Job ID = 1308543 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,037,254 reads read : 50,074,508 reads written : 25,037,254 reads 0-length : 25,037,254 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: 00:08:18 25037254 reads; of these: 25037254 (100.00%) were unpaired; of these: 9757038 (38.97%) aligned 0 times 10934867 (43.67%) aligned exactly 1 time 4345349 (17.36%) aligned >1 times 61.03% overall alignment rate Time searching: 00:08:18 Overall time: 00:08:18 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] 7524685 / 15280216 = 0.4924 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 23:10:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.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 23:10:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:10:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:10:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.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 23:10:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:10:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:10:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.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 23:10:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:10:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:10:33: 1000000 INFO @ Mon, 03 Jun 2019 23:10:33: 1000000 INFO @ Mon, 03 Jun 2019 23:10:34: 1000000 INFO @ Mon, 03 Jun 2019 23:10:42: 2000000 INFO @ Mon, 03 Jun 2019 23:10:42: 2000000 INFO @ Mon, 03 Jun 2019 23:10:42: 2000000 INFO @ Mon, 03 Jun 2019 23:10:49: 3000000 INFO @ Mon, 03 Jun 2019 23:10:49: 3000000 INFO @ Mon, 03 Jun 2019 23:10:50: 3000000 INFO @ Mon, 03 Jun 2019 23:10:56: 4000000 INFO @ Mon, 03 Jun 2019 23:10:57: 4000000 INFO @ Mon, 03 Jun 2019 23:10:57: 4000000 INFO @ Mon, 03 Jun 2019 23:11:03: 5000000 INFO @ Mon, 03 Jun 2019 23:11:05: 5000000 INFO @ Mon, 03 Jun 2019 23:11:05: 5000000 INFO @ Mon, 03 Jun 2019 23:11:10: 6000000 INFO @ Mon, 03 Jun 2019 23:11:13: 6000000 INFO @ Mon, 03 Jun 2019 23:11:13: 6000000 INFO @ Mon, 03 Jun 2019 23:11:17: 7000000 INFO @ Mon, 03 Jun 2019 23:11:20: 7000000 INFO @ Mon, 03 Jun 2019 23:11:21: 7000000 INFO @ Mon, 03 Jun 2019 23:11:22: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:11:22: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:11:22: #1 total tags in treatment: 7755531 INFO @ Mon, 03 Jun 2019 23:11:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:11:22: #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 23:11:22: #1 tags after filtering in treatment: 7755531 INFO @ Mon, 03 Jun 2019 23:11:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:11:22: #1 finished! INFO @ Mon, 03 Jun 2019 23:11:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:11:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:11:23: #2 number of paired peaks: 714 WARNING @ Mon, 03 Jun 2019 23:11:23: Fewer paired peaks (714) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 714 pairs to build model! INFO @ Mon, 03 Jun 2019 23:11:23: start model_add_line... INFO @ Mon, 03 Jun 2019 23:11:23: start X-correlation... INFO @ Mon, 03 Jun 2019 23:11:23: end of X-cor INFO @ Mon, 03 Jun 2019 23:11:23: #2 finished! INFO @ Mon, 03 Jun 2019 23:11:23: #2 predicted fragment length is 70 bps INFO @ Mon, 03 Jun 2019 23:11:23: #2 alternative fragment length(s) may be 70 bps INFO @ Mon, 03 Jun 2019 23:11:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.20_model.r WARNING @ Mon, 03 Jun 2019 23:11:23: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:11:23: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Mon, 03 Jun 2019 23:11:23: #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 23:11:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:11:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:11:26: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:11:26: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:11:26: #1 total tags in treatment: 7755531 INFO @ Mon, 03 Jun 2019 23:11:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:11:26: #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 23:11:26: #1 tags after filtering in treatment: 7755531 INFO @ Mon, 03 Jun 2019 23:11:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:11:26: #1 finished! INFO @ Mon, 03 Jun 2019 23:11:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:11:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:11:27: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:11:27: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:11:27: #1 total tags in treatment: 7755531 INFO @ Mon, 03 Jun 2019 23:11:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:11:27: #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 23:11:27: #1 tags after filtering in treatment: 7755531 INFO @ Mon, 03 Jun 2019 23:11:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:11:27: #1 finished! INFO @ Mon, 03 Jun 2019 23:11:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:11:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:11:27: #2 number of paired peaks: 714 WARNING @ Mon, 03 Jun 2019 23:11:27: Fewer paired peaks (714) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 714 pairs to build model! INFO @ Mon, 03 Jun 2019 23:11:27: start model_add_line... INFO @ Mon, 03 Jun 2019 23:11:27: start X-correlation... INFO @ Mon, 03 Jun 2019 23:11:27: end of X-cor INFO @ Mon, 03 Jun 2019 23:11:27: #2 finished! INFO @ Mon, 03 Jun 2019 23:11:27: #2 predicted fragment length is 70 bps INFO @ Mon, 03 Jun 2019 23:11:27: #2 alternative fragment length(s) may be 70 bps INFO @ Mon, 03 Jun 2019 23:11:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.10_model.r WARNING @ Mon, 03 Jun 2019 23:11:27: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:11:27: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Mon, 03 Jun 2019 23:11:27: #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 23:11:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:11:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:11:28: #2 number of paired peaks: 714 WARNING @ Mon, 03 Jun 2019 23:11:28: Fewer paired peaks (714) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 714 pairs to build model! INFO @ Mon, 03 Jun 2019 23:11:28: start model_add_line... INFO @ Mon, 03 Jun 2019 23:11:28: start X-correlation... INFO @ Mon, 03 Jun 2019 23:11:28: end of X-cor INFO @ Mon, 03 Jun 2019 23:11:28: #2 finished! INFO @ Mon, 03 Jun 2019 23:11:28: #2 predicted fragment length is 70 bps INFO @ Mon, 03 Jun 2019 23:11:28: #2 alternative fragment length(s) may be 70 bps INFO @ Mon, 03 Jun 2019 23:11:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.05_model.r WARNING @ Mon, 03 Jun 2019 23:11:28: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:11:28: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Mon, 03 Jun 2019 23:11:28: #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 23:11:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:11:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:11:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:11:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:11:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:11:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:11:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:11:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.20_summits.bed INFO @ Mon, 03 Jun 2019 23:11:56: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (745 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:12:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:12:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:12:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.10_summits.bed INFO @ Mon, 03 Jun 2019 23:12:00: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1152 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:12:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:12:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:12:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343150/SRX5343150.05_summits.bed INFO @ Mon, 03 Jun 2019 23:12:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2117 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。