Job ID = 1294401 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,903,645 reads read : 7,903,645 reads written : 7,903,645 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: 00:05:56 7903645 reads; of these: 7903645 (100.00%) were unpaired; of these: 159111 (2.01%) aligned 0 times 2919113 (36.93%) aligned exactly 1 time 4825421 (61.05%) aligned >1 times 97.99% overall alignment rate Time searching: 00:05:56 Overall time: 00:05:56 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] 1374967 / 7744534 = 0.1775 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 07:22:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.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 07:22:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:22:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:22:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.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 07:22:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:22:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:22:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.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 07:22:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:22:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:22:32: 1000000 INFO @ Mon, 03 Jun 2019 07:22:33: 1000000 INFO @ Mon, 03 Jun 2019 07:22:34: 1000000 INFO @ Mon, 03 Jun 2019 07:22:39: 2000000 INFO @ Mon, 03 Jun 2019 07:22:41: 2000000 INFO @ Mon, 03 Jun 2019 07:22:43: 2000000 INFO @ Mon, 03 Jun 2019 07:22:46: 3000000 INFO @ Mon, 03 Jun 2019 07:22:49: 3000000 INFO @ Mon, 03 Jun 2019 07:22:51: 3000000 INFO @ Mon, 03 Jun 2019 07:22:53: 4000000 INFO @ Mon, 03 Jun 2019 07:22:56: 4000000 INFO @ Mon, 03 Jun 2019 07:22:59: 4000000 INFO @ Mon, 03 Jun 2019 07:23:00: 5000000 INFO @ Mon, 03 Jun 2019 07:23:04: 5000000 INFO @ Mon, 03 Jun 2019 07:23:07: 6000000 INFO @ Mon, 03 Jun 2019 07:23:08: 5000000 INFO @ Mon, 03 Jun 2019 07:23:10: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 07:23:10: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 07:23:10: #1 total tags in treatment: 6369567 INFO @ Mon, 03 Jun 2019 07:23:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:23:10: #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 07:23:10: #1 tags after filtering in treatment: 6369567 INFO @ Mon, 03 Jun 2019 07:23:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:23:10: #1 finished! INFO @ Mon, 03 Jun 2019 07:23:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:23:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:23:11: #2 number of paired peaks: 1390 INFO @ Mon, 03 Jun 2019 07:23:11: start model_add_line... INFO @ Mon, 03 Jun 2019 07:23:11: start X-correlation... INFO @ Mon, 03 Jun 2019 07:23:11: end of X-cor INFO @ Mon, 03 Jun 2019 07:23:11: #2 finished! INFO @ Mon, 03 Jun 2019 07:23:11: #2 predicted fragment length is 58 bps INFO @ Mon, 03 Jun 2019 07:23:11: #2 alternative fragment length(s) may be 58 bps INFO @ Mon, 03 Jun 2019 07:23:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.10_model.r WARNING @ Mon, 03 Jun 2019 07:23:11: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:23:11: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Mon, 03 Jun 2019 07:23:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 07:23:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:23:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:23:12: 6000000 INFO @ Mon, 03 Jun 2019 07:23:15: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 07:23:15: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 07:23:15: #1 total tags in treatment: 6369567 INFO @ Mon, 03 Jun 2019 07:23:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:23:15: #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 07:23:15: #1 tags after filtering in treatment: 6369567 INFO @ Mon, 03 Jun 2019 07:23:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:23:15: #1 finished! INFO @ Mon, 03 Jun 2019 07:23:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:23:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:23:15: #2 number of paired peaks: 1390 INFO @ Mon, 03 Jun 2019 07:23:15: start model_add_line... INFO @ Mon, 03 Jun 2019 07:23:15: start X-correlation... INFO @ Mon, 03 Jun 2019 07:23:15: end of X-cor INFO @ Mon, 03 Jun 2019 07:23:15: #2 finished! INFO @ Mon, 03 Jun 2019 07:23:15: #2 predicted fragment length is 58 bps INFO @ Mon, 03 Jun 2019 07:23:15: #2 alternative fragment length(s) may be 58 bps INFO @ Mon, 03 Jun 2019 07:23:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.05_model.r WARNING @ Mon, 03 Jun 2019 07:23:15: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:23:15: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Mon, 03 Jun 2019 07:23:15: #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 07:23:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:23:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:23:17: 6000000 INFO @ Mon, 03 Jun 2019 07:23:20: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 07:23:20: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 07:23:20: #1 total tags in treatment: 6369567 INFO @ Mon, 03 Jun 2019 07:23:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:23:20: #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 07:23:20: #1 tags after filtering in treatment: 6369567 INFO @ Mon, 03 Jun 2019 07:23:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:23:20: #1 finished! INFO @ Mon, 03 Jun 2019 07:23:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:23:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:23:21: #2 number of paired peaks: 1390 INFO @ Mon, 03 Jun 2019 07:23:21: start model_add_line... INFO @ Mon, 03 Jun 2019 07:23:21: start X-correlation... INFO @ Mon, 03 Jun 2019 07:23:21: end of X-cor INFO @ Mon, 03 Jun 2019 07:23:21: #2 finished! INFO @ Mon, 03 Jun 2019 07:23:21: #2 predicted fragment length is 58 bps INFO @ Mon, 03 Jun 2019 07:23:21: #2 alternative fragment length(s) may be 58 bps INFO @ Mon, 03 Jun 2019 07:23:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.20_model.r WARNING @ Mon, 03 Jun 2019 07:23:21: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:23:21: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Mon, 03 Jun 2019 07:23:21: #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 07:23:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:23:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:23:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:23:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:23:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:23:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:23:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.10_summits.bed INFO @ Mon, 03 Jun 2019 07:23:40: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2417 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:23:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:23:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:23:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:23:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.05_summits.bed INFO @ Mon, 03 Jun 2019 07:23:46: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3791 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:23:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:23:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:23:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287575/SRX287575.20_summits.bed INFO @ Mon, 03 Jun 2019 07:23:50: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1522 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。