Job ID = 1290659 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,919,188 reads read : 25,838,376 reads written : 12,919,188 reads 0-length : 12,919,188 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: 00:03:10 12919188 reads; of these: 12919188 (100.00%) were unpaired; of these: 1421312 (11.00%) aligned 0 times 8807556 (68.17%) aligned exactly 1 time 2690320 (20.82%) aligned >1 times 89.00% overall alignment rate Time searching: 00:03:10 Overall time: 00:03:10 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] 4815470 / 11497876 = 0.4188 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 22:00:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.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 22:00:54: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:00:54: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:00:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.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 22:00:54: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:00:54: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:00:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.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 22:00:54: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:00:54: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:01:03: 1000000 INFO @ Sat, 01 Jun 2019 22:01:04: 1000000 INFO @ Sat, 01 Jun 2019 22:01:04: 1000000 INFO @ Sat, 01 Jun 2019 22:01:11: 2000000 INFO @ Sat, 01 Jun 2019 22:01:14: 2000000 INFO @ Sat, 01 Jun 2019 22:01:14: 2000000 INFO @ Sat, 01 Jun 2019 22:01:19: 3000000 INFO @ Sat, 01 Jun 2019 22:01:23: 3000000 INFO @ Sat, 01 Jun 2019 22:01:23: 3000000 INFO @ Sat, 01 Jun 2019 22:01:27: 4000000 INFO @ Sat, 01 Jun 2019 22:01:33: 4000000 INFO @ Sat, 01 Jun 2019 22:01:33: 4000000 INFO @ Sat, 01 Jun 2019 22:01:35: 5000000 INFO @ Sat, 01 Jun 2019 22:01:42: 5000000 INFO @ Sat, 01 Jun 2019 22:01:43: 5000000 INFO @ Sat, 01 Jun 2019 22:01:43: 6000000 INFO @ Sat, 01 Jun 2019 22:01:48: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 22:01:48: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 22:01:48: #1 total tags in treatment: 6682406 INFO @ Sat, 01 Jun 2019 22:01:48: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:01:48: #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 22:01:48: #1 tags after filtering in treatment: 6682406 INFO @ Sat, 01 Jun 2019 22:01:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 22:01:48: #1 finished! INFO @ Sat, 01 Jun 2019 22:01:48: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:01:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:01:49: #2 number of paired peaks: 652 WARNING @ Sat, 01 Jun 2019 22:01:49: Fewer paired peaks (652) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 652 pairs to build model! INFO @ Sat, 01 Jun 2019 22:01:49: start model_add_line... INFO @ Sat, 01 Jun 2019 22:01:49: start X-correlation... INFO @ Sat, 01 Jun 2019 22:01:49: end of X-cor INFO @ Sat, 01 Jun 2019 22:01:49: #2 finished! INFO @ Sat, 01 Jun 2019 22:01:49: #2 predicted fragment length is 49 bps INFO @ Sat, 01 Jun 2019 22:01:49: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sat, 01 Jun 2019 22:01:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.20_model.r WARNING @ Sat, 01 Jun 2019 22:01:49: #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 22:01:49: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sat, 01 Jun 2019 22:01:49: #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 22:01:49: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:01:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:01:52: 6000000 INFO @ Sat, 01 Jun 2019 22:01:53: 6000000 INFO @ Sat, 01 Jun 2019 22:01:58: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 22:01:58: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 22:01:58: #1 total tags in treatment: 6682406 INFO @ Sat, 01 Jun 2019 22:01:58: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:01:58: #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 22:01:59: #1 tags after filtering in treatment: 6682406 INFO @ Sat, 01 Jun 2019 22:01:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 22:01:59: #1 finished! INFO @ Sat, 01 Jun 2019 22:01:59: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:01:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:01:59: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 22:01:59: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 22:01:59: #1 total tags in treatment: 6682406 INFO @ Sat, 01 Jun 2019 22:01:59: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:01:59: #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 22:01:59: #1 tags after filtering in treatment: 6682406 INFO @ Sat, 01 Jun 2019 22:01:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 22:01:59: #1 finished! INFO @ Sat, 01 Jun 2019 22:01:59: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:01:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:01:59: #2 number of paired peaks: 652 WARNING @ Sat, 01 Jun 2019 22:01:59: Fewer paired peaks (652) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 652 pairs to build model! INFO @ Sat, 01 Jun 2019 22:01:59: start model_add_line... INFO @ Sat, 01 Jun 2019 22:01:59: start X-correlation... INFO @ Sat, 01 Jun 2019 22:01:59: end of X-cor INFO @ Sat, 01 Jun 2019 22:01:59: #2 finished! INFO @ Sat, 01 Jun 2019 22:01:59: #2 predicted fragment length is 49 bps INFO @ Sat, 01 Jun 2019 22:01:59: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sat, 01 Jun 2019 22:01:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.05_model.r WARNING @ Sat, 01 Jun 2019 22:01:59: #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 22:01:59: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sat, 01 Jun 2019 22:01:59: #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 22:01:59: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:01:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:02:00: #2 number of paired peaks: 652 WARNING @ Sat, 01 Jun 2019 22:02:00: Fewer paired peaks (652) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 652 pairs to build model! INFO @ Sat, 01 Jun 2019 22:02:00: start model_add_line... INFO @ Sat, 01 Jun 2019 22:02:00: start X-correlation... INFO @ Sat, 01 Jun 2019 22:02:00: end of X-cor INFO @ Sat, 01 Jun 2019 22:02:00: #2 finished! INFO @ Sat, 01 Jun 2019 22:02:00: #2 predicted fragment length is 49 bps INFO @ Sat, 01 Jun 2019 22:02:00: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sat, 01 Jun 2019 22:02:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.10_model.r WARNING @ Sat, 01 Jun 2019 22:02:00: #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 22:02:00: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sat, 01 Jun 2019 22:02:00: #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 22:02:00: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:02:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:02:08: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:02:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.20_peaks.xls INFO @ Sat, 01 Jun 2019 22:02:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:02:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.20_summits.bed INFO @ Sat, 01 Jun 2019 22:02:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (224 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 22:02:18: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:02:19: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:02:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.05_peaks.xls INFO @ Sat, 01 Jun 2019 22:02:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:02:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.05_summits.bed INFO @ Sat, 01 Jun 2019 22:02:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (814 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 22:02:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.10_peaks.xls INFO @ Sat, 01 Jun 2019 22:02:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:02:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082381/SRX4082381.10_summits.bed INFO @ Sat, 01 Jun 2019 22:02:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (476 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。