Job ID = 1290611 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,329,297 reads read : 11,329,297 reads written : 11,329,297 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: 00:02:59 11329297 reads; of these: 11329297 (100.00%) were unpaired; of these: 185454 (1.64%) aligned 0 times 9795476 (86.46%) aligned exactly 1 time 1348367 (11.90%) aligned >1 times 98.36% overall alignment rate Time searching: 00:02:59 Overall time: 00:02:59 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] 1376448 / 11143843 = 0.1235 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 @ Sat, 01 Jun 2019 21:51:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.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 @ Sat, 01 Jun 2019 21:51:47: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:47: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.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 @ Sat, 01 Jun 2019 21:51:47: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:47: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.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 @ Sat, 01 Jun 2019 21:51:47: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:47: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:54: 1000000 INFO @ Sat, 01 Jun 2019 21:51:55: 1000000 INFO @ Sat, 01 Jun 2019 21:51:56: 1000000 INFO @ Sat, 01 Jun 2019 21:52:02: 2000000 INFO @ Sat, 01 Jun 2019 21:52:02: 2000000 INFO @ Sat, 01 Jun 2019 21:52:04: 2000000 INFO @ Sat, 01 Jun 2019 21:52:10: 3000000 INFO @ Sat, 01 Jun 2019 21:52:10: 3000000 INFO @ Sat, 01 Jun 2019 21:52:12: 3000000 INFO @ Sat, 01 Jun 2019 21:52:17: 4000000 INFO @ Sat, 01 Jun 2019 21:52:18: 4000000 INFO @ Sat, 01 Jun 2019 21:52:20: 4000000 INFO @ Sat, 01 Jun 2019 21:52:25: 5000000 INFO @ Sat, 01 Jun 2019 21:52:26: 5000000 INFO @ Sat, 01 Jun 2019 21:52:28: 5000000 INFO @ Sat, 01 Jun 2019 21:52:32: 6000000 INFO @ Sat, 01 Jun 2019 21:52:33: 6000000 INFO @ Sat, 01 Jun 2019 21:52:36: 6000000 INFO @ Sat, 01 Jun 2019 21:52:39: 7000000 INFO @ Sat, 01 Jun 2019 21:52:41: 7000000 INFO @ Sat, 01 Jun 2019 21:52:43: 7000000 INFO @ Sat, 01 Jun 2019 21:52:46: 8000000 INFO @ Sat, 01 Jun 2019 21:52:48: 8000000 INFO @ Sat, 01 Jun 2019 21:52:50: 8000000 INFO @ Sat, 01 Jun 2019 21:52:52: 9000000 INFO @ Sat, 01 Jun 2019 21:52:55: 9000000 INFO @ Sat, 01 Jun 2019 21:52:58: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:52:58: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:52:58: #1 total tags in treatment: 9767395 INFO @ Sat, 01 Jun 2019 21:52:58: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:52:58: #1 tags after filtering in treatment: 9767395 INFO @ Sat, 01 Jun 2019 21:52:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:58: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:58: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:58: 9000000 INFO @ Sat, 01 Jun 2019 21:52:59: #2 number of paired peaks: 112 WARNING @ Sat, 01 Jun 2019 21:52:59: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 01 Jun 2019 21:52:59: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:59: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:59: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:59: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:59: #2 predicted fragment length is 49 bps INFO @ Sat, 01 Jun 2019 21:52:59: #2 alternative fragment length(s) may be 4,49,182,448,492 bps INFO @ Sat, 01 Jun 2019 21:52:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.20_model.r WARNING @ Sat, 01 Jun 2019 21:52:59: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:52:59: #2 You may need to consider one of the other alternative d(s): 4,49,182,448,492 WARNING @ Sat, 01 Jun 2019 21:52:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:52:59: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:53:01: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:53:01: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:53:01: #1 total tags in treatment: 9767395 INFO @ Sat, 01 Jun 2019 21:53:01: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:53:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:53:01: #1 tags after filtering in treatment: 9767395 INFO @ Sat, 01 Jun 2019 21:53:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:53:01: #1 finished! INFO @ Sat, 01 Jun 2019 21:53:01: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:53:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:53:02: #2 number of paired peaks: 112 WARNING @ Sat, 01 Jun 2019 21:53:02: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 01 Jun 2019 21:53:02: start model_add_line... INFO @ Sat, 01 Jun 2019 21:53:02: start X-correlation... INFO @ Sat, 01 Jun 2019 21:53:02: end of X-cor INFO @ Sat, 01 Jun 2019 21:53:02: #2 finished! INFO @ Sat, 01 Jun 2019 21:53:02: #2 predicted fragment length is 49 bps INFO @ Sat, 01 Jun 2019 21:53:02: #2 alternative fragment length(s) may be 4,49,182,448,492 bps INFO @ Sat, 01 Jun 2019 21:53:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.10_model.r WARNING @ Sat, 01 Jun 2019 21:53:02: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:53:02: #2 You may need to consider one of the other alternative d(s): 4,49,182,448,492 WARNING @ Sat, 01 Jun 2019 21:53:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:53:02: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:53:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:53:04: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:53:04: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:53:04: #1 total tags in treatment: 9767395 INFO @ Sat, 01 Jun 2019 21:53:04: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:53:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:53:04: #1 tags after filtering in treatment: 9767395 INFO @ Sat, 01 Jun 2019 21:53:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:53:04: #1 finished! INFO @ Sat, 01 Jun 2019 21:53:04: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:53:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:53:05: #2 number of paired peaks: 112 WARNING @ Sat, 01 Jun 2019 21:53:05: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 01 Jun 2019 21:53:05: start model_add_line... INFO @ Sat, 01 Jun 2019 21:53:05: start X-correlation... INFO @ Sat, 01 Jun 2019 21:53:05: end of X-cor INFO @ Sat, 01 Jun 2019 21:53:05: #2 finished! INFO @ Sat, 01 Jun 2019 21:53:05: #2 predicted fragment length is 49 bps INFO @ Sat, 01 Jun 2019 21:53:05: #2 alternative fragment length(s) may be 4,49,182,448,492 bps INFO @ Sat, 01 Jun 2019 21:53:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.05_model.r WARNING @ Sat, 01 Jun 2019 21:53:05: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:53:05: #2 You may need to consider one of the other alternative d(s): 4,49,182,448,492 WARNING @ Sat, 01 Jun 2019 21:53:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:53:05: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:53:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:53:25: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:28: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:32: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.20_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.20_summits.bed INFO @ Sat, 01 Jun 2019 21:53:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (64 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:53:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.10_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.10_summits.bed INFO @ Sat, 01 Jun 2019 21:53:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (176 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:53:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.05_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2350747/SRX2350747.05_summits.bed INFO @ Sat, 01 Jun 2019 21:53:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (554 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。