Job ID = 1294148 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,625,142 reads read : 23,625,142 reads written : 23,625,142 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: 00:09:01 23625142 reads; of these: 23625142 (100.00%) were unpaired; of these: 1330171 (5.63%) aligned 0 times 15349748 (64.97%) aligned exactly 1 time 6945223 (29.40%) aligned >1 times 94.37% overall alignment rate Time searching: 00:09:01 Overall time: 00:09:01 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] 2496001 / 22294971 = 0.1120 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 05:20:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.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 05:20:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.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 05:20:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.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 05:20:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:20:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:20:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:20:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:20:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:20:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:20:57: 1000000 INFO @ Mon, 03 Jun 2019 05:20:57: 1000000 INFO @ Mon, 03 Jun 2019 05:20:57: 1000000 INFO @ Mon, 03 Jun 2019 05:21:05: 2000000 INFO @ Mon, 03 Jun 2019 05:21:05: 2000000 INFO @ Mon, 03 Jun 2019 05:21:05: 2000000 INFO @ Mon, 03 Jun 2019 05:21:14: 3000000 INFO @ Mon, 03 Jun 2019 05:21:14: 3000000 INFO @ Mon, 03 Jun 2019 05:21:14: 3000000 INFO @ Mon, 03 Jun 2019 05:21:22: 4000000 INFO @ Mon, 03 Jun 2019 05:21:22: 4000000 INFO @ Mon, 03 Jun 2019 05:21:22: 4000000 INFO @ Mon, 03 Jun 2019 05:21:31: 5000000 INFO @ Mon, 03 Jun 2019 05:21:31: 5000000 INFO @ Mon, 03 Jun 2019 05:21:31: 5000000 INFO @ Mon, 03 Jun 2019 05:21:39: 6000000 INFO @ Mon, 03 Jun 2019 05:21:39: 6000000 INFO @ Mon, 03 Jun 2019 05:21:39: 6000000 INFO @ Mon, 03 Jun 2019 05:21:47: 7000000 INFO @ Mon, 03 Jun 2019 05:21:48: 7000000 INFO @ Mon, 03 Jun 2019 05:21:48: 7000000 INFO @ Mon, 03 Jun 2019 05:21:56: 8000000 INFO @ Mon, 03 Jun 2019 05:21:56: 8000000 INFO @ Mon, 03 Jun 2019 05:21:56: 8000000 INFO @ Mon, 03 Jun 2019 05:22:04: 9000000 INFO @ Mon, 03 Jun 2019 05:22:04: 9000000 INFO @ Mon, 03 Jun 2019 05:22:04: 9000000 INFO @ Mon, 03 Jun 2019 05:22:12: 10000000 INFO @ Mon, 03 Jun 2019 05:22:13: 10000000 INFO @ Mon, 03 Jun 2019 05:22:13: 10000000 INFO @ Mon, 03 Jun 2019 05:22:21: 11000000 INFO @ Mon, 03 Jun 2019 05:22:21: 11000000 INFO @ Mon, 03 Jun 2019 05:22:21: 11000000 INFO @ Mon, 03 Jun 2019 05:22:29: 12000000 INFO @ Mon, 03 Jun 2019 05:22:29: 12000000 INFO @ Mon, 03 Jun 2019 05:22:29: 12000000 INFO @ Mon, 03 Jun 2019 05:22:38: 13000000 INFO @ Mon, 03 Jun 2019 05:22:38: 13000000 INFO @ Mon, 03 Jun 2019 05:22:38: 13000000 INFO @ Mon, 03 Jun 2019 05:22:45: 14000000 INFO @ Mon, 03 Jun 2019 05:22:45: 14000000 INFO @ Mon, 03 Jun 2019 05:22:45: 14000000 INFO @ Mon, 03 Jun 2019 05:22:52: 15000000 INFO @ Mon, 03 Jun 2019 05:22:52: 15000000 INFO @ Mon, 03 Jun 2019 05:22:53: 15000000 INFO @ Mon, 03 Jun 2019 05:22:58: 16000000 INFO @ Mon, 03 Jun 2019 05:23:00: 16000000 INFO @ Mon, 03 Jun 2019 05:23:00: 16000000 INFO @ Mon, 03 Jun 2019 05:23:05: 17000000 INFO @ Mon, 03 Jun 2019 05:23:07: 17000000 INFO @ Mon, 03 Jun 2019 05:23:07: 17000000 INFO @ Mon, 03 Jun 2019 05:23:12: 18000000 INFO @ Mon, 03 Jun 2019 05:23:14: 18000000 INFO @ Mon, 03 Jun 2019 05:23:14: 18000000 INFO @ Mon, 03 Jun 2019 05:23:19: 19000000 INFO @ Mon, 03 Jun 2019 05:23:21: 19000000 INFO @ Mon, 03 Jun 2019 05:23:21: 19000000 INFO @ Mon, 03 Jun 2019 05:23:24: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:23:24: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:23:24: #1 total tags in treatment: 19798970 INFO @ Mon, 03 Jun 2019 05:23:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:23:24: #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 05:23:25: #1 tags after filtering in treatment: 19798970 INFO @ Mon, 03 Jun 2019 05:23:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:23:25: #1 finished! INFO @ Mon, 03 Jun 2019 05:23:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:23:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:23:26: #2 number of paired peaks: 304 WARNING @ Mon, 03 Jun 2019 05:23:26: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Mon, 03 Jun 2019 05:23:26: start model_add_line... INFO @ Mon, 03 Jun 2019 05:23:27: start X-correlation... INFO @ Mon, 03 Jun 2019 05:23:27: end of X-cor INFO @ Mon, 03 Jun 2019 05:23:27: #2 finished! INFO @ Mon, 03 Jun 2019 05:23:27: #2 predicted fragment length is 65 bps INFO @ Mon, 03 Jun 2019 05:23:27: #2 alternative fragment length(s) may be 4,65,574 bps INFO @ Mon, 03 Jun 2019 05:23:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.20_model.r WARNING @ Mon, 03 Jun 2019 05:23:27: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:23:27: #2 You may need to consider one of the other alternative d(s): 4,65,574 WARNING @ Mon, 03 Jun 2019 05:23:27: #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 05:23:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:23:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:23:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:23:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:23:27: #1 total tags in treatment: 19798970 INFO @ Mon, 03 Jun 2019 05:23:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:23:27: #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 05:23:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:23:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:23:27: #1 total tags in treatment: 19798970 INFO @ Mon, 03 Jun 2019 05:23:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:23:27: #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 05:23:27: #1 tags after filtering in treatment: 19798970 INFO @ Mon, 03 Jun 2019 05:23:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:23:27: #1 finished! INFO @ Mon, 03 Jun 2019 05:23:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:23:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:23:27: #1 tags after filtering in treatment: 19798970 INFO @ Mon, 03 Jun 2019 05:23:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:23:27: #1 finished! INFO @ Mon, 03 Jun 2019 05:23:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:23:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:23:29: #2 number of paired peaks: 304 WARNING @ Mon, 03 Jun 2019 05:23:29: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Mon, 03 Jun 2019 05:23:29: start model_add_line... INFO @ Mon, 03 Jun 2019 05:23:29: #2 number of paired peaks: 304 WARNING @ Mon, 03 Jun 2019 05:23:29: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Mon, 03 Jun 2019 05:23:29: start model_add_line... INFO @ Mon, 03 Jun 2019 05:23:29: start X-correlation... INFO @ Mon, 03 Jun 2019 05:23:29: end of X-cor INFO @ Mon, 03 Jun 2019 05:23:29: #2 finished! INFO @ Mon, 03 Jun 2019 05:23:29: #2 predicted fragment length is 65 bps INFO @ Mon, 03 Jun 2019 05:23:29: #2 alternative fragment length(s) may be 4,65,574 bps INFO @ Mon, 03 Jun 2019 05:23:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.10_model.r INFO @ Mon, 03 Jun 2019 05:23:29: start X-correlation... WARNING @ Mon, 03 Jun 2019 05:23:29: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:23:29: #2 You may need to consider one of the other alternative d(s): 4,65,574 WARNING @ Mon, 03 Jun 2019 05:23:29: #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 05:23:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:23:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:23:29: end of X-cor INFO @ Mon, 03 Jun 2019 05:23:29: #2 finished! INFO @ Mon, 03 Jun 2019 05:23:29: #2 predicted fragment length is 65 bps INFO @ Mon, 03 Jun 2019 05:23:29: #2 alternative fragment length(s) may be 4,65,574 bps INFO @ Mon, 03 Jun 2019 05:23:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.05_model.r WARNING @ Mon, 03 Jun 2019 05:23:29: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:23:29: #2 You may need to consider one of the other alternative d(s): 4,65,574 WARNING @ Mon, 03 Jun 2019 05:23:29: #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 05:23:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:23:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:24:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:24:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:24:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:24:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:24:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:24:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.20_summits.bed INFO @ Mon, 03 Jun 2019 05:24:41: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (846 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:24:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:24:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:24:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.05_summits.bed INFO @ Mon, 03 Jun 2019 05:24:44: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3169 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:24:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:24:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:24:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193326/SRX193326.10_summits.bed INFO @ Mon, 03 Jun 2019 05:24:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2027 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。