Job ID = 1292458 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,523,257 reads read : 18,523,257 reads written : 18,523,257 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: 00:03:31 18523257 reads; of these: 18523257 (100.00%) were unpaired; of these: 2608607 (14.08%) aligned 0 times 13498283 (72.87%) aligned exactly 1 time 2416367 (13.05%) aligned >1 times 85.92% overall alignment rate Time searching: 00:03:31 Overall time: 00:03:31 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_rmdupse_core] 9615374 / 15914650 = 0.6042 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 19:05:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.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 19:05:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:05:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:05:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.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 19:05:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:05:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:05:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.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 19:05:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:05:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:05:47: 1000000 INFO @ Sun, 02 Jun 2019 19:05:49: 1000000 INFO @ Sun, 02 Jun 2019 19:05:49: 1000000 INFO @ Sun, 02 Jun 2019 19:05:55: 2000000 INFO @ Sun, 02 Jun 2019 19:05:58: 2000000 INFO @ Sun, 02 Jun 2019 19:05:58: 2000000 INFO @ Sun, 02 Jun 2019 19:06:02: 3000000 INFO @ Sun, 02 Jun 2019 19:06:07: 3000000 INFO @ Sun, 02 Jun 2019 19:06:07: 3000000 INFO @ Sun, 02 Jun 2019 19:06:10: 4000000 INFO @ Sun, 02 Jun 2019 19:06:16: 4000000 INFO @ Sun, 02 Jun 2019 19:06:17: 4000000 INFO @ Sun, 02 Jun 2019 19:06:17: 5000000 INFO @ Sun, 02 Jun 2019 19:06:25: 6000000 INFO @ Sun, 02 Jun 2019 19:06:25: 5000000 INFO @ Sun, 02 Jun 2019 19:06:26: 5000000 INFO @ Sun, 02 Jun 2019 19:06:27: #1 tag size is determined as 40 bps INFO @ Sun, 02 Jun 2019 19:06:27: #1 tag size = 40 INFO @ Sun, 02 Jun 2019 19:06:27: #1 total tags in treatment: 6299276 INFO @ Sun, 02 Jun 2019 19:06:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:06:27: #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 19:06:27: #1 tags after filtering in treatment: 6299276 INFO @ Sun, 02 Jun 2019 19:06:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:06:27: #1 finished! INFO @ Sun, 02 Jun 2019 19:06:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:06:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:06:28: #2 number of paired peaks: 603 WARNING @ Sun, 02 Jun 2019 19:06:28: Fewer paired peaks (603) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 603 pairs to build model! INFO @ Sun, 02 Jun 2019 19:06:28: start model_add_line... INFO @ Sun, 02 Jun 2019 19:06:28: start X-correlation... INFO @ Sun, 02 Jun 2019 19:06:28: end of X-cor INFO @ Sun, 02 Jun 2019 19:06:28: #2 finished! INFO @ Sun, 02 Jun 2019 19:06:28: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 19:06:28: #2 alternative fragment length(s) may be 4,51,562 bps INFO @ Sun, 02 Jun 2019 19:06:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.20_model.r WARNING @ Sun, 02 Jun 2019 19:06:28: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:06:28: #2 You may need to consider one of the other alternative d(s): 4,51,562 WARNING @ Sun, 02 Jun 2019 19:06:28: #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 19:06:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:06:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:06:34: 6000000 INFO @ Sun, 02 Jun 2019 19:06:35: 6000000 INFO @ Sun, 02 Jun 2019 19:06:37: #1 tag size is determined as 40 bps INFO @ Sun, 02 Jun 2019 19:06:37: #1 tag size = 40 INFO @ Sun, 02 Jun 2019 19:06:37: #1 total tags in treatment: 6299276 INFO @ Sun, 02 Jun 2019 19:06:37: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:06:37: #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 19:06:37: #1 tag size is determined as 40 bps INFO @ Sun, 02 Jun 2019 19:06:37: #1 tag size = 40 INFO @ Sun, 02 Jun 2019 19:06:37: #1 total tags in treatment: 6299276 INFO @ Sun, 02 Jun 2019 19:06:37: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:06:37: #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 19:06:37: #1 tags after filtering in treatment: 6299276 INFO @ Sun, 02 Jun 2019 19:06:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:06:37: #1 finished! INFO @ Sun, 02 Jun 2019 19:06:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:06:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:06:37: #1 tags after filtering in treatment: 6299276 INFO @ Sun, 02 Jun 2019 19:06:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:06:37: #1 finished! INFO @ Sun, 02 Jun 2019 19:06:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:06:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:06:38: #2 number of paired peaks: 603 WARNING @ Sun, 02 Jun 2019 19:06:38: Fewer paired peaks (603) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 603 pairs to build model! INFO @ Sun, 02 Jun 2019 19:06:38: start model_add_line... INFO @ Sun, 02 Jun 2019 19:06:38: start X-correlation... INFO @ Sun, 02 Jun 2019 19:06:38: end of X-cor INFO @ Sun, 02 Jun 2019 19:06:38: #2 finished! INFO @ Sun, 02 Jun 2019 19:06:38: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 19:06:38: #2 alternative fragment length(s) may be 4,51,562 bps INFO @ Sun, 02 Jun 2019 19:06:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.10_model.r WARNING @ Sun, 02 Jun 2019 19:06:38: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:06:38: #2 You may need to consider one of the other alternative d(s): 4,51,562 WARNING @ Sun, 02 Jun 2019 19:06:38: #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 19:06:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:06:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:06:38: #2 number of paired peaks: 603 WARNING @ Sun, 02 Jun 2019 19:06:38: Fewer paired peaks (603) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 603 pairs to build model! INFO @ Sun, 02 Jun 2019 19:06:38: start model_add_line... INFO @ Sun, 02 Jun 2019 19:06:38: start X-correlation... INFO @ Sun, 02 Jun 2019 19:06:38: end of X-cor INFO @ Sun, 02 Jun 2019 19:06:38: #2 finished! INFO @ Sun, 02 Jun 2019 19:06:38: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 19:06:38: #2 alternative fragment length(s) may be 4,51,562 bps INFO @ Sun, 02 Jun 2019 19:06:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.05_model.r WARNING @ Sun, 02 Jun 2019 19:06:38: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:06:38: #2 You may need to consider one of the other alternative d(s): 4,51,562 WARNING @ Sun, 02 Jun 2019 19:06:38: #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 19:06:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:06:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:06:46: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:06:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:06:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:06:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.20_summits.bed INFO @ Sun, 02 Jun 2019 19:06:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (220 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:06:56: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:06:56: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:07:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:07:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:07:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.10_summits.bed INFO @ Sun, 02 Jun 2019 19:07:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (628 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:07:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:07:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:07:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4626832/SRX4626832.05_summits.bed INFO @ Sun, 02 Jun 2019 19:07:06: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1197 records, 4 fields): 36 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。