Job ID = 2590802 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,560,848 reads read : 49,121,696 reads written : 24,560,848 reads 0-length : 24,560,848 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:53 24560848 reads; of these: 24560848 (100.00%) were unpaired; of these: 497398 (2.03%) aligned 0 times 16777732 (68.31%) aligned exactly 1 time 7285718 (29.66%) aligned >1 times 97.97% overall alignment rate Time searching: 00:10:54 Overall time: 00:10:54 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] 11694829 / 24063450 = 0.4860 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, 12 Aug 2019 23:34:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.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, 12 Aug 2019 23:34:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:34:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:34:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.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, 12 Aug 2019 23:34:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:34:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:34:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.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, 12 Aug 2019 23:34:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:34:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:34:58: 1000000 INFO @ Mon, 12 Aug 2019 23:35:00: 1000000 INFO @ Mon, 12 Aug 2019 23:35:01: 1000000 INFO @ Mon, 12 Aug 2019 23:35:04: 2000000 INFO @ Mon, 12 Aug 2019 23:35:08: 2000000 INFO @ Mon, 12 Aug 2019 23:35:09: 2000000 INFO @ Mon, 12 Aug 2019 23:35:10: 3000000 INFO @ Mon, 12 Aug 2019 23:35:16: 3000000 INFO @ Mon, 12 Aug 2019 23:35:16: 4000000 INFO @ Mon, 12 Aug 2019 23:35:17: 3000000 INFO @ Mon, 12 Aug 2019 23:35:22: 5000000 INFO @ Mon, 12 Aug 2019 23:35:24: 4000000 INFO @ Mon, 12 Aug 2019 23:35:25: 4000000 INFO @ Mon, 12 Aug 2019 23:35:29: 6000000 INFO @ Mon, 12 Aug 2019 23:35:32: 5000000 INFO @ Mon, 12 Aug 2019 23:35:33: 5000000 INFO @ Mon, 12 Aug 2019 23:35:35: 7000000 INFO @ Mon, 12 Aug 2019 23:35:40: 6000000 INFO @ Mon, 12 Aug 2019 23:35:41: 6000000 INFO @ Mon, 12 Aug 2019 23:35:41: 8000000 INFO @ Mon, 12 Aug 2019 23:35:47: 9000000 INFO @ Mon, 12 Aug 2019 23:35:48: 7000000 INFO @ Mon, 12 Aug 2019 23:35:49: 7000000 INFO @ Mon, 12 Aug 2019 23:35:53: 10000000 INFO @ Mon, 12 Aug 2019 23:35:56: 8000000 INFO @ Mon, 12 Aug 2019 23:35:57: 8000000 INFO @ Mon, 12 Aug 2019 23:36:00: 11000000 INFO @ Mon, 12 Aug 2019 23:36:05: 9000000 INFO @ Mon, 12 Aug 2019 23:36:05: 9000000 INFO @ Mon, 12 Aug 2019 23:36:06: 12000000 INFO @ Mon, 12 Aug 2019 23:36:08: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:36:08: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:36:08: #1 total tags in treatment: 12368621 INFO @ Mon, 12 Aug 2019 23:36:08: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:36:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:36:08: #1 tags after filtering in treatment: 12368621 INFO @ Mon, 12 Aug 2019 23:36:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:36:08: #1 finished! INFO @ Mon, 12 Aug 2019 23:36:08: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:36:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:36:10: #2 number of paired peaks: 856 WARNING @ Mon, 12 Aug 2019 23:36:10: Fewer paired peaks (856) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 856 pairs to build model! INFO @ Mon, 12 Aug 2019 23:36:10: start model_add_line... INFO @ Mon, 12 Aug 2019 23:36:10: start X-correlation... INFO @ Mon, 12 Aug 2019 23:36:10: end of X-cor INFO @ Mon, 12 Aug 2019 23:36:10: #2 finished! INFO @ Mon, 12 Aug 2019 23:36:10: #2 predicted fragment length is 59 bps INFO @ Mon, 12 Aug 2019 23:36:10: #2 alternative fragment length(s) may be 59 bps INFO @ Mon, 12 Aug 2019 23:36:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.05_model.r WARNING @ Mon, 12 Aug 2019 23:36:10: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:36:10: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Mon, 12 Aug 2019 23:36:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:36:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:36:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:36:13: 10000000 INFO @ Mon, 12 Aug 2019 23:36:13: 10000000 INFO @ Mon, 12 Aug 2019 23:36:21: 11000000 INFO @ Mon, 12 Aug 2019 23:36:21: 11000000 INFO @ Mon, 12 Aug 2019 23:36:29: 12000000 INFO @ Mon, 12 Aug 2019 23:36:29: 12000000 INFO @ Mon, 12 Aug 2019 23:36:32: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:36:32: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:36:32: #1 total tags in treatment: 12368621 INFO @ Mon, 12 Aug 2019 23:36:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:36:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:36:32: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:36:32: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:36:32: #1 total tags in treatment: 12368621 INFO @ Mon, 12 Aug 2019 23:36:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:36:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:36:32: #1 tags after filtering in treatment: 12368621 INFO @ Mon, 12 Aug 2019 23:36:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:36:32: #1 finished! INFO @ Mon, 12 Aug 2019 23:36:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:36:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:36:32: #1 tags after filtering in treatment: 12368621 INFO @ Mon, 12 Aug 2019 23:36:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:36:32: #1 finished! INFO @ Mon, 12 Aug 2019 23:36:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:36:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:36:33: #2 number of paired peaks: 856 WARNING @ Mon, 12 Aug 2019 23:36:33: Fewer paired peaks (856) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 856 pairs to build model! INFO @ Mon, 12 Aug 2019 23:36:33: start model_add_line... INFO @ Mon, 12 Aug 2019 23:36:34: start X-correlation... INFO @ Mon, 12 Aug 2019 23:36:34: end of X-cor INFO @ Mon, 12 Aug 2019 23:36:34: #2 finished! INFO @ Mon, 12 Aug 2019 23:36:34: #2 predicted fragment length is 59 bps INFO @ Mon, 12 Aug 2019 23:36:34: #2 alternative fragment length(s) may be 59 bps INFO @ Mon, 12 Aug 2019 23:36:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.10_model.r WARNING @ Mon, 12 Aug 2019 23:36:34: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:36:34: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Mon, 12 Aug 2019 23:36:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:36:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:36:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:36:34: #2 number of paired peaks: 856 WARNING @ Mon, 12 Aug 2019 23:36:34: Fewer paired peaks (856) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 856 pairs to build model! INFO @ Mon, 12 Aug 2019 23:36:34: start model_add_line... INFO @ Mon, 12 Aug 2019 23:36:34: start X-correlation... INFO @ Mon, 12 Aug 2019 23:36:34: end of X-cor INFO @ Mon, 12 Aug 2019 23:36:34: #2 finished! INFO @ Mon, 12 Aug 2019 23:36:34: #2 predicted fragment length is 59 bps INFO @ Mon, 12 Aug 2019 23:36:34: #2 alternative fragment length(s) may be 59 bps INFO @ Mon, 12 Aug 2019 23:36:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.20_model.r WARNING @ Mon, 12 Aug 2019 23:36:34: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:36:34: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Mon, 12 Aug 2019 23:36:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:36:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:36:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:36:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:37:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:37:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:37:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.05_summits.bed INFO @ Mon, 12 Aug 2019 23:37:00: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3376 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:37:08: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:37:08: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:37:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:37:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:37:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.10_summits.bed INFO @ Mon, 12 Aug 2019 23:37:24: Done! INFO @ Mon, 12 Aug 2019 23:37:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.20_peaks.xls pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1914 records, 4 fields): 7 millis INFO @ Mon, 12 Aug 2019 23:37:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.20_peaks.narrowPeak CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:37:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011044/SRX5011044.20_summits.bed INFO @ Mon, 12 Aug 2019 23:37:24: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (994 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。