Job ID = 1294103 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,121,810 reads read : 13,121,810 reads written : 13,121,810 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:16 13121810 reads; of these: 13121810 (100.00%) were unpaired; of these: 3707349 (28.25%) aligned 0 times 6807261 (51.88%) aligned exactly 1 time 2607200 (19.87%) aligned >1 times 71.75% overall alignment rate Time searching: 00:03:17 Overall time: 00:03:17 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 2172818 / 9414461 = 0.2308 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 @ Mon, 03 Jun 2019 04:59:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 04:59:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:59:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:59:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 04:59:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:59:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:59:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 04:59:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:59:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:59:32: 1000000 INFO @ Mon, 03 Jun 2019 04:59:33: 1000000 INFO @ Mon, 03 Jun 2019 04:59:33: 1000000 INFO @ Mon, 03 Jun 2019 04:59:39: 2000000 INFO @ Mon, 03 Jun 2019 04:59:40: 2000000 INFO @ Mon, 03 Jun 2019 04:59:40: 2000000 INFO @ Mon, 03 Jun 2019 04:59:46: 3000000 INFO @ Mon, 03 Jun 2019 04:59:48: 3000000 INFO @ Mon, 03 Jun 2019 04:59:48: 3000000 INFO @ Mon, 03 Jun 2019 04:59:53: 4000000 INFO @ Mon, 03 Jun 2019 04:59:55: 4000000 INFO @ Mon, 03 Jun 2019 04:59:55: 4000000 INFO @ Mon, 03 Jun 2019 05:00:00: 5000000 INFO @ Mon, 03 Jun 2019 05:00:03: 5000000 INFO @ Mon, 03 Jun 2019 05:00:03: 5000000 INFO @ Mon, 03 Jun 2019 05:00:07: 6000000 INFO @ Mon, 03 Jun 2019 05:00:10: 6000000 INFO @ Mon, 03 Jun 2019 05:00:10: 6000000 INFO @ Mon, 03 Jun 2019 05:00:15: 7000000 INFO @ Mon, 03 Jun 2019 05:00:16: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:00:16: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:00:16: #1 total tags in treatment: 7241643 INFO @ Mon, 03 Jun 2019 05:00:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:00:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 05:00:16: #1 tags after filtering in treatment: 7241643 INFO @ Mon, 03 Jun 2019 05:00:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:00:16: #1 finished! INFO @ Mon, 03 Jun 2019 05:00:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:00:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:00:17: #2 number of paired peaks: 147 WARNING @ Mon, 03 Jun 2019 05:00:17: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Mon, 03 Jun 2019 05:00:17: start model_add_line... INFO @ Mon, 03 Jun 2019 05:00:17: start X-correlation... INFO @ Mon, 03 Jun 2019 05:00:17: end of X-cor INFO @ Mon, 03 Jun 2019 05:00:17: #2 finished! INFO @ Mon, 03 Jun 2019 05:00:17: #2 predicted fragment length is 35 bps INFO @ Mon, 03 Jun 2019 05:00:17: #2 alternative fragment length(s) may be 35,496,541 bps INFO @ Mon, 03 Jun 2019 05:00:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.10_model.r WARNING @ Mon, 03 Jun 2019 05:00:17: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:00:17: #2 You may need to consider one of the other alternative d(s): 35,496,541 WARNING @ Mon, 03 Jun 2019 05:00:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:00:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:00:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:00:18: 7000000 INFO @ Mon, 03 Jun 2019 05:00:18: 7000000 INFO @ Mon, 03 Jun 2019 05:00:20: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:00:20: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:00:20: #1 total tags in treatment: 7241643 INFO @ Mon, 03 Jun 2019 05:00:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:00:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 05:00:20: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:00:20: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:00:20: #1 total tags in treatment: 7241643 INFO @ Mon, 03 Jun 2019 05:00:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:00:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 05:00:20: #1 tags after filtering in treatment: 7241643 INFO @ Mon, 03 Jun 2019 05:00:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:00:20: #1 finished! INFO @ Mon, 03 Jun 2019 05:00:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:00:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:00:20: #1 tags after filtering in treatment: 7241643 INFO @ Mon, 03 Jun 2019 05:00:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:00:20: #1 finished! INFO @ Mon, 03 Jun 2019 05:00:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:00:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:00:21: #2 number of paired peaks: 147 WARNING @ Mon, 03 Jun 2019 05:00:21: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Mon, 03 Jun 2019 05:00:21: start model_add_line... INFO @ Mon, 03 Jun 2019 05:00:21: start X-correlation... INFO @ Mon, 03 Jun 2019 05:00:21: #2 number of paired peaks: 147 WARNING @ Mon, 03 Jun 2019 05:00:21: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Mon, 03 Jun 2019 05:00:21: start model_add_line... INFO @ Mon, 03 Jun 2019 05:00:21: end of X-cor INFO @ Mon, 03 Jun 2019 05:00:21: #2 finished! INFO @ Mon, 03 Jun 2019 05:00:21: #2 predicted fragment length is 35 bps INFO @ Mon, 03 Jun 2019 05:00:21: #2 alternative fragment length(s) may be 35,496,541 bps INFO @ Mon, 03 Jun 2019 05:00:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.20_model.r WARNING @ Mon, 03 Jun 2019 05:00:21: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:00:21: #2 You may need to consider one of the other alternative d(s): 35,496,541 WARNING @ Mon, 03 Jun 2019 05:00:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:00:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:00:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:00:21: start X-correlation... INFO @ Mon, 03 Jun 2019 05:00:21: end of X-cor INFO @ Mon, 03 Jun 2019 05:00:21: #2 finished! INFO @ Mon, 03 Jun 2019 05:00:21: #2 predicted fragment length is 35 bps INFO @ Mon, 03 Jun 2019 05:00:21: #2 alternative fragment length(s) may be 35,496,541 bps INFO @ Mon, 03 Jun 2019 05:00:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.05_model.r WARNING @ Mon, 03 Jun 2019 05:00:21: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:00:21: #2 You may need to consider one of the other alternative d(s): 35,496,541 WARNING @ Mon, 03 Jun 2019 05:00:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:00:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:00:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:00:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:00:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:00:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:00:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:00:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:00:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.10_summits.bed INFO @ Mon, 03 Jun 2019 05:00:48: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (490 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:00:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:00:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:00:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.20_summits.bed INFO @ Mon, 03 Jun 2019 05:00:52: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (277 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:00:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:00:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:00:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX186108/SRX186108.05_summits.bed INFO @ Mon, 03 Jun 2019 05:00:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (751 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。