Job ID = 1293179 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,344,770 reads read : 32,344,770 reads written : 32,344,770 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: 00:08:06 32344770 reads; of these: 32344770 (100.00%) were unpaired; of these: 9517918 (29.43%) aligned 0 times 14598643 (45.13%) aligned exactly 1 time 8228209 (25.44%) aligned >1 times 70.57% overall alignment rate Time searching: 00:08:06 Overall time: 00:08:06 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] 7529952 / 22826852 = 0.3299 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 22:39:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.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 22:39:24: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:39:24: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:39:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.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 22:39:24: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:39:24: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:39:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.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 22:39:24: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:39:24: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:39:31: 1000000 INFO @ Sun, 02 Jun 2019 22:39:31: 1000000 INFO @ Sun, 02 Jun 2019 22:39:33: 1000000 INFO @ Sun, 02 Jun 2019 22:39:38: 2000000 INFO @ Sun, 02 Jun 2019 22:39:38: 2000000 INFO @ Sun, 02 Jun 2019 22:39:42: 2000000 INFO @ Sun, 02 Jun 2019 22:39:47: 3000000 INFO @ Sun, 02 Jun 2019 22:39:47: 3000000 INFO @ Sun, 02 Jun 2019 22:39:52: 3000000 INFO @ Sun, 02 Jun 2019 22:39:55: 4000000 INFO @ Sun, 02 Jun 2019 22:39:55: 4000000 INFO @ Sun, 02 Jun 2019 22:40:01: 4000000 INFO @ Sun, 02 Jun 2019 22:40:03: 5000000 INFO @ Sun, 02 Jun 2019 22:40:03: 5000000 INFO @ Sun, 02 Jun 2019 22:40:10: 5000000 INFO @ Sun, 02 Jun 2019 22:40:11: 6000000 INFO @ Sun, 02 Jun 2019 22:40:11: 6000000 INFO @ Sun, 02 Jun 2019 22:40:19: 6000000 INFO @ Sun, 02 Jun 2019 22:40:19: 7000000 INFO @ Sun, 02 Jun 2019 22:40:19: 7000000 INFO @ Sun, 02 Jun 2019 22:40:27: 8000000 INFO @ Sun, 02 Jun 2019 22:40:27: 8000000 INFO @ Sun, 02 Jun 2019 22:40:28: 7000000 INFO @ Sun, 02 Jun 2019 22:40:35: 9000000 INFO @ Sun, 02 Jun 2019 22:40:35: 9000000 INFO @ Sun, 02 Jun 2019 22:40:37: 8000000 INFO @ Sun, 02 Jun 2019 22:40:42: 10000000 INFO @ Sun, 02 Jun 2019 22:40:42: 10000000 INFO @ Sun, 02 Jun 2019 22:40:46: 9000000 INFO @ Sun, 02 Jun 2019 22:40:50: 11000000 INFO @ Sun, 02 Jun 2019 22:40:50: 11000000 INFO @ Sun, 02 Jun 2019 22:40:55: 10000000 INFO @ Sun, 02 Jun 2019 22:40:58: 12000000 INFO @ Sun, 02 Jun 2019 22:40:58: 12000000 INFO @ Sun, 02 Jun 2019 22:41:04: 11000000 INFO @ Sun, 02 Jun 2019 22:41:06: 13000000 INFO @ Sun, 02 Jun 2019 22:41:06: 13000000 INFO @ Sun, 02 Jun 2019 22:41:12: 12000000 INFO @ Sun, 02 Jun 2019 22:41:14: 14000000 INFO @ Sun, 02 Jun 2019 22:41:14: 14000000 INFO @ Sun, 02 Jun 2019 22:41:21: 13000000 INFO @ Sun, 02 Jun 2019 22:41:21: 15000000 INFO @ Sun, 02 Jun 2019 22:41:21: 15000000 INFO @ Sun, 02 Jun 2019 22:41:24: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:41:24: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:41:24: #1 total tags in treatment: 15296900 INFO @ Sun, 02 Jun 2019 22:41:24: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:41:24: #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 22:41:24: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:41:24: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:41:24: #1 total tags in treatment: 15296900 INFO @ Sun, 02 Jun 2019 22:41:24: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:41:24: #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 22:41:24: #1 tags after filtering in treatment: 15296900 INFO @ Sun, 02 Jun 2019 22:41:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:41:24: #1 finished! INFO @ Sun, 02 Jun 2019 22:41:24: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:41:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:41:24: #1 tags after filtering in treatment: 15296900 INFO @ Sun, 02 Jun 2019 22:41:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:41:24: #1 finished! INFO @ Sun, 02 Jun 2019 22:41:24: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:41:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:41:26: #2 number of paired peaks: 1280 INFO @ Sun, 02 Jun 2019 22:41:26: start model_add_line... INFO @ Sun, 02 Jun 2019 22:41:26: #2 number of paired peaks: 1280 INFO @ Sun, 02 Jun 2019 22:41:26: start model_add_line... INFO @ Sun, 02 Jun 2019 22:41:26: start X-correlation... INFO @ Sun, 02 Jun 2019 22:41:26: end of X-cor INFO @ Sun, 02 Jun 2019 22:41:26: #2 finished! INFO @ Sun, 02 Jun 2019 22:41:26: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 22:41:26: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sun, 02 Jun 2019 22:41:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.05_model.r WARNING @ Sun, 02 Jun 2019 22:41:26: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:41:26: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sun, 02 Jun 2019 22:41:26: #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 22:41:26: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:41:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:41:26: start X-correlation... INFO @ Sun, 02 Jun 2019 22:41:26: end of X-cor INFO @ Sun, 02 Jun 2019 22:41:26: #2 finished! INFO @ Sun, 02 Jun 2019 22:41:26: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 22:41:26: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sun, 02 Jun 2019 22:41:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.20_model.r WARNING @ Sun, 02 Jun 2019 22:41:26: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:41:26: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sun, 02 Jun 2019 22:41:26: #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 22:41:26: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:41:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:41:30: 14000000 INFO @ Sun, 02 Jun 2019 22:41:38: 15000000 INFO @ Sun, 02 Jun 2019 22:41:41: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:41:41: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:41:41: #1 total tags in treatment: 15296900 INFO @ Sun, 02 Jun 2019 22:41:41: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:41:41: #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 22:41:41: #1 tags after filtering in treatment: 15296900 INFO @ Sun, 02 Jun 2019 22:41:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:41:41: #1 finished! INFO @ Sun, 02 Jun 2019 22:41:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:41:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:41:43: #2 number of paired peaks: 1280 INFO @ Sun, 02 Jun 2019 22:41:43: start model_add_line... INFO @ Sun, 02 Jun 2019 22:41:43: start X-correlation... INFO @ Sun, 02 Jun 2019 22:41:43: end of X-cor INFO @ Sun, 02 Jun 2019 22:41:43: #2 finished! INFO @ Sun, 02 Jun 2019 22:41:43: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 22:41:43: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sun, 02 Jun 2019 22:41:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.10_model.r WARNING @ Sun, 02 Jun 2019 22:41:43: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:41:43: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sun, 02 Jun 2019 22:41:43: #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 22:41:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:41:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:42:05: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:42:05: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:42:22: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:42:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:42:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:42:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.20_summits.bed INFO @ Sun, 02 Jun 2019 22:42:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (908 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:42:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:42:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:42:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.05_summits.bed INFO @ Sun, 02 Jun 2019 22:42:24: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8321 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:42:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:42:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:42:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402741/SRX5402741.10_summits.bed INFO @ Sun, 02 Jun 2019 22:42:40: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3642 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。