Job ID = 1293853 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,849,176 reads read : 12,849,176 reads written : 12,849,176 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: 00:04:53 12849176 reads; of these: 12849176 (100.00%) were unpaired; of these: 4180203 (32.53%) aligned 0 times 4657495 (36.25%) aligned exactly 1 time 4011478 (31.22%) aligned >1 times 67.47% overall alignment rate Time searching: 00:04:53 Overall time: 00:04:53 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] 2403391 / 8668973 = 0.2772 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 02:54:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.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 02:54:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:54:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:54:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.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 02:54:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:54:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:54:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.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 02:54:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:54:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:54:33: 1000000 INFO @ Mon, 03 Jun 2019 02:54:33: 1000000 INFO @ Mon, 03 Jun 2019 02:54:33: 1000000 INFO @ Mon, 03 Jun 2019 02:54:40: 2000000 INFO @ Mon, 03 Jun 2019 02:54:41: 2000000 INFO @ Mon, 03 Jun 2019 02:54:41: 2000000 INFO @ Mon, 03 Jun 2019 02:54:48: 3000000 INFO @ Mon, 03 Jun 2019 02:54:49: 3000000 INFO @ Mon, 03 Jun 2019 02:54:49: 3000000 INFO @ Mon, 03 Jun 2019 02:54:56: 4000000 INFO @ Mon, 03 Jun 2019 02:54:57: 4000000 INFO @ Mon, 03 Jun 2019 02:54:57: 4000000 INFO @ Mon, 03 Jun 2019 02:55:04: 5000000 INFO @ Mon, 03 Jun 2019 02:55:04: 5000000 INFO @ Mon, 03 Jun 2019 02:55:05: 5000000 INFO @ Mon, 03 Jun 2019 02:55:12: 6000000 INFO @ Mon, 03 Jun 2019 02:55:13: 6000000 INFO @ Mon, 03 Jun 2019 02:55:13: 6000000 INFO @ Mon, 03 Jun 2019 02:55:14: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 02:55:14: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 02:55:14: #1 total tags in treatment: 6265582 INFO @ Mon, 03 Jun 2019 02:55:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:55:14: #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 02:55:14: #1 tags after filtering in treatment: 6265582 INFO @ Mon, 03 Jun 2019 02:55:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:55:14: #1 finished! INFO @ Mon, 03 Jun 2019 02:55:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:55:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:55:15: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 02:55:15: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 02:55:15: #1 total tags in treatment: 6265582 INFO @ Mon, 03 Jun 2019 02:55:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:55:15: #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 02:55:15: #2 number of paired peaks: 1055 INFO @ Mon, 03 Jun 2019 02:55:15: start model_add_line... INFO @ Mon, 03 Jun 2019 02:55:15: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 02:55:15: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 02:55:15: #1 total tags in treatment: 6265582 INFO @ Mon, 03 Jun 2019 02:55:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:55:15: #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 02:55:15: #1 tags after filtering in treatment: 6265582 INFO @ Mon, 03 Jun 2019 02:55:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:55:15: #1 finished! INFO @ Mon, 03 Jun 2019 02:55:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:55:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:55:15: start X-correlation... INFO @ Mon, 03 Jun 2019 02:55:15: end of X-cor INFO @ Mon, 03 Jun 2019 02:55:15: #2 finished! INFO @ Mon, 03 Jun 2019 02:55:15: #2 predicted fragment length is 63 bps INFO @ Mon, 03 Jun 2019 02:55:15: #2 alternative fragment length(s) may be 63 bps INFO @ Mon, 03 Jun 2019 02:55:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.10_model.r WARNING @ Mon, 03 Jun 2019 02:55:15: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:55:15: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Mon, 03 Jun 2019 02:55:15: #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 02:55:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:55:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:55:15: #1 tags after filtering in treatment: 6265582 INFO @ Mon, 03 Jun 2019 02:55:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:55:15: #1 finished! INFO @ Mon, 03 Jun 2019 02:55:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:55:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:55:16: #2 number of paired peaks: 1055 INFO @ Mon, 03 Jun 2019 02:55:16: start model_add_line... INFO @ Mon, 03 Jun 2019 02:55:16: start X-correlation... INFO @ Mon, 03 Jun 2019 02:55:16: end of X-cor INFO @ Mon, 03 Jun 2019 02:55:16: #2 finished! INFO @ Mon, 03 Jun 2019 02:55:16: #2 predicted fragment length is 63 bps INFO @ Mon, 03 Jun 2019 02:55:16: #2 alternative fragment length(s) may be 63 bps INFO @ Mon, 03 Jun 2019 02:55:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.05_model.r INFO @ Mon, 03 Jun 2019 02:55:16: #2 number of paired peaks: 1055 INFO @ Mon, 03 Jun 2019 02:55:16: start model_add_line... WARNING @ Mon, 03 Jun 2019 02:55:16: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:55:16: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Mon, 03 Jun 2019 02:55:16: #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 02:55:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:55:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:55:16: start X-correlation... INFO @ Mon, 03 Jun 2019 02:55:16: end of X-cor INFO @ Mon, 03 Jun 2019 02:55:16: #2 finished! INFO @ Mon, 03 Jun 2019 02:55:16: #2 predicted fragment length is 63 bps INFO @ Mon, 03 Jun 2019 02:55:16: #2 alternative fragment length(s) may be 63 bps INFO @ Mon, 03 Jun 2019 02:55:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.20_model.r WARNING @ Mon, 03 Jun 2019 02:55:16: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:55:16: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Mon, 03 Jun 2019 02:55:16: #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 02:55:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:55:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:55:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:55:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:55:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:55:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:55:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:55:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.10_summits.bed INFO @ Mon, 03 Jun 2019 02:55:43: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1206 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:55:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:55:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:55:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.20_summits.bed INFO @ Mon, 03 Jun 2019 02:55:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:55:44: Done! INFO @ Mon, 03 Jun 2019 02:55:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:55:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299932/SRX1299932.05_summits.bed INFO @ Mon, 03 Jun 2019 02:55:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (764 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1988 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。