Job ID = 1291794 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,916,207 reads read : 10,916,207 reads written : 10,916,207 spots read : 14,166,298 reads read : 14,166,298 reads written : 14,166,298 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: 00:05:45 25082505 reads; of these: 25082505 (100.00%) were unpaired; of these: 4141340 (16.51%) aligned 0 times 17326571 (69.08%) aligned exactly 1 time 3614594 (14.41%) aligned >1 times 83.49% overall alignment rate Time searching: 00:05:45 Overall time: 00:05:45 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] 15208184 / 20941165 = 0.7262 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 16:51:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.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 16:51:34: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:51:34: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:51:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.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 16:51:34: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:51:34: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:51:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.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 16:51:34: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:51:34: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:51:42: 1000000 INFO @ Sun, 02 Jun 2019 16:51:43: 1000000 INFO @ Sun, 02 Jun 2019 16:51:46: 1000000 INFO @ Sun, 02 Jun 2019 16:51:50: 2000000 INFO @ Sun, 02 Jun 2019 16:51:52: 2000000 INFO @ Sun, 02 Jun 2019 16:51:56: 2000000 INFO @ Sun, 02 Jun 2019 16:51:58: 3000000 INFO @ Sun, 02 Jun 2019 16:52:00: 3000000 INFO @ Sun, 02 Jun 2019 16:52:06: 4000000 INFO @ Sun, 02 Jun 2019 16:52:07: 3000000 INFO @ Sun, 02 Jun 2019 16:52:09: 4000000 INFO @ Sun, 02 Jun 2019 16:52:14: 5000000 INFO @ Sun, 02 Jun 2019 16:52:17: 5000000 INFO @ Sun, 02 Jun 2019 16:52:18: 4000000 INFO @ Sun, 02 Jun 2019 16:52:19: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 16:52:19: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 16:52:19: #1 total tags in treatment: 5732981 INFO @ Sun, 02 Jun 2019 16:52:19: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:52:19: #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 16:52:19: #1 tags after filtering in treatment: 5732981 INFO @ Sun, 02 Jun 2019 16:52:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:52:19: #1 finished! INFO @ Sun, 02 Jun 2019 16:52:19: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:52:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:52:20: #2 number of paired peaks: 908 WARNING @ Sun, 02 Jun 2019 16:52:20: Fewer paired peaks (908) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 908 pairs to build model! INFO @ Sun, 02 Jun 2019 16:52:20: start model_add_line... INFO @ Sun, 02 Jun 2019 16:52:20: start X-correlation... INFO @ Sun, 02 Jun 2019 16:52:20: end of X-cor INFO @ Sun, 02 Jun 2019 16:52:20: #2 finished! INFO @ Sun, 02 Jun 2019 16:52:20: #2 predicted fragment length is 68 bps INFO @ Sun, 02 Jun 2019 16:52:20: #2 alternative fragment length(s) may be 68 bps INFO @ Sun, 02 Jun 2019 16:52:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.05_model.r WARNING @ Sun, 02 Jun 2019 16:52:20: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:52:20: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sun, 02 Jun 2019 16:52:20: #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 16:52:20: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:52:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:52:23: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 16:52:23: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 16:52:23: #1 total tags in treatment: 5732981 INFO @ Sun, 02 Jun 2019 16:52:23: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:52:23: #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 16:52:24: #1 tags after filtering in treatment: 5732981 INFO @ Sun, 02 Jun 2019 16:52:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:52:24: #1 finished! INFO @ Sun, 02 Jun 2019 16:52:24: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:52:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:52:24: #2 number of paired peaks: 908 WARNING @ Sun, 02 Jun 2019 16:52:24: Fewer paired peaks (908) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 908 pairs to build model! INFO @ Sun, 02 Jun 2019 16:52:24: start model_add_line... INFO @ Sun, 02 Jun 2019 16:52:24: start X-correlation... INFO @ Sun, 02 Jun 2019 16:52:24: end of X-cor INFO @ Sun, 02 Jun 2019 16:52:24: #2 finished! INFO @ Sun, 02 Jun 2019 16:52:24: #2 predicted fragment length is 68 bps INFO @ Sun, 02 Jun 2019 16:52:24: #2 alternative fragment length(s) may be 68 bps INFO @ Sun, 02 Jun 2019 16:52:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.10_model.r WARNING @ Sun, 02 Jun 2019 16:52:24: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:52:24: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sun, 02 Jun 2019 16:52:24: #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 16:52:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:52:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:52:28: 5000000 INFO @ Sun, 02 Jun 2019 16:52:35: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 16:52:35: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 16:52:35: #1 total tags in treatment: 5732981 INFO @ Sun, 02 Jun 2019 16:52:35: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:52:35: #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 16:52:36: #1 tags after filtering in treatment: 5732981 INFO @ Sun, 02 Jun 2019 16:52:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:52:36: #1 finished! INFO @ Sun, 02 Jun 2019 16:52:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:52:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:52:36: #2 number of paired peaks: 908 WARNING @ Sun, 02 Jun 2019 16:52:36: Fewer paired peaks (908) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 908 pairs to build model! INFO @ Sun, 02 Jun 2019 16:52:36: start model_add_line... INFO @ Sun, 02 Jun 2019 16:52:36: start X-correlation... INFO @ Sun, 02 Jun 2019 16:52:36: end of X-cor INFO @ Sun, 02 Jun 2019 16:52:36: #2 finished! INFO @ Sun, 02 Jun 2019 16:52:36: #2 predicted fragment length is 68 bps INFO @ Sun, 02 Jun 2019 16:52:36: #2 alternative fragment length(s) may be 68 bps INFO @ Sun, 02 Jun 2019 16:52:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.20_model.r WARNING @ Sun, 02 Jun 2019 16:52:36: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:52:36: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sun, 02 Jun 2019 16:52:36: #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 16:52:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:52:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:52:37: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:52:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:52:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:52:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:52:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.05_summits.bed INFO @ Sun, 02 Jun 2019 16:52:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1376 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:52:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:52:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:52:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.10_summits.bed INFO @ Sun, 02 Jun 2019 16:52:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (837 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:52:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:53:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:53:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:53:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257640/SRX257640.20_summits.bed INFO @ Sun, 02 Jun 2019 16:53:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (453 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。