Job ID = 1293888 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 88,628,439 reads read : 88,628,439 reads written : 88,628,439 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: 00:13:35 88628439 reads; of these: 88628439 (100.00%) were unpaired; of these: 70217328 (79.23%) aligned 0 times 13228144 (14.93%) aligned exactly 1 time 5182967 (5.85%) aligned >1 times 20.77% overall alignment rate Time searching: 00:13:35 Overall time: 00:13:35 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 8 files... [bam_rmdupse_core] 11833682 / 18411111 = 0.6427 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 03:22:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.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 03:22:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.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 03:22:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:22:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:22:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:22:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:22:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.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 03:22:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:22:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:22:09: 1000000 INFO @ Mon, 03 Jun 2019 03:22:10: 1000000 INFO @ Mon, 03 Jun 2019 03:22:12: 1000000 INFO @ Mon, 03 Jun 2019 03:22:16: 2000000 INFO @ Mon, 03 Jun 2019 03:22:17: 2000000 INFO @ Mon, 03 Jun 2019 03:22:21: 2000000 INFO @ Mon, 03 Jun 2019 03:22:22: 3000000 INFO @ Mon, 03 Jun 2019 03:22:24: 3000000 INFO @ Mon, 03 Jun 2019 03:22:29: 4000000 INFO @ Mon, 03 Jun 2019 03:22:30: 3000000 INFO @ Mon, 03 Jun 2019 03:22:32: 4000000 INFO @ Mon, 03 Jun 2019 03:22:36: 5000000 INFO @ Mon, 03 Jun 2019 03:22:39: 5000000 INFO @ Mon, 03 Jun 2019 03:22:39: 4000000 INFO @ Mon, 03 Jun 2019 03:22:42: 6000000 INFO @ Mon, 03 Jun 2019 03:22:46: 6000000 INFO @ Mon, 03 Jun 2019 03:22:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:22:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:22:46: #1 total tags in treatment: 6577429 INFO @ Mon, 03 Jun 2019 03:22:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:22:46: #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 03:22:46: #1 tags after filtering in treatment: 6577429 INFO @ Mon, 03 Jun 2019 03:22:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:22:46: #1 finished! INFO @ Mon, 03 Jun 2019 03:22:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:22:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:22:47: #2 number of paired peaks: 113 WARNING @ Mon, 03 Jun 2019 03:22:47: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Mon, 03 Jun 2019 03:22:47: start model_add_line... INFO @ Mon, 03 Jun 2019 03:22:47: start X-correlation... INFO @ Mon, 03 Jun 2019 03:22:47: end of X-cor INFO @ Mon, 03 Jun 2019 03:22:47: #2 finished! INFO @ Mon, 03 Jun 2019 03:22:47: #2 predicted fragment length is 59 bps INFO @ Mon, 03 Jun 2019 03:22:47: #2 alternative fragment length(s) may be 59 bps INFO @ Mon, 03 Jun 2019 03:22:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.05_model.r WARNING @ Mon, 03 Jun 2019 03:22:47: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:22:47: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Mon, 03 Jun 2019 03:22:47: #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 03:22:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:22:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:22:47: 5000000 INFO @ Mon, 03 Jun 2019 03:22:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:22:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:22:50: #1 total tags in treatment: 6577429 INFO @ Mon, 03 Jun 2019 03:22:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:22:50: #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 03:22:50: #1 tags after filtering in treatment: 6577429 INFO @ Mon, 03 Jun 2019 03:22:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:22:50: #1 finished! INFO @ Mon, 03 Jun 2019 03:22:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:22:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:22:50: #2 number of paired peaks: 113 WARNING @ Mon, 03 Jun 2019 03:22:50: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Mon, 03 Jun 2019 03:22:50: start model_add_line... INFO @ Mon, 03 Jun 2019 03:22:50: start X-correlation... INFO @ Mon, 03 Jun 2019 03:22:50: end of X-cor INFO @ Mon, 03 Jun 2019 03:22:50: #2 finished! INFO @ Mon, 03 Jun 2019 03:22:50: #2 predicted fragment length is 59 bps INFO @ Mon, 03 Jun 2019 03:22:50: #2 alternative fragment length(s) may be 59 bps INFO @ Mon, 03 Jun 2019 03:22:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.10_model.r WARNING @ Mon, 03 Jun 2019 03:22:50: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:22:50: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Mon, 03 Jun 2019 03:22:50: #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 03:22:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:22:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:22:55: 6000000 INFO @ Mon, 03 Jun 2019 03:23:00: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:23:00: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:23:00: #1 total tags in treatment: 6577429 INFO @ Mon, 03 Jun 2019 03:23:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:23:00: #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 03:23:00: #1 tags after filtering in treatment: 6577429 INFO @ Mon, 03 Jun 2019 03:23:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:23:00: #1 finished! INFO @ Mon, 03 Jun 2019 03:23:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:23:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:23:01: #2 number of paired peaks: 113 WARNING @ Mon, 03 Jun 2019 03:23:01: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Mon, 03 Jun 2019 03:23:01: start model_add_line... INFO @ Mon, 03 Jun 2019 03:23:01: start X-correlation... INFO @ Mon, 03 Jun 2019 03:23:01: end of X-cor INFO @ Mon, 03 Jun 2019 03:23:01: #2 finished! INFO @ Mon, 03 Jun 2019 03:23:01: #2 predicted fragment length is 59 bps INFO @ Mon, 03 Jun 2019 03:23:01: #2 alternative fragment length(s) may be 59 bps INFO @ Mon, 03 Jun 2019 03:23:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.20_model.r WARNING @ Mon, 03 Jun 2019 03:23:01: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:23:01: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Mon, 03 Jun 2019 03:23:01: #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 03:23:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:23:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:23:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:23:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:23:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:23:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:23:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.05_summits.bed INFO @ Mon, 03 Jun 2019 03:23:15: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1347 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:23:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:23:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:23:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.10_summits.bed INFO @ Mon, 03 Jun 2019 03:23:19: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (406 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:23:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:23:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:23:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:23:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX135530/SRX135530.20_summits.bed INFO @ Mon, 03 Jun 2019 03:23:30: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (207 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。