Job ID = 1293621 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,658,678 reads read : 16,658,678 reads written : 16,658,678 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: 00:06:01 16658678 reads; of these: 16658678 (100.00%) were unpaired; of these: 788976 (4.74%) aligned 0 times 11028287 (66.20%) aligned exactly 1 time 4841415 (29.06%) aligned >1 times 95.26% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 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] 1289747 / 15869702 = 0.0813 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 01:06:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.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 01:06:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:06:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:06:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.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 01:06:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:06:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:06:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.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 01:06:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:06:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:06:24: 1000000 INFO @ Mon, 03 Jun 2019 01:06:27: 1000000 INFO @ Mon, 03 Jun 2019 01:06:27: 1000000 INFO @ Mon, 03 Jun 2019 01:06:31: 2000000 INFO @ Mon, 03 Jun 2019 01:06:36: 2000000 INFO @ Mon, 03 Jun 2019 01:06:36: 2000000 INFO @ Mon, 03 Jun 2019 01:06:37: 3000000 INFO @ Mon, 03 Jun 2019 01:06:44: 4000000 INFO @ Mon, 03 Jun 2019 01:06:46: 3000000 INFO @ Mon, 03 Jun 2019 01:06:46: 3000000 INFO @ Mon, 03 Jun 2019 01:06:50: 5000000 INFO @ Mon, 03 Jun 2019 01:06:56: 4000000 INFO @ Mon, 03 Jun 2019 01:06:56: 4000000 INFO @ Mon, 03 Jun 2019 01:06:57: 6000000 INFO @ Mon, 03 Jun 2019 01:07:03: 7000000 INFO @ Mon, 03 Jun 2019 01:07:06: 5000000 INFO @ Mon, 03 Jun 2019 01:07:06: 5000000 INFO @ Mon, 03 Jun 2019 01:07:10: 8000000 INFO @ Mon, 03 Jun 2019 01:07:15: 6000000 INFO @ Mon, 03 Jun 2019 01:07:16: 6000000 INFO @ Mon, 03 Jun 2019 01:07:17: 9000000 INFO @ Mon, 03 Jun 2019 01:07:24: 10000000 INFO @ Mon, 03 Jun 2019 01:07:26: 7000000 INFO @ Mon, 03 Jun 2019 01:07:26: 7000000 INFO @ Mon, 03 Jun 2019 01:07:31: 11000000 INFO @ Mon, 03 Jun 2019 01:07:35: 8000000 INFO @ Mon, 03 Jun 2019 01:07:36: 8000000 INFO @ Mon, 03 Jun 2019 01:07:37: 12000000 INFO @ Mon, 03 Jun 2019 01:07:44: 13000000 INFO @ Mon, 03 Jun 2019 01:07:45: 9000000 INFO @ Mon, 03 Jun 2019 01:07:45: 9000000 INFO @ Mon, 03 Jun 2019 01:07:51: 14000000 INFO @ Mon, 03 Jun 2019 01:07:54: 10000000 INFO @ Mon, 03 Jun 2019 01:07:54: 10000000 INFO @ Mon, 03 Jun 2019 01:07:55: #1 tag size is determined as 33 bps INFO @ Mon, 03 Jun 2019 01:07:55: #1 tag size = 33 INFO @ Mon, 03 Jun 2019 01:07:55: #1 total tags in treatment: 14579955 INFO @ Mon, 03 Jun 2019 01:07:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:07:55: #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 01:07:55: #1 tags after filtering in treatment: 14579955 INFO @ Mon, 03 Jun 2019 01:07:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:07:55: #1 finished! INFO @ Mon, 03 Jun 2019 01:07:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:07:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:07:56: #2 number of paired peaks: 255 WARNING @ Mon, 03 Jun 2019 01:07:56: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Mon, 03 Jun 2019 01:07:56: start model_add_line... INFO @ Mon, 03 Jun 2019 01:07:56: start X-correlation... INFO @ Mon, 03 Jun 2019 01:07:56: end of X-cor INFO @ Mon, 03 Jun 2019 01:07:56: #2 finished! INFO @ Mon, 03 Jun 2019 01:07:56: #2 predicted fragment length is 29 bps INFO @ Mon, 03 Jun 2019 01:07:56: #2 alternative fragment length(s) may be 29 bps INFO @ Mon, 03 Jun 2019 01:07:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.20_model.r WARNING @ Mon, 03 Jun 2019 01:07:56: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:07:56: #2 You may need to consider one of the other alternative d(s): 29 WARNING @ Mon, 03 Jun 2019 01:07:56: #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 01:07:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:07:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:08:03: 11000000 INFO @ Mon, 03 Jun 2019 01:08:04: 11000000 INFO @ Mon, 03 Jun 2019 01:08:12: 12000000 INFO @ Mon, 03 Jun 2019 01:08:14: 12000000 INFO @ Mon, 03 Jun 2019 01:08:21: 13000000 INFO @ Mon, 03 Jun 2019 01:08:24: 13000000 INFO @ Mon, 03 Jun 2019 01:08:30: 14000000 INFO @ Mon, 03 Jun 2019 01:08:34: 14000000 INFO @ Mon, 03 Jun 2019 01:08:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:08:35: #1 tag size is determined as 33 bps INFO @ Mon, 03 Jun 2019 01:08:35: #1 tag size = 33 INFO @ Mon, 03 Jun 2019 01:08:35: #1 total tags in treatment: 14579955 INFO @ Mon, 03 Jun 2019 01:08:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:08:35: #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 01:08:36: #1 tags after filtering in treatment: 14579955 INFO @ Mon, 03 Jun 2019 01:08:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:08:36: #1 finished! INFO @ Mon, 03 Jun 2019 01:08:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:08:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:08:37: #2 number of paired peaks: 255 WARNING @ Mon, 03 Jun 2019 01:08:37: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Mon, 03 Jun 2019 01:08:37: start model_add_line... INFO @ Mon, 03 Jun 2019 01:08:37: start X-correlation... INFO @ Mon, 03 Jun 2019 01:08:37: end of X-cor INFO @ Mon, 03 Jun 2019 01:08:37: #2 finished! INFO @ Mon, 03 Jun 2019 01:08:37: #2 predicted fragment length is 29 bps INFO @ Mon, 03 Jun 2019 01:08:37: #2 alternative fragment length(s) may be 29 bps INFO @ Mon, 03 Jun 2019 01:08:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.05_model.r WARNING @ Mon, 03 Jun 2019 01:08:37: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:08:37: #2 You may need to consider one of the other alternative d(s): 29 WARNING @ Mon, 03 Jun 2019 01:08:37: #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 01:08:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:08:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:08:40: #1 tag size is determined as 33 bps INFO @ Mon, 03 Jun 2019 01:08:40: #1 tag size = 33 INFO @ Mon, 03 Jun 2019 01:08:40: #1 total tags in treatment: 14579955 INFO @ Mon, 03 Jun 2019 01:08:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:08:40: #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 01:08:40: #1 tags after filtering in treatment: 14579955 INFO @ Mon, 03 Jun 2019 01:08:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:08:40: #1 finished! INFO @ Mon, 03 Jun 2019 01:08:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:08:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:08:41: #2 number of paired peaks: 255 WARNING @ Mon, 03 Jun 2019 01:08:41: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Mon, 03 Jun 2019 01:08:41: start model_add_line... INFO @ Mon, 03 Jun 2019 01:08:41: start X-correlation... INFO @ Mon, 03 Jun 2019 01:08:41: end of X-cor INFO @ Mon, 03 Jun 2019 01:08:41: #2 finished! INFO @ Mon, 03 Jun 2019 01:08:41: #2 predicted fragment length is 29 bps INFO @ Mon, 03 Jun 2019 01:08:41: #2 alternative fragment length(s) may be 29 bps INFO @ Mon, 03 Jun 2019 01:08:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.10_model.r WARNING @ Mon, 03 Jun 2019 01:08:41: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:08:41: #2 You may need to consider one of the other alternative d(s): 29 WARNING @ Mon, 03 Jun 2019 01:08:41: #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 01:08:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:08:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:08:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:08:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:08:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.20_summits.bed INFO @ Mon, 03 Jun 2019 01:08:53: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (900 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:09:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:09:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:09:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:09:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:09:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.05_summits.bed INFO @ Mon, 03 Jun 2019 01:09:35: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1856 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:09:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:09:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:09:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032395/SRX1032395.10_summits.bed INFO @ Mon, 03 Jun 2019 01:09:39: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1520 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。