Job ID = 2590315 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,127,616 reads read : 18,127,616 reads written : 18,127,616 rm: cannot remove ‘[DSE]RR*’: 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: 00:09:04 18127616 reads; of these: 18127616 (100.00%) were unpaired; of these: 720384 (3.97%) aligned 0 times 10742543 (59.26%) aligned exactly 1 time 6664689 (36.77%) aligned >1 times 96.03% overall alignment rate Time searching: 00:09:04 Overall time: 00:09:04 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] 3067092 / 17407232 = 0.1762 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, 12 Aug 2019 21:00:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.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, 12 Aug 2019 21:00:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:00:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:00:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.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, 12 Aug 2019 21:00:19: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:00:19: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:00:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.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, 12 Aug 2019 21:00:20: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:00:20: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:00:26: 1000000 INFO @ Mon, 12 Aug 2019 21:00:28: 1000000 INFO @ Mon, 12 Aug 2019 21:00:28: 1000000 INFO @ Mon, 12 Aug 2019 21:00:34: 2000000 INFO @ Mon, 12 Aug 2019 21:00:36: 2000000 INFO @ Mon, 12 Aug 2019 21:00:37: 2000000 INFO @ Mon, 12 Aug 2019 21:00:42: 3000000 INFO @ Mon, 12 Aug 2019 21:00:45: 3000000 INFO @ Mon, 12 Aug 2019 21:00:45: 3000000 INFO @ Mon, 12 Aug 2019 21:00:50: 4000000 INFO @ Mon, 12 Aug 2019 21:00:53: 4000000 INFO @ Mon, 12 Aug 2019 21:00:53: 4000000 INFO @ Mon, 12 Aug 2019 21:00:59: 5000000 INFO @ Mon, 12 Aug 2019 21:01:01: 5000000 INFO @ Mon, 12 Aug 2019 21:01:02: 5000000 INFO @ Mon, 12 Aug 2019 21:01:07: 6000000 INFO @ Mon, 12 Aug 2019 21:01:10: 6000000 INFO @ Mon, 12 Aug 2019 21:01:11: 6000000 INFO @ Mon, 12 Aug 2019 21:01:16: 7000000 INFO @ Mon, 12 Aug 2019 21:01:18: 7000000 INFO @ Mon, 12 Aug 2019 21:01:20: 7000000 INFO @ Mon, 12 Aug 2019 21:01:24: 8000000 INFO @ Mon, 12 Aug 2019 21:01:26: 8000000 INFO @ Mon, 12 Aug 2019 21:01:29: 8000000 INFO @ Mon, 12 Aug 2019 21:01:32: 9000000 INFO @ Mon, 12 Aug 2019 21:01:35: 9000000 INFO @ Mon, 12 Aug 2019 21:01:37: 9000000 INFO @ Mon, 12 Aug 2019 21:01:41: 10000000 INFO @ Mon, 12 Aug 2019 21:01:43: 10000000 INFO @ Mon, 12 Aug 2019 21:01:46: 10000000 INFO @ Mon, 12 Aug 2019 21:01:49: 11000000 INFO @ Mon, 12 Aug 2019 21:01:51: 11000000 INFO @ Mon, 12 Aug 2019 21:01:55: 11000000 INFO @ Mon, 12 Aug 2019 21:01:57: 12000000 INFO @ Mon, 12 Aug 2019 21:02:00: 12000000 INFO @ Mon, 12 Aug 2019 21:02:03: 12000000 INFO @ Mon, 12 Aug 2019 21:02:06: 13000000 INFO @ Mon, 12 Aug 2019 21:02:08: 13000000 INFO @ Mon, 12 Aug 2019 21:02:12: 13000000 INFO @ Mon, 12 Aug 2019 21:02:14: 14000000 INFO @ Mon, 12 Aug 2019 21:02:16: 14000000 INFO @ Mon, 12 Aug 2019 21:02:17: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:02:17: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:02:17: #1 total tags in treatment: 14340140 INFO @ Mon, 12 Aug 2019 21:02:17: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:02:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:02:17: #1 tags after filtering in treatment: 14340140 INFO @ Mon, 12 Aug 2019 21:02:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:02:17: #1 finished! INFO @ Mon, 12 Aug 2019 21:02:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:02:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:02:19: #2 number of paired peaks: 791 WARNING @ Mon, 12 Aug 2019 21:02:19: Fewer paired peaks (791) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 791 pairs to build model! INFO @ Mon, 12 Aug 2019 21:02:19: start model_add_line... INFO @ Mon, 12 Aug 2019 21:02:19: start X-correlation... INFO @ Mon, 12 Aug 2019 21:02:19: end of X-cor INFO @ Mon, 12 Aug 2019 21:02:19: #2 finished! INFO @ Mon, 12 Aug 2019 21:02:19: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 21:02:19: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 12 Aug 2019 21:02:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.05_model.r WARNING @ Mon, 12 Aug 2019 21:02:19: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:02:19: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 12 Aug 2019 21:02:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 21:02:19: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:02:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:02:19: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:02:19: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:02:19: #1 total tags in treatment: 14340140 INFO @ Mon, 12 Aug 2019 21:02:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:02:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:02:19: #1 tags after filtering in treatment: 14340140 INFO @ Mon, 12 Aug 2019 21:02:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:02:19: #1 finished! INFO @ Mon, 12 Aug 2019 21:02:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:02:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:02:21: #2 number of paired peaks: 791 WARNING @ Mon, 12 Aug 2019 21:02:21: Fewer paired peaks (791) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 791 pairs to build model! INFO @ Mon, 12 Aug 2019 21:02:21: start model_add_line... INFO @ Mon, 12 Aug 2019 21:02:21: 14000000 INFO @ Mon, 12 Aug 2019 21:02:21: start X-correlation... INFO @ Mon, 12 Aug 2019 21:02:21: end of X-cor INFO @ Mon, 12 Aug 2019 21:02:21: #2 finished! INFO @ Mon, 12 Aug 2019 21:02:21: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 21:02:21: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 12 Aug 2019 21:02:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.20_model.r WARNING @ Mon, 12 Aug 2019 21:02:21: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:02:21: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 12 Aug 2019 21:02:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 21:02:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:02:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:02:24: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:02:24: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:02:24: #1 total tags in treatment: 14340140 INFO @ Mon, 12 Aug 2019 21:02:24: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:02:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:02:24: #1 tags after filtering in treatment: 14340140 INFO @ Mon, 12 Aug 2019 21:02:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:02:24: #1 finished! INFO @ Mon, 12 Aug 2019 21:02:24: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:02:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:02:25: #2 number of paired peaks: 791 WARNING @ Mon, 12 Aug 2019 21:02:25: Fewer paired peaks (791) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 791 pairs to build model! INFO @ Mon, 12 Aug 2019 21:02:25: start model_add_line... INFO @ Mon, 12 Aug 2019 21:02:26: start X-correlation... INFO @ Mon, 12 Aug 2019 21:02:26: end of X-cor INFO @ Mon, 12 Aug 2019 21:02:26: #2 finished! INFO @ Mon, 12 Aug 2019 21:02:26: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 21:02:26: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 12 Aug 2019 21:02:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.10_model.r WARNING @ Mon, 12 Aug 2019 21:02:26: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:02:26: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 12 Aug 2019 21:02:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 21:02:26: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:02:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:02:57: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:02:59: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:03:04: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:03:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:03:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:03:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.05_summits.bed INFO @ Mon, 12 Aug 2019 21:03:16: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3445 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:03:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:03:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:03:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.20_summits.bed INFO @ Mon, 12 Aug 2019 21:03:18: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1626 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:03:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:03:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:03:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331421/SRX331421.10_summits.bed INFO @ Mon, 12 Aug 2019 21:03:23: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2615 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。