Job ID = 1308141 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,568,287 reads read : 33,136,574 reads written : 16,568,287 reads 0-length : 16,568,287 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: 00:06:51 16568287 reads; of these: 16568287 (100.00%) were unpaired; of these: 2680243 (16.18%) aligned 0 times 10964854 (66.18%) aligned exactly 1 time 2923190 (17.64%) aligned >1 times 83.82% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 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] 4430332 / 13888044 = 0.3190 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 22:55:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.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 22:55:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:55:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:55:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.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 22:55:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:55:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:55:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.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 22:55:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:55:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:55:48: 1000000 INFO @ Mon, 03 Jun 2019 22:55:49: 1000000 INFO @ Mon, 03 Jun 2019 22:55:49: 1000000 INFO @ Mon, 03 Jun 2019 22:55:59: 2000000 INFO @ Mon, 03 Jun 2019 22:56:01: 2000000 INFO @ Mon, 03 Jun 2019 22:56:01: 2000000 INFO @ Mon, 03 Jun 2019 22:56:09: 3000000 INFO @ Mon, 03 Jun 2019 22:56:13: 3000000 INFO @ Mon, 03 Jun 2019 22:56:13: 3000000 INFO @ Mon, 03 Jun 2019 22:56:20: 4000000 INFO @ Mon, 03 Jun 2019 22:56:24: 4000000 INFO @ Mon, 03 Jun 2019 22:56:25: 4000000 INFO @ Mon, 03 Jun 2019 22:56:30: 5000000 INFO @ Mon, 03 Jun 2019 22:56:36: 5000000 INFO @ Mon, 03 Jun 2019 22:56:36: 5000000 INFO @ Mon, 03 Jun 2019 22:56:41: 6000000 INFO @ Mon, 03 Jun 2019 22:56:48: 6000000 INFO @ Mon, 03 Jun 2019 22:56:48: 6000000 INFO @ Mon, 03 Jun 2019 22:56:53: 7000000 INFO @ Mon, 03 Jun 2019 22:57:00: 7000000 INFO @ Mon, 03 Jun 2019 22:57:00: 7000000 INFO @ Mon, 03 Jun 2019 22:57:04: 8000000 INFO @ Mon, 03 Jun 2019 22:57:11: 8000000 INFO @ Mon, 03 Jun 2019 22:57:12: 8000000 INFO @ Mon, 03 Jun 2019 22:57:14: 9000000 INFO @ Mon, 03 Jun 2019 22:57:19: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:57:19: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:57:19: #1 total tags in treatment: 9457712 INFO @ Mon, 03 Jun 2019 22:57:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:57:19: #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 22:57:19: #1 tags after filtering in treatment: 9457712 INFO @ Mon, 03 Jun 2019 22:57:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:57:19: #1 finished! INFO @ Mon, 03 Jun 2019 22:57:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:57:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:57:20: #2 number of paired peaks: 355 WARNING @ Mon, 03 Jun 2019 22:57:20: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Mon, 03 Jun 2019 22:57:20: start model_add_line... INFO @ Mon, 03 Jun 2019 22:57:21: start X-correlation... INFO @ Mon, 03 Jun 2019 22:57:21: end of X-cor INFO @ Mon, 03 Jun 2019 22:57:21: #2 finished! INFO @ Mon, 03 Jun 2019 22:57:21: #2 predicted fragment length is 76 bps INFO @ Mon, 03 Jun 2019 22:57:21: #2 alternative fragment length(s) may be 76 bps INFO @ Mon, 03 Jun 2019 22:57:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.05_model.r WARNING @ Mon, 03 Jun 2019 22:57:21: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:57:21: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Mon, 03 Jun 2019 22:57:21: #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 22:57:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:57:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:57:23: 9000000 INFO @ Mon, 03 Jun 2019 22:57:24: 9000000 INFO @ Mon, 03 Jun 2019 22:57:28: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:57:28: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:57:28: #1 total tags in treatment: 9457712 INFO @ Mon, 03 Jun 2019 22:57:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:57:28: #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 22:57:29: #1 tags after filtering in treatment: 9457712 INFO @ Mon, 03 Jun 2019 22:57:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:57:29: #1 finished! INFO @ Mon, 03 Jun 2019 22:57:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:57:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:57:30: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:57:30: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:57:30: #1 total tags in treatment: 9457712 INFO @ Mon, 03 Jun 2019 22:57:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:57:30: #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 22:57:30: #2 number of paired peaks: 355 WARNING @ Mon, 03 Jun 2019 22:57:30: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Mon, 03 Jun 2019 22:57:30: start model_add_line... INFO @ Mon, 03 Jun 2019 22:57:30: start X-correlation... INFO @ Mon, 03 Jun 2019 22:57:30: end of X-cor INFO @ Mon, 03 Jun 2019 22:57:30: #2 finished! INFO @ Mon, 03 Jun 2019 22:57:30: #2 predicted fragment length is 76 bps INFO @ Mon, 03 Jun 2019 22:57:30: #2 alternative fragment length(s) may be 76 bps INFO @ Mon, 03 Jun 2019 22:57:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.20_model.r WARNING @ Mon, 03 Jun 2019 22:57:30: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:57:30: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Mon, 03 Jun 2019 22:57:30: #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 22:57:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:57:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:57:30: #1 tags after filtering in treatment: 9457712 INFO @ Mon, 03 Jun 2019 22:57:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:57:30: #1 finished! INFO @ Mon, 03 Jun 2019 22:57:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:57:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:57:31: #2 number of paired peaks: 355 WARNING @ Mon, 03 Jun 2019 22:57:31: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Mon, 03 Jun 2019 22:57:31: start model_add_line... INFO @ Mon, 03 Jun 2019 22:57:31: start X-correlation... INFO @ Mon, 03 Jun 2019 22:57:31: end of X-cor INFO @ Mon, 03 Jun 2019 22:57:31: #2 finished! INFO @ Mon, 03 Jun 2019 22:57:31: #2 predicted fragment length is 76 bps INFO @ Mon, 03 Jun 2019 22:57:31: #2 alternative fragment length(s) may be 76 bps INFO @ Mon, 03 Jun 2019 22:57:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.10_model.r WARNING @ Mon, 03 Jun 2019 22:57:31: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:57:31: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Mon, 03 Jun 2019 22:57:31: #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 22:57:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:57:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:57:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:57:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:58:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:58:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:58:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:58:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.05_summits.bed INFO @ Mon, 03 Jun 2019 22:58:05: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3329 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:58:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:58:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:58:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.20_summits.bed INFO @ Mon, 03 Jun 2019 22:58:14: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (746 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:58:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:58:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:58:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343132/SRX5343132.10_summits.bed INFO @ Mon, 03 Jun 2019 22:58:15: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1430 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。