Job ID = 2590277 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,176,975 reads read : 13,176,975 reads written : 13,176,975 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:55 13176975 reads; of these: 13176975 (100.00%) were unpaired; of these: 384111 (2.92%) aligned 0 times 8530936 (64.74%) aligned exactly 1 time 4261928 (32.34%) aligned >1 times 97.08% overall alignment rate Time searching: 00:04:55 Overall time: 00:04:55 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_rmdupse_core] 1092624 / 12792864 = 0.0854 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 20:38:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.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 20:38:43: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:38:43: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:38:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.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 20:38:44: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:38:44: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:38:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.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 20:38:45: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:38:45: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:38:51: 1000000 INFO @ Mon, 12 Aug 2019 20:38:52: 1000000 INFO @ Mon, 12 Aug 2019 20:38:52: 1000000 INFO @ Mon, 12 Aug 2019 20:38:58: 2000000 INFO @ Mon, 12 Aug 2019 20:38:59: 2000000 INFO @ Mon, 12 Aug 2019 20:39:00: 2000000 INFO @ Mon, 12 Aug 2019 20:39:06: 3000000 INFO @ Mon, 12 Aug 2019 20:39:07: 3000000 INFO @ Mon, 12 Aug 2019 20:39:07: 3000000 INFO @ Mon, 12 Aug 2019 20:39:14: 4000000 INFO @ Mon, 12 Aug 2019 20:39:14: 4000000 INFO @ Mon, 12 Aug 2019 20:39:15: 4000000 INFO @ Mon, 12 Aug 2019 20:39:21: 5000000 INFO @ Mon, 12 Aug 2019 20:39:21: 5000000 INFO @ Mon, 12 Aug 2019 20:39:22: 5000000 INFO @ Mon, 12 Aug 2019 20:39:28: 6000000 INFO @ Mon, 12 Aug 2019 20:39:29: 6000000 INFO @ Mon, 12 Aug 2019 20:39:30: 6000000 INFO @ Mon, 12 Aug 2019 20:39:35: 7000000 INFO @ Mon, 12 Aug 2019 20:39:36: 7000000 INFO @ Mon, 12 Aug 2019 20:39:37: 7000000 INFO @ Mon, 12 Aug 2019 20:39:41: 8000000 INFO @ Mon, 12 Aug 2019 20:39:44: 8000000 INFO @ Mon, 12 Aug 2019 20:39:45: 8000000 INFO @ Mon, 12 Aug 2019 20:39:48: 9000000 INFO @ Mon, 12 Aug 2019 20:39:51: 9000000 INFO @ Mon, 12 Aug 2019 20:39:52: 9000000 INFO @ Mon, 12 Aug 2019 20:39:55: 10000000 INFO @ Mon, 12 Aug 2019 20:39:58: 10000000 INFO @ Mon, 12 Aug 2019 20:40:00: 10000000 INFO @ Mon, 12 Aug 2019 20:40:02: 11000000 INFO @ Mon, 12 Aug 2019 20:40:05: 11000000 INFO @ Mon, 12 Aug 2019 20:40:07: 11000000 INFO @ Mon, 12 Aug 2019 20:40:08: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 20:40:08: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 20:40:08: #1 total tags in treatment: 11700240 INFO @ Mon, 12 Aug 2019 20:40:08: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:40:08: #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 20:40:08: #1 tags after filtering in treatment: 11700240 INFO @ Mon, 12 Aug 2019 20:40:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:40:08: #1 finished! INFO @ Mon, 12 Aug 2019 20:40:08: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:40:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:40:09: #2 number of paired peaks: 971 WARNING @ Mon, 12 Aug 2019 20:40:09: Fewer paired peaks (971) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 971 pairs to build model! INFO @ Mon, 12 Aug 2019 20:40:09: start model_add_line... INFO @ Mon, 12 Aug 2019 20:40:09: start X-correlation... INFO @ Mon, 12 Aug 2019 20:40:09: end of X-cor INFO @ Mon, 12 Aug 2019 20:40:09: #2 finished! INFO @ Mon, 12 Aug 2019 20:40:09: #2 predicted fragment length is 40 bps INFO @ Mon, 12 Aug 2019 20:40:09: #2 alternative fragment length(s) may be 4,40,524 bps INFO @ Mon, 12 Aug 2019 20:40:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.20_model.r WARNING @ Mon, 12 Aug 2019 20:40:09: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:40:09: #2 You may need to consider one of the other alternative d(s): 4,40,524 WARNING @ Mon, 12 Aug 2019 20:40:09: #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 20:40:09: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:40:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:40:10: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 20:40:10: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 20:40:10: #1 total tags in treatment: 11700240 INFO @ Mon, 12 Aug 2019 20:40:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:40:10: #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 20:40:10: #1 tags after filtering in treatment: 11700240 INFO @ Mon, 12 Aug 2019 20:40:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:40:10: #1 finished! INFO @ Mon, 12 Aug 2019 20:40:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:40:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:40:11: #2 number of paired peaks: 971 WARNING @ Mon, 12 Aug 2019 20:40:11: Fewer paired peaks (971) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 971 pairs to build model! INFO @ Mon, 12 Aug 2019 20:40:11: start model_add_line... INFO @ Mon, 12 Aug 2019 20:40:11: start X-correlation... INFO @ Mon, 12 Aug 2019 20:40:11: end of X-cor INFO @ Mon, 12 Aug 2019 20:40:11: #2 finished! INFO @ Mon, 12 Aug 2019 20:40:11: #2 predicted fragment length is 40 bps INFO @ Mon, 12 Aug 2019 20:40:11: #2 alternative fragment length(s) may be 4,40,524 bps INFO @ Mon, 12 Aug 2019 20:40:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.05_model.r WARNING @ Mon, 12 Aug 2019 20:40:11: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:40:11: #2 You may need to consider one of the other alternative d(s): 4,40,524 WARNING @ Mon, 12 Aug 2019 20:40:11: #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 20:40:11: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:40:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:40:12: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 20:40:12: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 20:40:12: #1 total tags in treatment: 11700240 INFO @ Mon, 12 Aug 2019 20:40:12: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:40:12: #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 20:40:12: #1 tags after filtering in treatment: 11700240 INFO @ Mon, 12 Aug 2019 20:40:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:40:12: #1 finished! INFO @ Mon, 12 Aug 2019 20:40:12: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:40:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:40:13: #2 number of paired peaks: 971 WARNING @ Mon, 12 Aug 2019 20:40:13: Fewer paired peaks (971) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 971 pairs to build model! INFO @ Mon, 12 Aug 2019 20:40:13: start model_add_line... INFO @ Mon, 12 Aug 2019 20:40:13: start X-correlation... INFO @ Mon, 12 Aug 2019 20:40:13: end of X-cor INFO @ Mon, 12 Aug 2019 20:40:13: #2 finished! INFO @ Mon, 12 Aug 2019 20:40:13: #2 predicted fragment length is 40 bps INFO @ Mon, 12 Aug 2019 20:40:13: #2 alternative fragment length(s) may be 4,40,524 bps INFO @ Mon, 12 Aug 2019 20:40:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.10_model.r WARNING @ Mon, 12 Aug 2019 20:40:13: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:40:13: #2 You may need to consider one of the other alternative d(s): 4,40,524 WARNING @ Mon, 12 Aug 2019 20:40:13: #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 20:40:13: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:40:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:40:41: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:40:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:40:46: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:40:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:40:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:40:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.20_summits.bed INFO @ Mon, 12 Aug 2019 20:40:56: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1078 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:40:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:40:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:40:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.05_summits.bed INFO @ Mon, 12 Aug 2019 20:40:59: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3450 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:41:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:41:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:41:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287562/SRX287562.10_summits.bed INFO @ Mon, 12 Aug 2019 20:41:01: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2145 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。