Job ID = 4303048 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,666,016 reads read : 29,666,016 reads written : 29,666,016 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1198445.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: 00:07:03 29666016 reads; of these: 29666016 (100.00%) were unpaired; of these: 2183384 (7.36%) aligned 0 times 22670698 (76.42%) aligned exactly 1 time 4811934 (16.22%) aligned >1 times 92.64% overall alignment rate Time searching: 00:07:03 Overall time: 00:07:03 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] 17076317 / 27482632 = 0.6213 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:50:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.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 @ Thu, 12 Dec 2019 00:50:16: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:50:16: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:50:24: 1000000 INFO @ Thu, 12 Dec 2019 00:50:32: 2000000 INFO @ Thu, 12 Dec 2019 00:50:40: 3000000 INFO @ Thu, 12 Dec 2019 00:50:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.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 @ Thu, 12 Dec 2019 00:50:45: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:50:45: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:50:48: 4000000 INFO @ Thu, 12 Dec 2019 00:50:53: 1000000 INFO @ Thu, 12 Dec 2019 00:50:55: 5000000 INFO @ Thu, 12 Dec 2019 00:51:02: 2000000 INFO @ Thu, 12 Dec 2019 00:51:03: 6000000 INFO @ Thu, 12 Dec 2019 00:51:10: 7000000 INFO @ Thu, 12 Dec 2019 00:51:11: 3000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:51:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.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 @ Thu, 12 Dec 2019 00:51:15: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:51:15: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:51:18: 8000000 INFO @ Thu, 12 Dec 2019 00:51:20: 4000000 INFO @ Thu, 12 Dec 2019 00:51:25: 1000000 INFO @ Thu, 12 Dec 2019 00:51:25: 9000000 INFO @ Thu, 12 Dec 2019 00:51:30: 5000000 INFO @ Thu, 12 Dec 2019 00:51:33: 10000000 INFO @ Thu, 12 Dec 2019 00:51:35: 2000000 INFO @ Thu, 12 Dec 2019 00:51:36: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:51:36: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:51:36: #1 total tags in treatment: 10406315 INFO @ Thu, 12 Dec 2019 00:51:36: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:51:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:51:36: #1 tags after filtering in treatment: 10406315 INFO @ Thu, 12 Dec 2019 00:51:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:51:36: #1 finished! INFO @ Thu, 12 Dec 2019 00:51:36: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:51:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:51:37: #2 number of paired peaks: 752 WARNING @ Thu, 12 Dec 2019 00:51:37: Fewer paired peaks (752) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 752 pairs to build model! INFO @ Thu, 12 Dec 2019 00:51:37: start model_add_line... INFO @ Thu, 12 Dec 2019 00:51:37: start X-correlation... INFO @ Thu, 12 Dec 2019 00:51:38: end of X-cor INFO @ Thu, 12 Dec 2019 00:51:38: #2 finished! INFO @ Thu, 12 Dec 2019 00:51:38: #2 predicted fragment length is 54 bps INFO @ Thu, 12 Dec 2019 00:51:38: #2 alternative fragment length(s) may be 3,54 bps INFO @ Thu, 12 Dec 2019 00:51:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.05_model.r WARNING @ Thu, 12 Dec 2019 00:51:38: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:51:38: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Thu, 12 Dec 2019 00:51:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:51:38: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:51:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:51:40: 6000000 INFO @ Thu, 12 Dec 2019 00:51:45: 3000000 INFO @ Thu, 12 Dec 2019 00:51:50: 7000000 INFO @ Thu, 12 Dec 2019 00:51:54: 4000000 INFO @ Thu, 12 Dec 2019 00:51:59: 8000000 INFO @ Thu, 12 Dec 2019 00:52:04: 5000000 INFO @ Thu, 12 Dec 2019 00:52:07: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:52:08: 9000000 INFO @ Thu, 12 Dec 2019 00:52:14: 6000000 INFO @ Thu, 12 Dec 2019 00:52:17: 10000000 INFO @ Thu, 12 Dec 2019 00:52:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:52:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:52:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.05_summits.bed INFO @ Thu, 12 Dec 2019 00:52:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1691 records, 4 fields): 63 millis INFO @ Thu, 12 Dec 2019 00:52:21: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:52:21: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:52:21: #1 total tags in treatment: 10406315 INFO @ Thu, 12 Dec 2019 00:52:21: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:52:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:52:21: #1 tags after filtering in treatment: 10406315 INFO @ Thu, 12 Dec 2019 00:52:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:52:21: #1 finished! INFO @ Thu, 12 Dec 2019 00:52:21: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:52:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:52:22: #2 number of paired peaks: 752 WARNING @ Thu, 12 Dec 2019 00:52:22: Fewer paired peaks (752) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 752 pairs to build model! INFO @ Thu, 12 Dec 2019 00:52:22: start model_add_line... INFO @ Thu, 12 Dec 2019 00:52:22: start X-correlation... INFO @ Thu, 12 Dec 2019 00:52:22: end of X-cor INFO @ Thu, 12 Dec 2019 00:52:22: #2 finished! INFO @ Thu, 12 Dec 2019 00:52:22: #2 predicted fragment length is 54 bps INFO @ Thu, 12 Dec 2019 00:52:22: #2 alternative fragment length(s) may be 3,54 bps INFO @ Thu, 12 Dec 2019 00:52:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.10_model.r WARNING @ Thu, 12 Dec 2019 00:52:22: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:52:22: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Thu, 12 Dec 2019 00:52:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:52:22: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:52:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:52:23: 7000000 INFO @ Thu, 12 Dec 2019 00:52:32: 8000000 INFO @ Thu, 12 Dec 2019 00:52:41: 9000000 INFO @ Thu, 12 Dec 2019 00:52:50: 10000000 INFO @ Thu, 12 Dec 2019 00:52:50: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:52:54: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:52:54: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:52:54: #1 total tags in treatment: 10406315 INFO @ Thu, 12 Dec 2019 00:52:54: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:52:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:52:54: #1 tags after filtering in treatment: 10406315 INFO @ Thu, 12 Dec 2019 00:52:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:52:54: #1 finished! INFO @ Thu, 12 Dec 2019 00:52:54: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:52:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:52:55: #2 number of paired peaks: 752 WARNING @ Thu, 12 Dec 2019 00:52:55: Fewer paired peaks (752) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 752 pairs to build model! INFO @ Thu, 12 Dec 2019 00:52:55: start model_add_line... INFO @ Thu, 12 Dec 2019 00:52:55: start X-correlation... INFO @ Thu, 12 Dec 2019 00:52:55: end of X-cor INFO @ Thu, 12 Dec 2019 00:52:55: #2 finished! INFO @ Thu, 12 Dec 2019 00:52:55: #2 predicted fragment length is 54 bps INFO @ Thu, 12 Dec 2019 00:52:55: #2 alternative fragment length(s) may be 3,54 bps INFO @ Thu, 12 Dec 2019 00:52:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.20_model.r WARNING @ Thu, 12 Dec 2019 00:52:55: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:52:55: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Thu, 12 Dec 2019 00:52:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:52:55: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:52:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:53:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:53:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:53:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.10_summits.bed INFO @ Thu, 12 Dec 2019 00:53:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (937 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:53:24: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:53:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:53:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:53:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494913/SRX494913.20_summits.bed INFO @ Thu, 12 Dec 2019 00:53:38: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (388 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。