Job ID = 1301280 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,543,178 reads read : 10,543,178 reads written : 10,543,178 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: 00:03:10 10543178 reads; of these: 10543178 (100.00%) were unpaired; of these: 1028856 (9.76%) aligned 0 times 8155287 (77.35%) aligned exactly 1 time 1359035 (12.89%) aligned >1 times 90.24% overall alignment rate Time searching: 00:03:10 Overall time: 00:03:10 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] 891167 / 9514322 = 0.0937 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 19:55:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.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 19:55:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:55:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:55:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.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 19:55:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:55:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:55:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.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 19:55:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:55:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:56:05: 1000000 INFO @ Mon, 03 Jun 2019 19:56:05: 1000000 INFO @ Mon, 03 Jun 2019 19:56:07: 1000000 INFO @ Mon, 03 Jun 2019 19:56:17: 2000000 INFO @ Mon, 03 Jun 2019 19:56:17: 2000000 INFO @ Mon, 03 Jun 2019 19:56:20: 2000000 INFO @ Mon, 03 Jun 2019 19:56:29: 3000000 INFO @ Mon, 03 Jun 2019 19:56:30: 3000000 INFO @ Mon, 03 Jun 2019 19:56:33: 3000000 INFO @ Mon, 03 Jun 2019 19:56:40: 4000000 INFO @ Mon, 03 Jun 2019 19:56:42: 4000000 INFO @ Mon, 03 Jun 2019 19:56:46: 4000000 INFO @ Mon, 03 Jun 2019 19:56:52: 5000000 INFO @ Mon, 03 Jun 2019 19:56:54: 5000000 INFO @ Mon, 03 Jun 2019 19:56:59: 5000000 INFO @ Mon, 03 Jun 2019 19:57:03: 6000000 INFO @ Mon, 03 Jun 2019 19:57:07: 6000000 INFO @ Mon, 03 Jun 2019 19:57:12: 6000000 INFO @ Mon, 03 Jun 2019 19:57:15: 7000000 INFO @ Mon, 03 Jun 2019 19:57:20: 7000000 INFO @ Mon, 03 Jun 2019 19:57:24: 7000000 INFO @ Mon, 03 Jun 2019 19:57:27: 8000000 INFO @ Mon, 03 Jun 2019 19:57:32: 8000000 INFO @ Mon, 03 Jun 2019 19:57:35: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:57:35: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:57:35: #1 total tags in treatment: 8623155 INFO @ Mon, 03 Jun 2019 19:57:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:57:35: #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 19:57:35: #1 tags after filtering in treatment: 8623155 INFO @ Mon, 03 Jun 2019 19:57:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:57:35: #1 finished! INFO @ Mon, 03 Jun 2019 19:57:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:57:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:57:36: #2 number of paired peaks: 228 WARNING @ Mon, 03 Jun 2019 19:57:36: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Mon, 03 Jun 2019 19:57:36: start model_add_line... INFO @ Mon, 03 Jun 2019 19:57:36: start X-correlation... INFO @ Mon, 03 Jun 2019 19:57:36: end of X-cor INFO @ Mon, 03 Jun 2019 19:57:36: #2 finished! INFO @ Mon, 03 Jun 2019 19:57:36: #2 predicted fragment length is 216 bps INFO @ Mon, 03 Jun 2019 19:57:36: #2 alternative fragment length(s) may be 4,216,232 bps INFO @ Mon, 03 Jun 2019 19:57:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.10_model.r INFO @ Mon, 03 Jun 2019 19:57:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:57:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:57:36: 8000000 INFO @ Mon, 03 Jun 2019 19:57:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:57:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:57:39: #1 total tags in treatment: 8623155 INFO @ Mon, 03 Jun 2019 19:57:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:57:39: #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 19:57:39: #1 tags after filtering in treatment: 8623155 INFO @ Mon, 03 Jun 2019 19:57:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:57:39: #1 finished! INFO @ Mon, 03 Jun 2019 19:57:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:57:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:57:40: #2 number of paired peaks: 228 WARNING @ Mon, 03 Jun 2019 19:57:40: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Mon, 03 Jun 2019 19:57:40: start model_add_line... INFO @ Mon, 03 Jun 2019 19:57:40: start X-correlation... INFO @ Mon, 03 Jun 2019 19:57:40: end of X-cor INFO @ Mon, 03 Jun 2019 19:57:40: #2 finished! INFO @ Mon, 03 Jun 2019 19:57:40: #2 predicted fragment length is 216 bps INFO @ Mon, 03 Jun 2019 19:57:40: #2 alternative fragment length(s) may be 4,216,232 bps INFO @ Mon, 03 Jun 2019 19:57:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.20_model.r INFO @ Mon, 03 Jun 2019 19:57:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:57:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:57:44: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:57:44: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:57:44: #1 total tags in treatment: 8623155 INFO @ Mon, 03 Jun 2019 19:57:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:57:44: #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 19:57:44: #1 tags after filtering in treatment: 8623155 INFO @ Mon, 03 Jun 2019 19:57:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:57:44: #1 finished! INFO @ Mon, 03 Jun 2019 19:57:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:57:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:57:45: #2 number of paired peaks: 228 WARNING @ Mon, 03 Jun 2019 19:57:45: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Mon, 03 Jun 2019 19:57:45: start model_add_line... INFO @ Mon, 03 Jun 2019 19:57:45: start X-correlation... INFO @ Mon, 03 Jun 2019 19:57:45: end of X-cor INFO @ Mon, 03 Jun 2019 19:57:45: #2 finished! INFO @ Mon, 03 Jun 2019 19:57:45: #2 predicted fragment length is 216 bps INFO @ Mon, 03 Jun 2019 19:57:45: #2 alternative fragment length(s) may be 4,216,232 bps INFO @ Mon, 03 Jun 2019 19:57:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.05_model.r INFO @ Mon, 03 Jun 2019 19:57:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:57:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:58:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:58:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:58:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:58:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:58:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:58:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.10_summits.bed INFO @ Mon, 03 Jun 2019 19:58:14: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (185 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:58:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:58:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:58:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.20_summits.bed INFO @ Mon, 03 Jun 2019 19:58:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (68 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:58:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:58:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:58:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485210/SRX485210.05_summits.bed INFO @ Mon, 03 Jun 2019 19:58:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (428 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。