Job ID = 1293269 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,462,340 reads read : 23,462,340 reads written : 23,462,340 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:51 23462340 reads; of these: 23462340 (100.00%) were unpaired; of these: 638318 (2.72%) aligned 0 times 16734139 (71.32%) aligned exactly 1 time 6089883 (25.96%) aligned >1 times 97.28% overall alignment rate Time searching: 00:07:52 Overall time: 00:07:52 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] 5352342 / 22824022 = 0.2345 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 @ Sun, 02 Jun 2019 22:58:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.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 @ Sun, 02 Jun 2019 22:58:37: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:58:37: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:58:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.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 @ Sun, 02 Jun 2019 22:58:37: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:58:37: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:58:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.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 @ Sun, 02 Jun 2019 22:58:37: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:58:37: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:58:46: 1000000 INFO @ Sun, 02 Jun 2019 22:58:46: 1000000 INFO @ Sun, 02 Jun 2019 22:58:47: 1000000 INFO @ Sun, 02 Jun 2019 22:58:54: 2000000 INFO @ Sun, 02 Jun 2019 22:58:54: 2000000 INFO @ Sun, 02 Jun 2019 22:58:57: 2000000 INFO @ Sun, 02 Jun 2019 22:59:02: 3000000 INFO @ Sun, 02 Jun 2019 22:59:02: 3000000 INFO @ Sun, 02 Jun 2019 22:59:06: 3000000 INFO @ Sun, 02 Jun 2019 22:59:10: 4000000 INFO @ Sun, 02 Jun 2019 22:59:10: 4000000 INFO @ Sun, 02 Jun 2019 22:59:16: 4000000 INFO @ Sun, 02 Jun 2019 22:59:18: 5000000 INFO @ Sun, 02 Jun 2019 22:59:18: 5000000 INFO @ Sun, 02 Jun 2019 22:59:25: 5000000 INFO @ Sun, 02 Jun 2019 22:59:26: 6000000 INFO @ Sun, 02 Jun 2019 22:59:26: 6000000 INFO @ Sun, 02 Jun 2019 22:59:34: 7000000 INFO @ Sun, 02 Jun 2019 22:59:35: 7000000 INFO @ Sun, 02 Jun 2019 22:59:35: 6000000 INFO @ Sun, 02 Jun 2019 22:59:42: 8000000 INFO @ Sun, 02 Jun 2019 22:59:43: 8000000 INFO @ Sun, 02 Jun 2019 22:59:44: 7000000 INFO @ Sun, 02 Jun 2019 22:59:50: 9000000 INFO @ Sun, 02 Jun 2019 22:59:51: 9000000 INFO @ Sun, 02 Jun 2019 22:59:54: 8000000 INFO @ Sun, 02 Jun 2019 22:59:58: 10000000 INFO @ Sun, 02 Jun 2019 23:00:00: 10000000 INFO @ Sun, 02 Jun 2019 23:00:04: 9000000 INFO @ Sun, 02 Jun 2019 23:00:06: 11000000 INFO @ Sun, 02 Jun 2019 23:00:08: 11000000 INFO @ Sun, 02 Jun 2019 23:00:13: 10000000 INFO @ Sun, 02 Jun 2019 23:00:13: 12000000 INFO @ Sun, 02 Jun 2019 23:00:16: 12000000 INFO @ Sun, 02 Jun 2019 23:00:21: 13000000 INFO @ Sun, 02 Jun 2019 23:00:22: 11000000 INFO @ Sun, 02 Jun 2019 23:00:24: 13000000 INFO @ Sun, 02 Jun 2019 23:00:29: 14000000 INFO @ Sun, 02 Jun 2019 23:00:32: 12000000 INFO @ Sun, 02 Jun 2019 23:00:33: 14000000 INFO @ Sun, 02 Jun 2019 23:00:37: 15000000 INFO @ Sun, 02 Jun 2019 23:00:40: 13000000 INFO @ Sun, 02 Jun 2019 23:00:41: 15000000 INFO @ Sun, 02 Jun 2019 23:00:45: 16000000 INFO @ Sun, 02 Jun 2019 23:00:49: 16000000 INFO @ Sun, 02 Jun 2019 23:00:49: 14000000 INFO @ Sun, 02 Jun 2019 23:00:52: 17000000 INFO @ Sun, 02 Jun 2019 23:00:56: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:00:56: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:00:56: #1 total tags in treatment: 17471680 INFO @ Sun, 02 Jun 2019 23:00:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:00:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:00:57: #1 tags after filtering in treatment: 17471680 INFO @ Sun, 02 Jun 2019 23:00:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:00:57: #1 finished! INFO @ Sun, 02 Jun 2019 23:00:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:00:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:00:57: 17000000 INFO @ Sun, 02 Jun 2019 23:00:58: #2 number of paired peaks: 104 WARNING @ Sun, 02 Jun 2019 23:00:58: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Sun, 02 Jun 2019 23:00:58: start model_add_line... INFO @ Sun, 02 Jun 2019 23:00:58: start X-correlation... INFO @ Sun, 02 Jun 2019 23:00:58: end of X-cor INFO @ Sun, 02 Jun 2019 23:00:58: #2 finished! INFO @ Sun, 02 Jun 2019 23:00:58: #2 predicted fragment length is 30 bps INFO @ Sun, 02 Jun 2019 23:00:58: #2 alternative fragment length(s) may be 30 bps INFO @ Sun, 02 Jun 2019 23:00:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.10_model.r WARNING @ Sun, 02 Jun 2019 23:00:58: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:00:58: #2 You may need to consider one of the other alternative d(s): 30 WARNING @ Sun, 02 Jun 2019 23:00:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:00:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:00:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:00:58: 15000000 INFO @ Sun, 02 Jun 2019 23:01:01: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:01:01: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:01:01: #1 total tags in treatment: 17471680 INFO @ Sun, 02 Jun 2019 23:01:01: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:01:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:01:01: #1 tags after filtering in treatment: 17471680 INFO @ Sun, 02 Jun 2019 23:01:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:01:01: #1 finished! INFO @ Sun, 02 Jun 2019 23:01:01: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:01:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:01:03: #2 number of paired peaks: 104 WARNING @ Sun, 02 Jun 2019 23:01:03: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Sun, 02 Jun 2019 23:01:03: start model_add_line... INFO @ Sun, 02 Jun 2019 23:01:03: start X-correlation... INFO @ Sun, 02 Jun 2019 23:01:03: end of X-cor INFO @ Sun, 02 Jun 2019 23:01:03: #2 finished! INFO @ Sun, 02 Jun 2019 23:01:03: #2 predicted fragment length is 30 bps INFO @ Sun, 02 Jun 2019 23:01:03: #2 alternative fragment length(s) may be 30 bps INFO @ Sun, 02 Jun 2019 23:01:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.20_model.r WARNING @ Sun, 02 Jun 2019 23:01:03: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:01:03: #2 You may need to consider one of the other alternative d(s): 30 WARNING @ Sun, 02 Jun 2019 23:01:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:01:03: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:01:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:01:07: 16000000 INFO @ Sun, 02 Jun 2019 23:01:15: 17000000 INFO @ Sun, 02 Jun 2019 23:01:19: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:01:19: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:01:19: #1 total tags in treatment: 17471680 INFO @ Sun, 02 Jun 2019 23:01:19: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:01:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:01:19: #1 tags after filtering in treatment: 17471680 INFO @ Sun, 02 Jun 2019 23:01:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:01:20: #1 finished! INFO @ Sun, 02 Jun 2019 23:01:20: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:01:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:01:21: #2 number of paired peaks: 104 WARNING @ Sun, 02 Jun 2019 23:01:21: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Sun, 02 Jun 2019 23:01:21: start model_add_line... INFO @ Sun, 02 Jun 2019 23:01:21: start X-correlation... INFO @ Sun, 02 Jun 2019 23:01:21: end of X-cor INFO @ Sun, 02 Jun 2019 23:01:21: #2 finished! INFO @ Sun, 02 Jun 2019 23:01:21: #2 predicted fragment length is 30 bps INFO @ Sun, 02 Jun 2019 23:01:21: #2 alternative fragment length(s) may be 30 bps INFO @ Sun, 02 Jun 2019 23:01:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.05_model.r WARNING @ Sun, 02 Jun 2019 23:01:21: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:01:21: #2 You may need to consider one of the other alternative d(s): 30 WARNING @ Sun, 02 Jun 2019 23:01:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:01:21: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:01:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:01:42: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:01:47: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:02:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:02:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:02:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.10_summits.bed INFO @ Sun, 02 Jun 2019 23:02:04: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1456 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:02:05: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:02:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:02:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:02:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.20_summits.bed INFO @ Sun, 02 Jun 2019 23:02:09: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (739 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:02:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:02:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:02:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011408/ERX011408.05_summits.bed INFO @ Sun, 02 Jun 2019 23:02:27: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2420 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。