Job ID = 1293089 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,794,530 reads read : 51,589,060 reads written : 25,794,530 reads 0-length : 25,794,530 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: 00:05:39 25794530 reads; of these: 25794530 (100.00%) were unpaired; of these: 1593226 (6.18%) aligned 0 times 20556139 (79.69%) aligned exactly 1 time 3645165 (14.13%) aligned >1 times 93.82% overall alignment rate Time searching: 00:05:39 Overall time: 00:05:39 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] 7592415 / 24201304 = 0.3137 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 21:59:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.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 21:59:29: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:59:29: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:59:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.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 21:59:29: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:59:29: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:59:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.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 21:59:29: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:59:29: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:59:37: 1000000 INFO @ Sun, 02 Jun 2019 21:59:39: 1000000 INFO @ Sun, 02 Jun 2019 21:59:39: 1000000 INFO @ Sun, 02 Jun 2019 21:59:43: 2000000 INFO @ Sun, 02 Jun 2019 21:59:47: 2000000 INFO @ Sun, 02 Jun 2019 21:59:48: 2000000 INFO @ Sun, 02 Jun 2019 21:59:50: 3000000 INFO @ Sun, 02 Jun 2019 21:59:55: 3000000 INFO @ Sun, 02 Jun 2019 21:59:56: 4000000 INFO @ Sun, 02 Jun 2019 21:59:56: 3000000 INFO @ Sun, 02 Jun 2019 22:00:02: 5000000 INFO @ Sun, 02 Jun 2019 22:00:03: 4000000 INFO @ Sun, 02 Jun 2019 22:00:04: 4000000 INFO @ Sun, 02 Jun 2019 22:00:09: 6000000 INFO @ Sun, 02 Jun 2019 22:00:11: 5000000 INFO @ Sun, 02 Jun 2019 22:00:13: 5000000 INFO @ Sun, 02 Jun 2019 22:00:16: 7000000 INFO @ Sun, 02 Jun 2019 22:00:19: 6000000 INFO @ Sun, 02 Jun 2019 22:00:21: 6000000 INFO @ Sun, 02 Jun 2019 22:00:22: 8000000 INFO @ Sun, 02 Jun 2019 22:00:27: 7000000 INFO @ Sun, 02 Jun 2019 22:00:28: 9000000 INFO @ Sun, 02 Jun 2019 22:00:29: 7000000 INFO @ Sun, 02 Jun 2019 22:00:35: 10000000 INFO @ Sun, 02 Jun 2019 22:00:35: 8000000 INFO @ Sun, 02 Jun 2019 22:00:38: 8000000 INFO @ Sun, 02 Jun 2019 22:00:41: 11000000 INFO @ Sun, 02 Jun 2019 22:00:43: 9000000 INFO @ Sun, 02 Jun 2019 22:00:46: 9000000 INFO @ Sun, 02 Jun 2019 22:00:48: 12000000 INFO @ Sun, 02 Jun 2019 22:00:51: 10000000 INFO @ Sun, 02 Jun 2019 22:00:54: 13000000 INFO @ Sun, 02 Jun 2019 22:00:54: 10000000 INFO @ Sun, 02 Jun 2019 22:00:59: 11000000 INFO @ Sun, 02 Jun 2019 22:01:01: 14000000 INFO @ Sun, 02 Jun 2019 22:01:04: 11000000 INFO @ Sun, 02 Jun 2019 22:01:07: 15000000 INFO @ Sun, 02 Jun 2019 22:01:07: 12000000 INFO @ Sun, 02 Jun 2019 22:01:13: 12000000 INFO @ Sun, 02 Jun 2019 22:01:13: 16000000 INFO @ Sun, 02 Jun 2019 22:01:16: 13000000 INFO @ Sun, 02 Jun 2019 22:01:17: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:01:17: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:01:17: #1 total tags in treatment: 16608889 INFO @ Sun, 02 Jun 2019 22:01:17: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:01:17: #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 22:01:18: #1 tags after filtering in treatment: 16608889 INFO @ Sun, 02 Jun 2019 22:01:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:01:18: #1 finished! INFO @ Sun, 02 Jun 2019 22:01:18: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:01:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:01:19: #2 number of paired peaks: 173 WARNING @ Sun, 02 Jun 2019 22:01:19: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sun, 02 Jun 2019 22:01:19: start model_add_line... INFO @ Sun, 02 Jun 2019 22:01:19: start X-correlation... INFO @ Sun, 02 Jun 2019 22:01:19: end of X-cor INFO @ Sun, 02 Jun 2019 22:01:19: #2 finished! INFO @ Sun, 02 Jun 2019 22:01:19: #2 predicted fragment length is 63 bps INFO @ Sun, 02 Jun 2019 22:01:19: #2 alternative fragment length(s) may be 1,41,63 bps INFO @ Sun, 02 Jun 2019 22:01:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.20_model.r WARNING @ Sun, 02 Jun 2019 22:01:19: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:01:19: #2 You may need to consider one of the other alternative d(s): 1,41,63 WARNING @ Sun, 02 Jun 2019 22:01:19: #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 22:01:19: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:01:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:01:22: 13000000 INFO @ Sun, 02 Jun 2019 22:01:24: 14000000 INFO @ Sun, 02 Jun 2019 22:01:31: 14000000 INFO @ Sun, 02 Jun 2019 22:01:32: 15000000 INFO @ Sun, 02 Jun 2019 22:01:39: 15000000 INFO @ Sun, 02 Jun 2019 22:01:40: 16000000 INFO @ Sun, 02 Jun 2019 22:01:46: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:01:46: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:01:46: #1 total tags in treatment: 16608889 INFO @ Sun, 02 Jun 2019 22:01:46: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:01:46: #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 22:01:46: #1 tags after filtering in treatment: 16608889 INFO @ Sun, 02 Jun 2019 22:01:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:01:46: #1 finished! INFO @ Sun, 02 Jun 2019 22:01:46: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:01:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:01:47: #2 number of paired peaks: 173 WARNING @ Sun, 02 Jun 2019 22:01:47: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sun, 02 Jun 2019 22:01:47: start model_add_line... INFO @ Sun, 02 Jun 2019 22:01:47: start X-correlation... INFO @ Sun, 02 Jun 2019 22:01:47: 16000000 INFO @ Sun, 02 Jun 2019 22:01:47: end of X-cor INFO @ Sun, 02 Jun 2019 22:01:47: #2 finished! INFO @ Sun, 02 Jun 2019 22:01:47: #2 predicted fragment length is 63 bps INFO @ Sun, 02 Jun 2019 22:01:47: #2 alternative fragment length(s) may be 1,41,63 bps INFO @ Sun, 02 Jun 2019 22:01:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.05_model.r WARNING @ Sun, 02 Jun 2019 22:01:47: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:01:47: #2 You may need to consider one of the other alternative d(s): 1,41,63 WARNING @ Sun, 02 Jun 2019 22:01:47: #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 22:01:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:01:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:01:52: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:01:52: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:01:52: #1 total tags in treatment: 16608889 INFO @ Sun, 02 Jun 2019 22:01:52: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:01:52: #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 22:01:53: #1 tags after filtering in treatment: 16608889 INFO @ Sun, 02 Jun 2019 22:01:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:01:53: #1 finished! INFO @ Sun, 02 Jun 2019 22:01:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:01:54: #2 number of paired peaks: 173 WARNING @ Sun, 02 Jun 2019 22:01:54: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sun, 02 Jun 2019 22:01:54: start model_add_line... INFO @ Sun, 02 Jun 2019 22:01:54: start X-correlation... INFO @ Sun, 02 Jun 2019 22:01:54: end of X-cor INFO @ Sun, 02 Jun 2019 22:01:54: #2 finished! INFO @ Sun, 02 Jun 2019 22:01:54: #2 predicted fragment length is 63 bps INFO @ Sun, 02 Jun 2019 22:01:54: #2 alternative fragment length(s) may be 1,41,63 bps INFO @ Sun, 02 Jun 2019 22:01:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.10_model.r WARNING @ Sun, 02 Jun 2019 22:01:54: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:01:54: #2 You may need to consider one of the other alternative d(s): 1,41,63 WARNING @ Sun, 02 Jun 2019 22:01:54: #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 22:01:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:01:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:02:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:02:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:02:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:02:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.20_summits.bed INFO @ Sun, 02 Jun 2019 22:02:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (127 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:02:28: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:02:35: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:02:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:02:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:02:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.05_summits.bed INFO @ Sun, 02 Jun 2019 22:02:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1551 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:02:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:02:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:02:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5073497/SRX5073497.10_summits.bed INFO @ Sun, 02 Jun 2019 22:02:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (427 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。