Job ID = 4178417 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,075,044 reads read : 4,150,088 reads written : 4,150,088 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:01 Multiseed full-index search: 00:04:44 2075044 reads; of these: 2075044 (100.00%) were paired; of these: 512456 (24.70%) aligned concordantly 0 times 1270486 (61.23%) aligned concordantly exactly 1 time 292102 (14.08%) aligned concordantly >1 times ---- 512456 pairs aligned concordantly 0 times; of these: 248251 (48.44%) aligned discordantly 1 time ---- 264205 pairs aligned 0 times concordantly or discordantly; of these: 528410 mates make up the pairs; of these: 369563 (69.94%) aligned 0 times 77511 (14.67%) aligned exactly 1 time 81336 (15.39%) aligned >1 times 91.10% overall alignment rate Time searching: 00:04:45 Overall time: 00:04:46 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 153587 / 1807469 = 0.0850 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:25:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.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 @ Thu, 05 Dec 2019 12:25:52: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:25:52: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:25:59: 1000000 INFO @ Thu, 05 Dec 2019 12:26:07: 2000000 INFO @ Thu, 05 Dec 2019 12:26:14: 3000000 INFO @ Thu, 05 Dec 2019 12:26:17: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:26:17: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:26:17: #1 total tags in treatment: 1424694 INFO @ Thu, 05 Dec 2019 12:26:17: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:26:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:26:17: #1 tags after filtering in treatment: 1396870 INFO @ Thu, 05 Dec 2019 12:26:17: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 05 Dec 2019 12:26:17: #1 finished! INFO @ Thu, 05 Dec 2019 12:26:17: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:26:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:26:17: #2 number of paired peaks: 149 WARNING @ Thu, 05 Dec 2019 12:26:17: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Thu, 05 Dec 2019 12:26:17: start model_add_line... INFO @ Thu, 05 Dec 2019 12:26:17: start X-correlation... INFO @ Thu, 05 Dec 2019 12:26:17: end of X-cor INFO @ Thu, 05 Dec 2019 12:26:17: #2 finished! INFO @ Thu, 05 Dec 2019 12:26:17: #2 predicted fragment length is 118 bps INFO @ Thu, 05 Dec 2019 12:26:17: #2 alternative fragment length(s) may be 118 bps INFO @ Thu, 05 Dec 2019 12:26:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.05_model.r WARNING @ Thu, 05 Dec 2019 12:26:17: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:26:17: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Thu, 05 Dec 2019 12:26:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:26:17: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:26:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:26:20: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:26:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.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 @ Thu, 05 Dec 2019 12:26:21: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:26:21: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:26:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:26:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:26:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.05_summits.bed INFO @ Thu, 05 Dec 2019 12:26:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (356 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:26:28: 1000000 INFO @ Thu, 05 Dec 2019 12:26:34: 2000000 INFO @ Thu, 05 Dec 2019 12:26:41: 3000000 INFO @ Thu, 05 Dec 2019 12:26:44: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:26:44: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:26:44: #1 total tags in treatment: 1424694 INFO @ Thu, 05 Dec 2019 12:26:44: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:26:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:26:44: #1 tags after filtering in treatment: 1396870 INFO @ Thu, 05 Dec 2019 12:26:44: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 05 Dec 2019 12:26:44: #1 finished! INFO @ Thu, 05 Dec 2019 12:26:44: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:26:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:26:44: #2 number of paired peaks: 149 WARNING @ Thu, 05 Dec 2019 12:26:44: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Thu, 05 Dec 2019 12:26:44: start model_add_line... INFO @ Thu, 05 Dec 2019 12:26:44: start X-correlation... INFO @ Thu, 05 Dec 2019 12:26:44: end of X-cor INFO @ Thu, 05 Dec 2019 12:26:44: #2 finished! INFO @ Thu, 05 Dec 2019 12:26:44: #2 predicted fragment length is 118 bps INFO @ Thu, 05 Dec 2019 12:26:44: #2 alternative fragment length(s) may be 118 bps INFO @ Thu, 05 Dec 2019 12:26:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.10_model.r WARNING @ Thu, 05 Dec 2019 12:26:44: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:26:44: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Thu, 05 Dec 2019 12:26:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:26:44: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:26:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:26:47: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:26:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:26:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:26:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.10_summits.bed INFO @ Thu, 05 Dec 2019 12:26:48: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (247 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:26:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.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 @ Thu, 05 Dec 2019 12:26:51: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:26:51: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:26:58: 1000000 INFO @ Thu, 05 Dec 2019 12:27:04: 2000000 INFO @ Thu, 05 Dec 2019 12:27:11: 3000000 INFO @ Thu, 05 Dec 2019 12:27:14: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:27:14: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:27:14: #1 total tags in treatment: 1424694 INFO @ Thu, 05 Dec 2019 12:27:14: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:27:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:27:14: #1 tags after filtering in treatment: 1396870 INFO @ Thu, 05 Dec 2019 12:27:14: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 05 Dec 2019 12:27:14: #1 finished! INFO @ Thu, 05 Dec 2019 12:27:14: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:27:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:27:14: #2 number of paired peaks: 149 WARNING @ Thu, 05 Dec 2019 12:27:14: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Thu, 05 Dec 2019 12:27:14: start model_add_line... INFO @ Thu, 05 Dec 2019 12:27:14: start X-correlation... INFO @ Thu, 05 Dec 2019 12:27:14: end of X-cor INFO @ Thu, 05 Dec 2019 12:27:14: #2 finished! INFO @ Thu, 05 Dec 2019 12:27:14: #2 predicted fragment length is 118 bps INFO @ Thu, 05 Dec 2019 12:27:14: #2 alternative fragment length(s) may be 118 bps INFO @ Thu, 05 Dec 2019 12:27:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.20_model.r WARNING @ Thu, 05 Dec 2019 12:27:14: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:27:14: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Thu, 05 Dec 2019 12:27:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:27:14: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:27:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:27:17: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:27:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:27:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:27:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2095156/SRX2095156.20_summits.bed INFO @ Thu, 05 Dec 2019 12:27:18: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (148 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。