Job ID = 1293129 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,023,518 reads read : 38,047,036 reads written : 19,023,518 reads 0-length : 19,023,518 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: 00:05:25 19023518 reads; of these: 19023518 (100.00%) were unpaired; of these: 185258 (0.97%) aligned 0 times 14195317 (74.62%) aligned exactly 1 time 4642943 (24.41%) aligned >1 times 99.03% overall alignment rate Time searching: 00:05:25 Overall time: 00:05:25 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] 8697514 / 18838260 = 0.4617 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 22:09:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.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 22:09:10: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:09:10: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:09:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.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 22:09:10: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:09:10: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:09:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.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 22:09:10: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:09:10: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:09:18: 1000000 INFO @ Sun, 02 Jun 2019 22:09:18: 1000000 INFO @ Sun, 02 Jun 2019 22:09:20: 1000000 INFO @ Sun, 02 Jun 2019 22:09:25: 2000000 INFO @ Sun, 02 Jun 2019 22:09:26: 2000000 INFO @ Sun, 02 Jun 2019 22:09:29: 2000000 INFO @ Sun, 02 Jun 2019 22:09:33: 3000000 INFO @ Sun, 02 Jun 2019 22:09:34: 3000000 INFO @ Sun, 02 Jun 2019 22:09:39: 3000000 INFO @ Sun, 02 Jun 2019 22:09:41: 4000000 INFO @ Sun, 02 Jun 2019 22:09:43: 4000000 INFO @ Sun, 02 Jun 2019 22:09:48: 5000000 INFO @ Sun, 02 Jun 2019 22:09:49: 4000000 INFO @ Sun, 02 Jun 2019 22:09:50: 5000000 INFO @ Sun, 02 Jun 2019 22:09:55: 6000000 INFO @ Sun, 02 Jun 2019 22:09:58: 5000000 INFO @ Sun, 02 Jun 2019 22:09:58: 6000000 INFO @ Sun, 02 Jun 2019 22:10:02: 7000000 INFO @ Sun, 02 Jun 2019 22:10:07: 7000000 INFO @ Sun, 02 Jun 2019 22:10:08: 6000000 INFO @ Sun, 02 Jun 2019 22:10:13: 8000000 INFO @ Sun, 02 Jun 2019 22:10:16: 8000000 INFO @ Sun, 02 Jun 2019 22:10:18: 7000000 INFO @ Sun, 02 Jun 2019 22:10:20: 9000000 INFO @ Sun, 02 Jun 2019 22:10:23: 9000000 INFO @ Sun, 02 Jun 2019 22:10:27: 10000000 INFO @ Sun, 02 Jun 2019 22:10:28: 8000000 INFO @ Sun, 02 Jun 2019 22:10:28: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:10:28: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:10:28: #1 total tags in treatment: 10140746 INFO @ Sun, 02 Jun 2019 22:10:28: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:10:28: #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 22:10:29: #1 tags after filtering in treatment: 10140746 INFO @ Sun, 02 Jun 2019 22:10:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:10:29: #1 finished! INFO @ Sun, 02 Jun 2019 22:10:29: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:10:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:10:30: #2 number of paired peaks: 795 WARNING @ Sun, 02 Jun 2019 22:10:30: Fewer paired peaks (795) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 795 pairs to build model! INFO @ Sun, 02 Jun 2019 22:10:30: start model_add_line... INFO @ Sun, 02 Jun 2019 22:10:30: start X-correlation... INFO @ Sun, 02 Jun 2019 22:10:30: end of X-cor INFO @ Sun, 02 Jun 2019 22:10:30: #2 finished! INFO @ Sun, 02 Jun 2019 22:10:30: #2 predicted fragment length is 53 bps INFO @ Sun, 02 Jun 2019 22:10:30: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 02 Jun 2019 22:10:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.20_model.r WARNING @ Sun, 02 Jun 2019 22:10:30: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:10:30: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 02 Jun 2019 22:10:30: #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 22:10:30: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:10:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:10:31: 10000000 INFO @ Sun, 02 Jun 2019 22:10:32: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:10:32: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:10:32: #1 total tags in treatment: 10140746 INFO @ Sun, 02 Jun 2019 22:10:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:10:32: #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 22:10:33: #1 tags after filtering in treatment: 10140746 INFO @ Sun, 02 Jun 2019 22:10:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:10:33: #1 finished! INFO @ Sun, 02 Jun 2019 22:10:33: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:10:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:10:34: #2 number of paired peaks: 795 WARNING @ Sun, 02 Jun 2019 22:10:34: Fewer paired peaks (795) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 795 pairs to build model! INFO @ Sun, 02 Jun 2019 22:10:34: start model_add_line... INFO @ Sun, 02 Jun 2019 22:10:34: start X-correlation... INFO @ Sun, 02 Jun 2019 22:10:34: end of X-cor INFO @ Sun, 02 Jun 2019 22:10:34: #2 finished! INFO @ Sun, 02 Jun 2019 22:10:34: #2 predicted fragment length is 53 bps INFO @ Sun, 02 Jun 2019 22:10:34: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 02 Jun 2019 22:10:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.05_model.r WARNING @ Sun, 02 Jun 2019 22:10:34: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:10:34: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 02 Jun 2019 22:10:34: #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 22:10:34: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:10:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:10:38: 9000000 INFO @ Sun, 02 Jun 2019 22:10:46: 10000000 INFO @ Sun, 02 Jun 2019 22:10:48: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:10:48: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:10:48: #1 total tags in treatment: 10140746 INFO @ Sun, 02 Jun 2019 22:10:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:10:48: #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 22:10:48: #1 tags after filtering in treatment: 10140746 INFO @ Sun, 02 Jun 2019 22:10:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:10:48: #1 finished! INFO @ Sun, 02 Jun 2019 22:10:48: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:10:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:10:49: #2 number of paired peaks: 795 WARNING @ Sun, 02 Jun 2019 22:10:49: Fewer paired peaks (795) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 795 pairs to build model! INFO @ Sun, 02 Jun 2019 22:10:49: start model_add_line... INFO @ Sun, 02 Jun 2019 22:10:49: start X-correlation... INFO @ Sun, 02 Jun 2019 22:10:49: end of X-cor INFO @ Sun, 02 Jun 2019 22:10:49: #2 finished! INFO @ Sun, 02 Jun 2019 22:10:49: #2 predicted fragment length is 53 bps INFO @ Sun, 02 Jun 2019 22:10:49: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 02 Jun 2019 22:10:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.10_model.r WARNING @ Sun, 02 Jun 2019 22:10:49: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:10:49: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 02 Jun 2019 22:10:49: #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 22:10:49: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:10:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:10:58: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:11:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:11:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:11:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:11:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.20_summits.bed INFO @ Sun, 02 Jun 2019 22:11:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (274 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:11:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:11:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:11:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.05_summits.bed INFO @ Sun, 02 Jun 2019 22:11:15: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1763 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:11:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:11:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:11:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:11:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402704/SRX5402704.10_summits.bed INFO @ Sun, 02 Jun 2019 22:11:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (746 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。