Job ID = 1291799 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,172,133 reads read : 16,172,133 reads written : 16,172,133 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:04:44 16172133 reads; of these: 16172133 (100.00%) were unpaired; of these: 283776 (1.75%) aligned 0 times 13078381 (80.87%) aligned exactly 1 time 2809976 (17.38%) aligned >1 times 98.25% overall alignment rate Time searching: 00:04:44 Overall time: 00:04:44 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] 5750507 / 15888357 = 0.3619 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 @ Sun, 02 Jun 2019 16:46:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.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 @ Sun, 02 Jun 2019 16:46:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:46:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:46:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.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 @ Sun, 02 Jun 2019 16:46:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:46:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:46:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.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 @ Sun, 02 Jun 2019 16:46:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:46:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:46:56: 1000000 INFO @ Sun, 02 Jun 2019 16:46:56: 1000000 INFO @ Sun, 02 Jun 2019 16:46:56: 1000000 INFO @ Sun, 02 Jun 2019 16:47:05: 2000000 INFO @ Sun, 02 Jun 2019 16:47:05: 2000000 INFO @ Sun, 02 Jun 2019 16:47:07: 2000000 INFO @ Sun, 02 Jun 2019 16:47:15: 3000000 INFO @ Sun, 02 Jun 2019 16:47:15: 3000000 INFO @ Sun, 02 Jun 2019 16:47:17: 3000000 INFO @ Sun, 02 Jun 2019 16:47:23: 4000000 INFO @ Sun, 02 Jun 2019 16:47:24: 4000000 INFO @ Sun, 02 Jun 2019 16:47:27: 4000000 INFO @ Sun, 02 Jun 2019 16:47:33: 5000000 INFO @ Sun, 02 Jun 2019 16:47:33: 5000000 INFO @ Sun, 02 Jun 2019 16:47:37: 5000000 INFO @ Sun, 02 Jun 2019 16:47:42: 6000000 INFO @ Sun, 02 Jun 2019 16:47:43: 6000000 INFO @ Sun, 02 Jun 2019 16:47:47: 6000000 INFO @ Sun, 02 Jun 2019 16:47:51: 7000000 INFO @ Sun, 02 Jun 2019 16:47:53: 7000000 INFO @ Sun, 02 Jun 2019 16:47:56: 7000000 INFO @ Sun, 02 Jun 2019 16:48:00: 8000000 INFO @ Sun, 02 Jun 2019 16:48:02: 8000000 INFO @ Sun, 02 Jun 2019 16:48:06: 8000000 INFO @ Sun, 02 Jun 2019 16:48:10: 9000000 INFO @ Sun, 02 Jun 2019 16:48:11: 9000000 INFO @ Sun, 02 Jun 2019 16:48:16: 9000000 INFO @ Sun, 02 Jun 2019 16:48:19: 10000000 INFO @ Sun, 02 Jun 2019 16:48:20: 10000000 INFO @ Sun, 02 Jun 2019 16:48:20: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 16:48:20: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 16:48:20: #1 total tags in treatment: 10137850 INFO @ Sun, 02 Jun 2019 16:48:20: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:48:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:48:20: #1 tags after filtering in treatment: 10137850 INFO @ Sun, 02 Jun 2019 16:48:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:48:20: #1 finished! INFO @ Sun, 02 Jun 2019 16:48:20: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:48:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:48:21: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 16:48:21: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 16:48:21: #1 total tags in treatment: 10137850 INFO @ Sun, 02 Jun 2019 16:48:21: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:48:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:48:21: #2 number of paired peaks: 425 WARNING @ Sun, 02 Jun 2019 16:48:21: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Sun, 02 Jun 2019 16:48:21: start model_add_line... INFO @ Sun, 02 Jun 2019 16:48:21: start X-correlation... INFO @ Sun, 02 Jun 2019 16:48:21: end of X-cor INFO @ Sun, 02 Jun 2019 16:48:21: #2 finished! INFO @ Sun, 02 Jun 2019 16:48:21: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 16:48:21: #2 alternative fragment length(s) may be 2,51,556,577 bps INFO @ Sun, 02 Jun 2019 16:48:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.10_model.r WARNING @ Sun, 02 Jun 2019 16:48:21: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:48:21: #2 You may need to consider one of the other alternative d(s): 2,51,556,577 WARNING @ Sun, 02 Jun 2019 16:48:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 16:48:21: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:48:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:48:21: #1 tags after filtering in treatment: 10137850 INFO @ Sun, 02 Jun 2019 16:48:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:48:21: #1 finished! INFO @ Sun, 02 Jun 2019 16:48:21: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:48:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:48:22: #2 number of paired peaks: 425 WARNING @ Sun, 02 Jun 2019 16:48:22: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Sun, 02 Jun 2019 16:48:22: start model_add_line... INFO @ Sun, 02 Jun 2019 16:48:22: start X-correlation... INFO @ Sun, 02 Jun 2019 16:48:22: end of X-cor INFO @ Sun, 02 Jun 2019 16:48:22: #2 finished! INFO @ Sun, 02 Jun 2019 16:48:22: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 16:48:22: #2 alternative fragment length(s) may be 2,51,556,577 bps INFO @ Sun, 02 Jun 2019 16:48:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.20_model.r WARNING @ Sun, 02 Jun 2019 16:48:22: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:48:22: #2 You may need to consider one of the other alternative d(s): 2,51,556,577 WARNING @ Sun, 02 Jun 2019 16:48:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 16:48:22: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:48:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:48:26: 10000000 INFO @ Sun, 02 Jun 2019 16:48:27: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 16:48:27: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 16:48:27: #1 total tags in treatment: 10137850 INFO @ Sun, 02 Jun 2019 16:48:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:48:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:48:27: #1 tags after filtering in treatment: 10137850 INFO @ Sun, 02 Jun 2019 16:48:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:48:27: #1 finished! INFO @ Sun, 02 Jun 2019 16:48:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:48:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:48:28: #2 number of paired peaks: 425 WARNING @ Sun, 02 Jun 2019 16:48:28: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Sun, 02 Jun 2019 16:48:28: start model_add_line... INFO @ Sun, 02 Jun 2019 16:48:28: start X-correlation... INFO @ Sun, 02 Jun 2019 16:48:28: end of X-cor INFO @ Sun, 02 Jun 2019 16:48:28: #2 finished! INFO @ Sun, 02 Jun 2019 16:48:28: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 16:48:28: #2 alternative fragment length(s) may be 2,51,556,577 bps INFO @ Sun, 02 Jun 2019 16:48:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.05_model.r WARNING @ Sun, 02 Jun 2019 16:48:28: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:48:28: #2 You may need to consider one of the other alternative d(s): 2,51,556,577 WARNING @ Sun, 02 Jun 2019 16:48:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 16:48:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:48:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:48:49: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:48:50: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:48:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:49:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:49:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:49:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.10_summits.bed INFO @ Sun, 02 Jun 2019 16:49:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (558 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:49:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:49:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:49:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.20_summits.bed INFO @ Sun, 02 Jun 2019 16:49:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (220 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:49:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:49:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:49:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257645/SRX257645.05_summits.bed INFO @ Sun, 02 Jun 2019 16:49:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (861 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。