Job ID = 1293911 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,320,767 reads read : 16,320,767 reads written : 16,320,767 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: 00:07:00 16320767 reads; of these: 16320767 (100.00%) were unpaired; of these: 292433 (1.79%) aligned 0 times 11291366 (69.18%) aligned exactly 1 time 4736968 (29.02%) aligned >1 times 98.21% overall alignment rate Time searching: 00:07:00 Overall time: 00:07:00 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] 1942165 / 16028334 = 0.1212 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 03:23:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.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 03:23:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:23:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:23:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.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 03:23:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.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 03:23:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:23:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:23:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:23:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:24:02: 1000000 INFO @ Mon, 03 Jun 2019 03:24:03: 1000000 INFO @ Mon, 03 Jun 2019 03:24:03: 1000000 INFO @ Mon, 03 Jun 2019 03:24:09: 2000000 INFO @ Mon, 03 Jun 2019 03:24:11: 2000000 INFO @ Mon, 03 Jun 2019 03:24:11: 2000000 INFO @ Mon, 03 Jun 2019 03:24:15: 3000000 INFO @ Mon, 03 Jun 2019 03:24:18: 3000000 INFO @ Mon, 03 Jun 2019 03:24:18: 3000000 INFO @ Mon, 03 Jun 2019 03:24:22: 4000000 INFO @ Mon, 03 Jun 2019 03:24:26: 4000000 INFO @ Mon, 03 Jun 2019 03:24:26: 4000000 INFO @ Mon, 03 Jun 2019 03:24:29: 5000000 INFO @ Mon, 03 Jun 2019 03:24:33: 5000000 INFO @ Mon, 03 Jun 2019 03:24:33: 5000000 INFO @ Mon, 03 Jun 2019 03:24:35: 6000000 INFO @ Mon, 03 Jun 2019 03:24:40: 6000000 INFO @ Mon, 03 Jun 2019 03:24:40: 6000000 INFO @ Mon, 03 Jun 2019 03:24:41: 7000000 INFO @ Mon, 03 Jun 2019 03:24:48: 7000000 INFO @ Mon, 03 Jun 2019 03:24:48: 8000000 INFO @ Mon, 03 Jun 2019 03:24:48: 7000000 INFO @ Mon, 03 Jun 2019 03:24:55: 8000000 INFO @ Mon, 03 Jun 2019 03:24:55: 9000000 INFO @ Mon, 03 Jun 2019 03:24:55: 8000000 INFO @ Mon, 03 Jun 2019 03:25:01: 10000000 INFO @ Mon, 03 Jun 2019 03:25:02: 9000000 INFO @ Mon, 03 Jun 2019 03:25:02: 9000000 INFO @ Mon, 03 Jun 2019 03:25:08: 11000000 INFO @ Mon, 03 Jun 2019 03:25:09: 10000000 INFO @ Mon, 03 Jun 2019 03:25:09: 10000000 INFO @ Mon, 03 Jun 2019 03:25:14: 12000000 INFO @ Mon, 03 Jun 2019 03:25:15: 11000000 INFO @ Mon, 03 Jun 2019 03:25:16: 11000000 INFO @ Mon, 03 Jun 2019 03:25:20: 13000000 INFO @ Mon, 03 Jun 2019 03:25:22: 12000000 INFO @ Mon, 03 Jun 2019 03:25:23: 12000000 INFO @ Mon, 03 Jun 2019 03:25:27: 14000000 INFO @ Mon, 03 Jun 2019 03:25:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:25:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:25:27: #1 total tags in treatment: 14086169 INFO @ Mon, 03 Jun 2019 03:25:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:25:27: #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 03:25:28: #1 tags after filtering in treatment: 14086169 INFO @ Mon, 03 Jun 2019 03:25:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:25:28: #1 finished! INFO @ Mon, 03 Jun 2019 03:25:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:25:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:25:29: #2 number of paired peaks: 662 WARNING @ Mon, 03 Jun 2019 03:25:29: Fewer paired peaks (662) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 662 pairs to build model! INFO @ Mon, 03 Jun 2019 03:25:29: start model_add_line... INFO @ Mon, 03 Jun 2019 03:25:29: start X-correlation... INFO @ Mon, 03 Jun 2019 03:25:29: end of X-cor INFO @ Mon, 03 Jun 2019 03:25:29: #2 finished! INFO @ Mon, 03 Jun 2019 03:25:29: #2 predicted fragment length is 74 bps INFO @ Mon, 03 Jun 2019 03:25:29: #2 alternative fragment length(s) may be 74 bps INFO @ Mon, 03 Jun 2019 03:25:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.20_model.r WARNING @ Mon, 03 Jun 2019 03:25:29: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:25:29: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Mon, 03 Jun 2019 03:25:29: #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 03:25:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:25:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:25:29: 13000000 INFO @ Mon, 03 Jun 2019 03:25:30: 13000000 INFO @ Mon, 03 Jun 2019 03:25:36: 14000000 INFO @ Mon, 03 Jun 2019 03:25:37: 14000000 INFO @ Mon, 03 Jun 2019 03:25:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:25:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:25:37: #1 total tags in treatment: 14086169 INFO @ Mon, 03 Jun 2019 03:25:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:25:37: #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 03:25:37: #1 tags after filtering in treatment: 14086169 INFO @ Mon, 03 Jun 2019 03:25:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:25:37: #1 finished! INFO @ Mon, 03 Jun 2019 03:25:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:25:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:25:38: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:25:38: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:25:38: #1 total tags in treatment: 14086169 INFO @ Mon, 03 Jun 2019 03:25:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:25:38: #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 03:25:38: #1 tags after filtering in treatment: 14086169 INFO @ Mon, 03 Jun 2019 03:25:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:25:38: #1 finished! INFO @ Mon, 03 Jun 2019 03:25:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:25:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:25:39: #2 number of paired peaks: 662 WARNING @ Mon, 03 Jun 2019 03:25:39: Fewer paired peaks (662) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 662 pairs to build model! INFO @ Mon, 03 Jun 2019 03:25:39: start model_add_line... INFO @ Mon, 03 Jun 2019 03:25:39: start X-correlation... INFO @ Mon, 03 Jun 2019 03:25:39: end of X-cor INFO @ Mon, 03 Jun 2019 03:25:39: #2 finished! INFO @ Mon, 03 Jun 2019 03:25:39: #2 predicted fragment length is 74 bps INFO @ Mon, 03 Jun 2019 03:25:39: #2 alternative fragment length(s) may be 74 bps INFO @ Mon, 03 Jun 2019 03:25:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.10_model.r WARNING @ Mon, 03 Jun 2019 03:25:39: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:25:39: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Mon, 03 Jun 2019 03:25:39: #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 03:25:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:25:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:25:39: #2 number of paired peaks: 662 WARNING @ Mon, 03 Jun 2019 03:25:39: Fewer paired peaks (662) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 662 pairs to build model! INFO @ Mon, 03 Jun 2019 03:25:39: start model_add_line... INFO @ Mon, 03 Jun 2019 03:25:39: start X-correlation... INFO @ Mon, 03 Jun 2019 03:25:39: end of X-cor INFO @ Mon, 03 Jun 2019 03:25:39: #2 finished! INFO @ Mon, 03 Jun 2019 03:25:39: #2 predicted fragment length is 74 bps INFO @ Mon, 03 Jun 2019 03:25:39: #2 alternative fragment length(s) may be 74 bps INFO @ Mon, 03 Jun 2019 03:25:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.05_model.r WARNING @ Mon, 03 Jun 2019 03:25:39: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:25:39: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Mon, 03 Jun 2019 03:25:39: #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 03:25:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:25:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:26:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:26:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:26:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:26:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:26:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:26:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.20_summits.bed INFO @ Mon, 03 Jun 2019 03:26:27: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1214 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:26:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:26:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:26:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.10_summits.bed INFO @ Mon, 03 Jun 2019 03:26:36: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2270 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:26:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:26:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:26:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX147005/SRX147005.05_summits.bed INFO @ Mon, 03 Jun 2019 03:26:37: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4402 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。