Job ID = 1294915 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,809,114 reads read : 13,809,114 reads written : 13,809,114 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: 00:06:40 13809114 reads; of these: 13809114 (100.00%) were unpaired; of these: 547858 (3.97%) aligned 0 times 8994315 (65.13%) aligned exactly 1 time 4266941 (30.90%) aligned >1 times 96.03% overall alignment rate Time searching: 00:06:40 Overall time: 00:06:40 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] 1852093 / 13261256 = 0.1397 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 10:57:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.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 10:57:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:57:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:57:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.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 10:57:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:57:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:57:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.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 10:57:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:57:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:57:16: 1000000 INFO @ Mon, 03 Jun 2019 10:57:18: 1000000 INFO @ Mon, 03 Jun 2019 10:57:18: 1000000 INFO @ Mon, 03 Jun 2019 10:57:24: 2000000 INFO @ Mon, 03 Jun 2019 10:57:28: 2000000 INFO @ Mon, 03 Jun 2019 10:57:28: 2000000 INFO @ Mon, 03 Jun 2019 10:57:32: 3000000 INFO @ Mon, 03 Jun 2019 10:57:37: 3000000 INFO @ Mon, 03 Jun 2019 10:57:38: 3000000 INFO @ Mon, 03 Jun 2019 10:57:40: 4000000 INFO @ Mon, 03 Jun 2019 10:57:47: 4000000 INFO @ Mon, 03 Jun 2019 10:57:47: 4000000 INFO @ Mon, 03 Jun 2019 10:57:48: 5000000 INFO @ Mon, 03 Jun 2019 10:57:55: 6000000 INFO @ Mon, 03 Jun 2019 10:57:56: 5000000 INFO @ Mon, 03 Jun 2019 10:57:56: 5000000 INFO @ Mon, 03 Jun 2019 10:58:03: 7000000 INFO @ Mon, 03 Jun 2019 10:58:06: 6000000 INFO @ Mon, 03 Jun 2019 10:58:06: 6000000 INFO @ Mon, 03 Jun 2019 10:58:11: 8000000 INFO @ Mon, 03 Jun 2019 10:58:15: 7000000 INFO @ Mon, 03 Jun 2019 10:58:15: 7000000 INFO @ Mon, 03 Jun 2019 10:58:18: 9000000 INFO @ Mon, 03 Jun 2019 10:58:24: 8000000 INFO @ Mon, 03 Jun 2019 10:58:25: 8000000 INFO @ Mon, 03 Jun 2019 10:58:26: 10000000 INFO @ Mon, 03 Jun 2019 10:58:34: 9000000 INFO @ Mon, 03 Jun 2019 10:58:34: 9000000 INFO @ Mon, 03 Jun 2019 10:58:34: 11000000 INFO @ Mon, 03 Jun 2019 10:58:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:58:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:58:37: #1 total tags in treatment: 11409163 INFO @ Mon, 03 Jun 2019 10:58:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:58:37: #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 10:58:38: #1 tags after filtering in treatment: 11409163 INFO @ Mon, 03 Jun 2019 10:58:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:58:38: #1 finished! INFO @ Mon, 03 Jun 2019 10:58:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:58:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:58:39: #2 number of paired peaks: 423 WARNING @ Mon, 03 Jun 2019 10:58:39: Fewer paired peaks (423) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 423 pairs to build model! INFO @ Mon, 03 Jun 2019 10:58:39: start model_add_line... INFO @ Mon, 03 Jun 2019 10:58:39: start X-correlation... INFO @ Mon, 03 Jun 2019 10:58:39: end of X-cor INFO @ Mon, 03 Jun 2019 10:58:39: #2 finished! INFO @ Mon, 03 Jun 2019 10:58:39: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 10:58:39: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 10:58:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.20_model.r WARNING @ Mon, 03 Jun 2019 10:58:39: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:58:39: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 10:58:39: #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 10:58:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:58:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:58:43: 10000000 INFO @ Mon, 03 Jun 2019 10:58:43: 10000000 INFO @ Mon, 03 Jun 2019 10:58:53: 11000000 INFO @ Mon, 03 Jun 2019 10:58:53: 11000000 INFO @ Mon, 03 Jun 2019 10:58:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:58:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:58:57: #1 total tags in treatment: 11409163 INFO @ Mon, 03 Jun 2019 10:58:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:58:57: #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 10:58:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:58:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:58:57: #1 total tags in treatment: 11409163 INFO @ Mon, 03 Jun 2019 10:58:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:58:57: #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 10:58:57: #1 tags after filtering in treatment: 11409163 INFO @ Mon, 03 Jun 2019 10:58:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:58:57: #1 finished! INFO @ Mon, 03 Jun 2019 10:58:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:58:57: #1 tags after filtering in treatment: 11409163 INFO @ Mon, 03 Jun 2019 10:58:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:58:57: #1 finished! INFO @ Mon, 03 Jun 2019 10:58:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:58:58: #2 number of paired peaks: 423 WARNING @ Mon, 03 Jun 2019 10:58:58: Fewer paired peaks (423) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 423 pairs to build model! INFO @ Mon, 03 Jun 2019 10:58:58: start model_add_line... INFO @ Mon, 03 Jun 2019 10:58:58: start X-correlation... INFO @ Mon, 03 Jun 2019 10:58:58: end of X-cor INFO @ Mon, 03 Jun 2019 10:58:58: #2 finished! INFO @ Mon, 03 Jun 2019 10:58:58: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 10:58:58: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 10:58:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.05_model.r WARNING @ Mon, 03 Jun 2019 10:58:58: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:58:58: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 10:58:58: #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 10:58:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:58:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:58:58: #2 number of paired peaks: 423 WARNING @ Mon, 03 Jun 2019 10:58:58: Fewer paired peaks (423) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 423 pairs to build model! INFO @ Mon, 03 Jun 2019 10:58:58: start model_add_line... INFO @ Mon, 03 Jun 2019 10:58:58: start X-correlation... INFO @ Mon, 03 Jun 2019 10:58:59: end of X-cor INFO @ Mon, 03 Jun 2019 10:58:59: #2 finished! INFO @ Mon, 03 Jun 2019 10:58:59: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 10:58:59: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 10:58:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.10_model.r WARNING @ Mon, 03 Jun 2019 10:58:59: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:58:59: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 10:58:59: #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 10:58:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:58:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:59:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:59:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:59:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:59:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.20_summits.bed INFO @ Mon, 03 Jun 2019 10:59:25: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1414 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:59:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:59:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:59:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:59:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:59:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.10_summits.bed INFO @ Mon, 03 Jun 2019 10:59:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:59:45: Done! INFO @ Mon, 03 Jun 2019 10:59:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:59:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287987/SRX287987.05_summits.bed INFO @ Mon, 03 Jun 2019 10:59:45: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1845 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2084 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。