29: #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 17:54:29: #1 tags after filtering in treatment: 7403640 INFO @ Mon, 12 Aug 2019 17:54:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:54:29: #1 finished! INFO @ Mon, 12 Aug 2019 17:54:29: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:54:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:54:29: #2 number of paired peaks: 402 WARNING @ Mon, 12 Aug 2019 17:54:29: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Mon, 12 Aug 2019 17:54:29: start model_add_line... INFO @ Mon, 12 Aug 2019 17:54:29: start X-correlation... INFO @ Mon, 12 Aug 2019 17:54:29: end of X-cor INFO @ Mon, 12 Aug 2019 17:54:29: #2 finished! INFO @ Mon, 12 Aug 2019 17:54:29: #2 predicted fragment length is 32 bps INFO @ Mon, 12 Aug 2019 17:54:29: #2 alternative fragment length(s) may be 2,32,575 bps INFO @ Mon, 12 Aug 2019 17:54:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.10_model.r WARNING @ Mon, 12 Aug 2019 17:54:29: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:54:29: #2 You may need to consider one of the other alternative d(s): 2,32,575 WARNING @ Mon, 12 Aug 2019 17:54:29: #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 17:54:29: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:54:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:54:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:54:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:54:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:54:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:54:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.05_summits.bed INFO @ Mon, 12 Aug 2019 17:54:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (511 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:54:50: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:54:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:54:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:54:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.20_summits.bed INFO @ Mon, 12 Aug 2019 17:54:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (59 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:55:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:55:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:55:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX222640/SRX222640.10_summits.bed INFO @ Mon, 12 Aug 2019 17:55:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (235 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。