Job ID = 1308566 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,267,185 reads read : 56,534,370 reads written : 28,267,185 reads 0-length : 28,267,185 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: 00:11:05 28267185 reads; of these: 28267185 (100.00%) were unpaired; of these: 5110054 (18.08%) aligned 0 times 16820752 (59.51%) aligned exactly 1 time 6336379 (22.42%) aligned >1 times 81.92% overall alignment rate Time searching: 00:11:05 Overall time: 00:11:05 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 12 files... [bam_rmdupse_core] 11161065 / 23157131 = 0.4820 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 23:16:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.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 23:16:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:16:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:16:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.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 23:16:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:16:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:16:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.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 23:16:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:16:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:16:31: 1000000 INFO @ Mon, 03 Jun 2019 23:16:31: 1000000 INFO @ Mon, 03 Jun 2019 23:16:34: 1000000 INFO @ Mon, 03 Jun 2019 23:16:39: 2000000 INFO @ Mon, 03 Jun 2019 23:16:41: 2000000 INFO @ Mon, 03 Jun 2019 23:16:46: 2000000 INFO @ Mon, 03 Jun 2019 23:16:48: 3000000 INFO @ Mon, 03 Jun 2019 23:16:51: 3000000 INFO @ Mon, 03 Jun 2019 23:16:56: 4000000 INFO @ Mon, 03 Jun 2019 23:16:58: 3000000 INFO @ Mon, 03 Jun 2019 23:17:00: 4000000 INFO @ Mon, 03 Jun 2019 23:17:05: 5000000 INFO @ Mon, 03 Jun 2019 23:17:10: 4000000 INFO @ Mon, 03 Jun 2019 23:17:10: 5000000 INFO @ Mon, 03 Jun 2019 23:17:13: 6000000 INFO @ Mon, 03 Jun 2019 23:17:20: 6000000 INFO @ Mon, 03 Jun 2019 23:17:22: 5000000 INFO @ Mon, 03 Jun 2019 23:17:22: 7000000 INFO @ Mon, 03 Jun 2019 23:17:30: 7000000 INFO @ Mon, 03 Jun 2019 23:17:30: 8000000 INFO @ Mon, 03 Jun 2019 23:17:34: 6000000 INFO @ Mon, 03 Jun 2019 23:17:38: 9000000 INFO @ Mon, 03 Jun 2019 23:17:39: 8000000 INFO @ Mon, 03 Jun 2019 23:17:45: 7000000 INFO @ Mon, 03 Jun 2019 23:17:47: 10000000 INFO @ Mon, 03 Jun 2019 23:17:49: 9000000 INFO @ Mon, 03 Jun 2019 23:17:55: 11000000 INFO @ Mon, 03 Jun 2019 23:17:57: 8000000 INFO @ Mon, 03 Jun 2019 23:17:59: 10000000 INFO @ Mon, 03 Jun 2019 23:18:03: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:18:03: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:18:03: #1 total tags in treatment: 11996066 INFO @ Mon, 03 Jun 2019 23:18:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:18:03: #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 23:18:04: #1 tags after filtering in treatment: 11996066 INFO @ Mon, 03 Jun 2019 23:18:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:18:04: #1 finished! INFO @ Mon, 03 Jun 2019 23:18:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:18:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:18:05: #2 number of paired peaks: 688 WARNING @ Mon, 03 Jun 2019 23:18:05: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Mon, 03 Jun 2019 23:18:05: start model_add_line... INFO @ Mon, 03 Jun 2019 23:18:05: start X-correlation... INFO @ Mon, 03 Jun 2019 23:18:05: end of X-cor INFO @ Mon, 03 Jun 2019 23:18:05: #2 finished! INFO @ Mon, 03 Jun 2019 23:18:05: #2 predicted fragment length is 79 bps INFO @ Mon, 03 Jun 2019 23:18:05: #2 alternative fragment length(s) may be 79 bps INFO @ Mon, 03 Jun 2019 23:18:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.10_model.r WARNING @ Mon, 03 Jun 2019 23:18:05: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:18:05: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Mon, 03 Jun 2019 23:18:05: #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 23:18:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:18:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:18:08: 11000000 INFO @ Mon, 03 Jun 2019 23:18:09: 9000000 INFO @ Mon, 03 Jun 2019 23:18:17: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:18:17: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:18:17: #1 total tags in treatment: 11996066 INFO @ Mon, 03 Jun 2019 23:18:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:18:17: #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 23:18:17: #1 tags after filtering in treatment: 11996066 INFO @ Mon, 03 Jun 2019 23:18:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:18:17: #1 finished! INFO @ Mon, 03 Jun 2019 23:18:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:18:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:18:18: #2 number of paired peaks: 688 WARNING @ Mon, 03 Jun 2019 23:18:18: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Mon, 03 Jun 2019 23:18:18: start model_add_line... INFO @ Mon, 03 Jun 2019 23:18:18: start X-correlation... INFO @ Mon, 03 Jun 2019 23:18:18: end of X-cor INFO @ Mon, 03 Jun 2019 23:18:18: #2 finished! INFO @ Mon, 03 Jun 2019 23:18:18: #2 predicted fragment length is 79 bps INFO @ Mon, 03 Jun 2019 23:18:18: #2 alternative fragment length(s) may be 79 bps INFO @ Mon, 03 Jun 2019 23:18:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.05_model.r WARNING @ Mon, 03 Jun 2019 23:18:18: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:18:18: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Mon, 03 Jun 2019 23:18:18: #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 23:18:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:18:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:18:21: 10000000 INFO @ Mon, 03 Jun 2019 23:18:33: 11000000 INFO @ Mon, 03 Jun 2019 23:18:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:18:45: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:18:45: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:18:45: #1 total tags in treatment: 11996066 INFO @ Mon, 03 Jun 2019 23:18:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:18:45: #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 23:18:45: #1 tags after filtering in treatment: 11996066 INFO @ Mon, 03 Jun 2019 23:18:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:18:45: #1 finished! INFO @ Mon, 03 Jun 2019 23:18:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:18:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:18:46: #2 number of paired peaks: 688 WARNING @ Mon, 03 Jun 2019 23:18:46: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Mon, 03 Jun 2019 23:18:46: start model_add_line... INFO @ Mon, 03 Jun 2019 23:18:46: start X-correlation... INFO @ Mon, 03 Jun 2019 23:18:46: end of X-cor INFO @ Mon, 03 Jun 2019 23:18:46: #2 finished! INFO @ Mon, 03 Jun 2019 23:18:46: #2 predicted fragment length is 79 bps INFO @ Mon, 03 Jun 2019 23:18:46: #2 alternative fragment length(s) may be 79 bps INFO @ Mon, 03 Jun 2019 23:18:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.20_model.r WARNING @ Mon, 03 Jun 2019 23:18:46: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:18:46: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Mon, 03 Jun 2019 23:18:46: #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 23:18:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:18:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:18:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:18:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:18:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:18:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.10_summits.bed INFO @ Mon, 03 Jun 2019 23:18:55: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1415 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:19:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:19:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:19:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.05_summits.bed INFO @ Mon, 03 Jun 2019 23:19:08: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3121 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:19:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:19:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:19:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:19:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343152/SRX5343152.20_summits.bed INFO @ Mon, 03 Jun 2019 23:19:37: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (781 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。