Job ID = 1301974 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,994,684 reads read : 20,994,684 reads written : 20,994,684 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: 00:08:02 20994684 reads; of these: 20994684 (100.00%) were unpaired; of these: 4416348 (21.04%) aligned 0 times 11433401 (54.46%) aligned exactly 1 time 5144935 (24.51%) aligned >1 times 78.96% overall alignment rate Time searching: 00:08:02 Overall time: 00:08:02 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_sort_core] merging from 8 files... [bam_rmdupse_core] 6113182 / 16578336 = 0.3687 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 20:25:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.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 20:25:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:25:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:25:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.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 20:25:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:25:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:25:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.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 20:25:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:25:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:25:12: 1000000 INFO @ Mon, 03 Jun 2019 20:25:14: 1000000 INFO @ Mon, 03 Jun 2019 20:25:14: 1000000 INFO @ Mon, 03 Jun 2019 20:25:21: 2000000 INFO @ Mon, 03 Jun 2019 20:25:24: 2000000 INFO @ Mon, 03 Jun 2019 20:25:24: 2000000 INFO @ Mon, 03 Jun 2019 20:25:29: 3000000 INFO @ Mon, 03 Jun 2019 20:25:33: 3000000 INFO @ Mon, 03 Jun 2019 20:25:33: 3000000 INFO @ Mon, 03 Jun 2019 20:25:37: 4000000 INFO @ Mon, 03 Jun 2019 20:25:43: 4000000 INFO @ Mon, 03 Jun 2019 20:25:43: 4000000 INFO @ Mon, 03 Jun 2019 20:25:45: 5000000 INFO @ Mon, 03 Jun 2019 20:25:52: 5000000 INFO @ Mon, 03 Jun 2019 20:25:52: 5000000 INFO @ Mon, 03 Jun 2019 20:25:53: 6000000 INFO @ Mon, 03 Jun 2019 20:26:01: 7000000 INFO @ Mon, 03 Jun 2019 20:26:02: 6000000 INFO @ Mon, 03 Jun 2019 20:26:02: 6000000 INFO @ Mon, 03 Jun 2019 20:26:10: 8000000 INFO @ Mon, 03 Jun 2019 20:26:12: 7000000 INFO @ Mon, 03 Jun 2019 20:26:12: 7000000 INFO @ Mon, 03 Jun 2019 20:26:18: 9000000 INFO @ Mon, 03 Jun 2019 20:26:22: 8000000 INFO @ Mon, 03 Jun 2019 20:26:22: 8000000 INFO @ Mon, 03 Jun 2019 20:26:27: 10000000 INFO @ Mon, 03 Jun 2019 20:26:31: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 20:26:31: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 20:26:31: #1 total tags in treatment: 10465154 INFO @ Mon, 03 Jun 2019 20:26:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:26:31: #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 20:26:31: #1 tags after filtering in treatment: 10465154 INFO @ Mon, 03 Jun 2019 20:26:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:26:31: #1 finished! INFO @ Mon, 03 Jun 2019 20:26:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:26:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:26:32: #2 number of paired peaks: 318 WARNING @ Mon, 03 Jun 2019 20:26:32: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Mon, 03 Jun 2019 20:26:32: start model_add_line... INFO @ Mon, 03 Jun 2019 20:26:32: start X-correlation... INFO @ Mon, 03 Jun 2019 20:26:32: end of X-cor INFO @ Mon, 03 Jun 2019 20:26:32: #2 finished! INFO @ Mon, 03 Jun 2019 20:26:32: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 20:26:32: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 20:26:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.05_model.r WARNING @ Mon, 03 Jun 2019 20:26:32: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:26:32: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 20:26:32: #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 20:26:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:26:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:26:32: 9000000 INFO @ Mon, 03 Jun 2019 20:26:32: 9000000 INFO @ Mon, 03 Jun 2019 20:26:42: 10000000 INFO @ Mon, 03 Jun 2019 20:26:42: 10000000 INFO @ Mon, 03 Jun 2019 20:26:47: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 20:26:47: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 20:26:47: #1 total tags in treatment: 10465154 INFO @ Mon, 03 Jun 2019 20:26:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:26:47: #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 20:26:47: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 20:26:47: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 20:26:47: #1 total tags in treatment: 10465154 INFO @ Mon, 03 Jun 2019 20:26:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:26:47: #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 20:26:47: #1 tags after filtering in treatment: 10465154 INFO @ Mon, 03 Jun 2019 20:26:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:26:47: #1 finished! INFO @ Mon, 03 Jun 2019 20:26:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:26:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:26:47: #1 tags after filtering in treatment: 10465154 INFO @ Mon, 03 Jun 2019 20:26:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:26:47: #1 finished! INFO @ Mon, 03 Jun 2019 20:26:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:26:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:26:48: #2 number of paired peaks: 318 WARNING @ Mon, 03 Jun 2019 20:26:48: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Mon, 03 Jun 2019 20:26:48: start model_add_line... INFO @ Mon, 03 Jun 2019 20:26:48: #2 number of paired peaks: 318 WARNING @ Mon, 03 Jun 2019 20:26:48: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Mon, 03 Jun 2019 20:26:48: start model_add_line... INFO @ Mon, 03 Jun 2019 20:26:48: start X-correlation... INFO @ Mon, 03 Jun 2019 20:26:48: end of X-cor INFO @ Mon, 03 Jun 2019 20:26:48: #2 finished! INFO @ Mon, 03 Jun 2019 20:26:48: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 20:26:48: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 20:26:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.10_model.r INFO @ Mon, 03 Jun 2019 20:26:48: start X-correlation... WARNING @ Mon, 03 Jun 2019 20:26:48: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:26:48: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 20:26:48: #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 20:26:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:26:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:26:48: end of X-cor INFO @ Mon, 03 Jun 2019 20:26:48: #2 finished! INFO @ Mon, 03 Jun 2019 20:26:48: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 20:26:48: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 20:26:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.20_model.r WARNING @ Mon, 03 Jun 2019 20:26:48: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:26:48: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 20:26:48: #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 20:26:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:26:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:27:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:27:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:27:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:27:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.05_summits.bed INFO @ Mon, 03 Jun 2019 20:27:15: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1726 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:27:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:27:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:27:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:27:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:27:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.20_summits.bed INFO @ Mon, 03 Jun 2019 20:27:31: Done! INFO @ Mon, 03 Jun 2019 20:27:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:27:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:27:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933875/SRX4933875.10_summits.bed pass1 - making usageList (8 chroms): 1 millis INFO @ Mon, 03 Jun 2019 20:27:31: Done! pass2 - checking and writing primary data (951 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1292 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。