Job ID = 1291839 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,555,829 reads read : 10,555,829 reads written : 10,555,829 spots read : 13,496,288 reads read : 13,496,288 reads written : 13,496,288 spots read : 9,037,675 reads read : 9,037,675 reads written : 9,037,675 spots read : 11,628,948 reads read : 11,628,948 reads written : 11,628,948 spots read : 9,069,939 reads read : 9,069,939 reads written : 9,069,939 spots read : 7,065,825 reads read : 7,065,825 reads written : 7,065,825 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: 00:13:38 60854504 reads; of these: 60854504 (100.00%) were unpaired; of these: 13657399 (22.44%) aligned 0 times 38017079 (62.47%) aligned exactly 1 time 9180026 (15.09%) aligned >1 times 77.56% overall alignment rate Time searching: 00:13:38 Overall time: 00:13:38 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 20 files... [bam_rmdupse_core] 28005094 / 47197105 = 0.5934 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 17:32:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.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 17:32:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:32:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:32:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.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 17:32:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:32:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:32:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.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 17:32:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:32:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:32:57: 1000000 INFO @ Sun, 02 Jun 2019 17:32:57: 1000000 INFO @ Sun, 02 Jun 2019 17:32:57: 1000000 INFO @ Sun, 02 Jun 2019 17:33:05: 2000000 INFO @ Sun, 02 Jun 2019 17:33:05: 2000000 INFO @ Sun, 02 Jun 2019 17:33:05: 2000000 INFO @ Sun, 02 Jun 2019 17:33:12: 3000000 INFO @ Sun, 02 Jun 2019 17:33:13: 3000000 INFO @ Sun, 02 Jun 2019 17:33:13: 3000000 INFO @ Sun, 02 Jun 2019 17:33:20: 4000000 INFO @ Sun, 02 Jun 2019 17:33:20: 4000000 INFO @ Sun, 02 Jun 2019 17:33:20: 4000000 INFO @ Sun, 02 Jun 2019 17:33:27: 5000000 INFO @ Sun, 02 Jun 2019 17:33:28: 5000000 INFO @ Sun, 02 Jun 2019 17:33:28: 5000000 INFO @ Sun, 02 Jun 2019 17:33:34: 6000000 INFO @ Sun, 02 Jun 2019 17:33:36: 6000000 INFO @ Sun, 02 Jun 2019 17:33:36: 6000000 INFO @ Sun, 02 Jun 2019 17:33:42: 7000000 INFO @ Sun, 02 Jun 2019 17:33:44: 7000000 INFO @ Sun, 02 Jun 2019 17:33:44: 7000000 INFO @ Sun, 02 Jun 2019 17:33:50: 8000000 INFO @ Sun, 02 Jun 2019 17:33:52: 8000000 INFO @ Sun, 02 Jun 2019 17:33:52: 8000000 INFO @ Sun, 02 Jun 2019 17:33:57: 9000000 INFO @ Sun, 02 Jun 2019 17:33:59: 9000000 INFO @ Sun, 02 Jun 2019 17:33:59: 9000000 INFO @ Sun, 02 Jun 2019 17:34:05: 10000000 INFO @ Sun, 02 Jun 2019 17:34:07: 10000000 INFO @ Sun, 02 Jun 2019 17:34:08: 10000000 INFO @ Sun, 02 Jun 2019 17:34:12: 11000000 INFO @ Sun, 02 Jun 2019 17:34:15: 11000000 INFO @ Sun, 02 Jun 2019 17:34:16: 11000000 INFO @ Sun, 02 Jun 2019 17:34:20: 12000000 INFO @ Sun, 02 Jun 2019 17:34:23: 12000000 INFO @ Sun, 02 Jun 2019 17:34:23: 12000000 INFO @ Sun, 02 Jun 2019 17:34:27: 13000000 INFO @ Sun, 02 Jun 2019 17:34:31: 13000000 INFO @ Sun, 02 Jun 2019 17:34:31: 13000000 INFO @ Sun, 02 Jun 2019 17:34:35: 14000000 INFO @ Sun, 02 Jun 2019 17:34:38: 14000000 INFO @ Sun, 02 Jun 2019 17:34:39: 14000000 INFO @ Sun, 02 Jun 2019 17:34:43: 15000000 INFO @ Sun, 02 Jun 2019 17:34:47: 15000000 INFO @ Sun, 02 Jun 2019 17:34:47: 15000000 INFO @ Sun, 02 Jun 2019 17:34:50: 16000000 INFO @ Sun, 02 Jun 2019 17:34:54: 16000000 INFO @ Sun, 02 Jun 2019 17:34:55: 16000000 INFO @ Sun, 02 Jun 2019 17:34:58: 17000000 INFO @ Sun, 02 Jun 2019 17:35:02: 17000000 INFO @ Sun, 02 Jun 2019 17:35:03: 17000000 INFO @ Sun, 02 Jun 2019 17:35:06: 18000000 INFO @ Sun, 02 Jun 2019 17:35:10: 18000000 INFO @ Sun, 02 Jun 2019 17:35:11: 18000000 INFO @ Sun, 02 Jun 2019 17:35:13: 19000000 INFO @ Sun, 02 Jun 2019 17:35:15: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:35:15: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:35:15: #1 total tags in treatment: 19192011 INFO @ Sun, 02 Jun 2019 17:35:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:35:15: #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 17:35:15: #1 tags after filtering in treatment: 19192011 INFO @ Sun, 02 Jun 2019 17:35:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:35:15: #1 finished! INFO @ Sun, 02 Jun 2019 17:35:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:35:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:35:17: #2 number of paired peaks: 435 WARNING @ Sun, 02 Jun 2019 17:35:17: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Sun, 02 Jun 2019 17:35:17: start model_add_line... INFO @ Sun, 02 Jun 2019 17:35:17: start X-correlation... INFO @ Sun, 02 Jun 2019 17:35:17: end of X-cor INFO @ Sun, 02 Jun 2019 17:35:17: #2 finished! INFO @ Sun, 02 Jun 2019 17:35:17: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 17:35:17: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sun, 02 Jun 2019 17:35:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.20_model.r WARNING @ Sun, 02 Jun 2019 17:35:17: #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 17:35:17: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sun, 02 Jun 2019 17:35:17: #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 17:35:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:35:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:35:18: 19000000 INFO @ Sun, 02 Jun 2019 17:35:19: 19000000 INFO @ Sun, 02 Jun 2019 17:35:20: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:35:20: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:35:20: #1 total tags in treatment: 19192011 INFO @ Sun, 02 Jun 2019 17:35:20: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:35:20: #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 17:35:20: #1 tags after filtering in treatment: 19192011 INFO @ Sun, 02 Jun 2019 17:35:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:35:20: #1 finished! INFO @ Sun, 02 Jun 2019 17:35:20: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:35:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:35:20: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:35:20: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:35:20: #1 total tags in treatment: 19192011 INFO @ Sun, 02 Jun 2019 17:35:20: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:35:20: #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 17:35:21: #1 tags after filtering in treatment: 19192011 INFO @ Sun, 02 Jun 2019 17:35:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:35:21: #1 finished! INFO @ Sun, 02 Jun 2019 17:35:21: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:35:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:35:22: #2 number of paired peaks: 435 WARNING @ Sun, 02 Jun 2019 17:35:22: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Sun, 02 Jun 2019 17:35:22: start model_add_line... INFO @ Sun, 02 Jun 2019 17:35:22: start X-correlation... INFO @ Sun, 02 Jun 2019 17:35:22: end of X-cor INFO @ Sun, 02 Jun 2019 17:35:22: #2 finished! INFO @ Sun, 02 Jun 2019 17:35:22: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 17:35:22: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sun, 02 Jun 2019 17:35:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.10_model.r WARNING @ Sun, 02 Jun 2019 17:35:22: #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 17:35:22: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sun, 02 Jun 2019 17:35:22: #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 17:35:22: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:35:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:35:22: #2 number of paired peaks: 435 WARNING @ Sun, 02 Jun 2019 17:35:22: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Sun, 02 Jun 2019 17:35:22: start model_add_line... INFO @ Sun, 02 Jun 2019 17:35:22: start X-correlation... INFO @ Sun, 02 Jun 2019 17:35:22: end of X-cor INFO @ Sun, 02 Jun 2019 17:35:22: #2 finished! INFO @ Sun, 02 Jun 2019 17:35:22: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 17:35:22: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sun, 02 Jun 2019 17:35:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.05_model.r WARNING @ Sun, 02 Jun 2019 17:35:22: #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 17:35:22: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sun, 02 Jun 2019 17:35:22: #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 17:35:22: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:35:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:36:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:36:06: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:36:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:36:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:36:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:36:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.20_summits.bed INFO @ Sun, 02 Jun 2019 17:36:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (439 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:36:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:36:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:36:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.10_summits.bed INFO @ Sun, 02 Jun 2019 17:36:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1094 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:36:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:36:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:36:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257675/SRX257675.05_summits.bed INFO @ Sun, 02 Jun 2019 17:36:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2219 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。