Job ID = 1294405 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,172,821 reads read : 19,172,821 reads written : 19,172,821 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: 00:08:45 19172821 reads; of these: 19172821 (100.00%) were unpaired; of these: 728086 (3.80%) aligned 0 times 12514184 (65.27%) aligned exactly 1 time 5930551 (30.93%) aligned >1 times 96.20% overall alignment rate Time searching: 00:08:45 Overall time: 00:08:45 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] 2854592 / 18444735 = 0.1548 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 07:39:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.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 07:39:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:39:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:39:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.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 07:39:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:39:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:39:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.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 07:39:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:39:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:39:39: 1000000 INFO @ Mon, 03 Jun 2019 07:39:39: 1000000 INFO @ Mon, 03 Jun 2019 07:39:40: 1000000 INFO @ Mon, 03 Jun 2019 07:39:47: 2000000 INFO @ Mon, 03 Jun 2019 07:39:47: 2000000 INFO @ Mon, 03 Jun 2019 07:39:49: 2000000 INFO @ Mon, 03 Jun 2019 07:39:55: 3000000 INFO @ Mon, 03 Jun 2019 07:39:55: 3000000 INFO @ Mon, 03 Jun 2019 07:39:58: 3000000 INFO @ Mon, 03 Jun 2019 07:40:03: 4000000 INFO @ Mon, 03 Jun 2019 07:40:03: 4000000 INFO @ Mon, 03 Jun 2019 07:40:07: 4000000 INFO @ Mon, 03 Jun 2019 07:40:11: 5000000 INFO @ Mon, 03 Jun 2019 07:40:11: 5000000 INFO @ Mon, 03 Jun 2019 07:40:16: 5000000 INFO @ Mon, 03 Jun 2019 07:40:19: 6000000 INFO @ Mon, 03 Jun 2019 07:40:19: 6000000 INFO @ Mon, 03 Jun 2019 07:40:25: 6000000 INFO @ Mon, 03 Jun 2019 07:40:27: 7000000 INFO @ Mon, 03 Jun 2019 07:40:27: 7000000 INFO @ Mon, 03 Jun 2019 07:40:34: 7000000 INFO @ Mon, 03 Jun 2019 07:40:35: 8000000 INFO @ Mon, 03 Jun 2019 07:40:35: 8000000 INFO @ Mon, 03 Jun 2019 07:40:43: 8000000 INFO @ Mon, 03 Jun 2019 07:40:43: 9000000 INFO @ Mon, 03 Jun 2019 07:40:44: 9000000 INFO @ Mon, 03 Jun 2019 07:40:51: 10000000 INFO @ Mon, 03 Jun 2019 07:40:51: 10000000 INFO @ Mon, 03 Jun 2019 07:40:52: 9000000 INFO @ Mon, 03 Jun 2019 07:40:59: 11000000 INFO @ Mon, 03 Jun 2019 07:40:59: 11000000 INFO @ Mon, 03 Jun 2019 07:41:01: 10000000 INFO @ Mon, 03 Jun 2019 07:41:07: 12000000 INFO @ Mon, 03 Jun 2019 07:41:07: 12000000 INFO @ Mon, 03 Jun 2019 07:41:10: 11000000 INFO @ Mon, 03 Jun 2019 07:41:15: 13000000 INFO @ Mon, 03 Jun 2019 07:41:15: 13000000 INFO @ Mon, 03 Jun 2019 07:41:19: 12000000 INFO @ Mon, 03 Jun 2019 07:41:23: 14000000 INFO @ Mon, 03 Jun 2019 07:41:23: 14000000 INFO @ Mon, 03 Jun 2019 07:41:28: 13000000 INFO @ Mon, 03 Jun 2019 07:41:31: 15000000 INFO @ Mon, 03 Jun 2019 07:41:31: 15000000 INFO @ Mon, 03 Jun 2019 07:41:36: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:41:36: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:41:36: #1 total tags in treatment: 15590143 INFO @ Mon, 03 Jun 2019 07:41:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:41:36: #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 07:41:36: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:41:36: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:41:36: #1 total tags in treatment: 15590143 INFO @ Mon, 03 Jun 2019 07:41:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:41:36: #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 07:41:36: #1 tags after filtering in treatment: 15590143 INFO @ Mon, 03 Jun 2019 07:41:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:41:36: #1 finished! INFO @ Mon, 03 Jun 2019 07:41:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:41:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:41:36: #1 tags after filtering in treatment: 15590143 INFO @ Mon, 03 Jun 2019 07:41:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:41:36: #1 finished! INFO @ Mon, 03 Jun 2019 07:41:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:41:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:41:37: 14000000 INFO @ Mon, 03 Jun 2019 07:41:37: #2 number of paired peaks: 258 WARNING @ Mon, 03 Jun 2019 07:41:37: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Mon, 03 Jun 2019 07:41:37: start model_add_line... INFO @ Mon, 03 Jun 2019 07:41:37: start X-correlation... INFO @ Mon, 03 Jun 2019 07:41:37: end of X-cor INFO @ Mon, 03 Jun 2019 07:41:37: #2 finished! INFO @ Mon, 03 Jun 2019 07:41:37: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 07:41:37: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 07:41:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.05_model.r WARNING @ Mon, 03 Jun 2019 07:41:37: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:41:37: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 07:41:37: #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 07:41:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:41:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:41:38: #2 number of paired peaks: 258 WARNING @ Mon, 03 Jun 2019 07:41:38: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Mon, 03 Jun 2019 07:41:38: start model_add_line... INFO @ Mon, 03 Jun 2019 07:41:38: start X-correlation... INFO @ Mon, 03 Jun 2019 07:41:38: end of X-cor INFO @ Mon, 03 Jun 2019 07:41:38: #2 finished! INFO @ Mon, 03 Jun 2019 07:41:38: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 07:41:38: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 07:41:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.10_model.r WARNING @ Mon, 03 Jun 2019 07:41:38: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:41:38: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 07:41:38: #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 07:41:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:41:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:41:45: 15000000 INFO @ Mon, 03 Jun 2019 07:41:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:41:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:41:50: #1 total tags in treatment: 15590143 INFO @ Mon, 03 Jun 2019 07:41:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:41:50: #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 07:41:51: #1 tags after filtering in treatment: 15590143 INFO @ Mon, 03 Jun 2019 07:41:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:41:51: #1 finished! INFO @ Mon, 03 Jun 2019 07:41:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:41:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:41:52: #2 number of paired peaks: 258 WARNING @ Mon, 03 Jun 2019 07:41:52: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Mon, 03 Jun 2019 07:41:52: start model_add_line... INFO @ Mon, 03 Jun 2019 07:41:52: start X-correlation... INFO @ Mon, 03 Jun 2019 07:41:52: end of X-cor INFO @ Mon, 03 Jun 2019 07:41:52: #2 finished! INFO @ Mon, 03 Jun 2019 07:41:52: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 07:41:52: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 07:41:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.20_model.r WARNING @ Mon, 03 Jun 2019 07:41:52: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:41:52: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 07:41:52: #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 07:41:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:41:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:42:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:42:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:42:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:42:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:42:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:42:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.10_summits.bed INFO @ Mon, 03 Jun 2019 07:42:38: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1648 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:42:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:42:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:42:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.05_summits.bed INFO @ Mon, 03 Jun 2019 07:42:38: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1975 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:42:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:42:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:42:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287579/SRX287579.20_summits.bed INFO @ Mon, 03 Jun 2019 07:42:53: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1258 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。