Job ID = 2590626 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,892,168 reads read : 18,892,168 reads written : 18,892,168 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1198774.sra.cache’: 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 18892168 reads; of these: 18892168 (100.00%) were unpaired; of these: 2120381 (11.22%) aligned 0 times 12078502 (63.93%) aligned exactly 1 time 4693285 (24.84%) aligned >1 times 88.78% 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3854618 / 16771787 = 0.2298 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 22:56:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.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 22:56:41: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:56:41: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:56:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.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 22:56:42: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:56:42: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:56:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.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 22:56:43: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:56:43: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:56:49: 1000000 INFO @ Mon, 12 Aug 2019 22:56:51: 1000000 INFO @ Mon, 12 Aug 2019 22:56:53: 1000000 INFO @ Mon, 12 Aug 2019 22:56:56: 2000000 INFO @ Mon, 12 Aug 2019 22:56:59: 2000000 INFO @ Mon, 12 Aug 2019 22:57:02: 2000000 INFO @ Mon, 12 Aug 2019 22:57:03: 3000000 INFO @ Mon, 12 Aug 2019 22:57:07: 3000000 INFO @ Mon, 12 Aug 2019 22:57:11: 4000000 INFO @ Mon, 12 Aug 2019 22:57:11: 3000000 INFO @ Mon, 12 Aug 2019 22:57:15: 4000000 INFO @ Mon, 12 Aug 2019 22:57:18: 5000000 INFO @ Mon, 12 Aug 2019 22:57:20: 4000000 INFO @ Mon, 12 Aug 2019 22:57:23: 5000000 INFO @ Mon, 12 Aug 2019 22:57:25: 6000000 INFO @ Mon, 12 Aug 2019 22:57:30: 5000000 INFO @ Mon, 12 Aug 2019 22:57:31: 6000000 INFO @ Mon, 12 Aug 2019 22:57:32: 7000000 INFO @ Mon, 12 Aug 2019 22:57:39: 6000000 INFO @ Mon, 12 Aug 2019 22:57:39: 7000000 INFO @ Mon, 12 Aug 2019 22:57:40: 8000000 INFO @ Mon, 12 Aug 2019 22:57:47: 9000000 INFO @ Mon, 12 Aug 2019 22:57:47: 8000000 INFO @ Mon, 12 Aug 2019 22:57:48: 7000000 INFO @ Mon, 12 Aug 2019 22:57:54: 10000000 INFO @ Mon, 12 Aug 2019 22:57:55: 9000000 INFO @ Mon, 12 Aug 2019 22:57:57: 8000000 INFO @ Mon, 12 Aug 2019 22:58:01: 11000000 INFO @ Mon, 12 Aug 2019 22:58:03: 10000000 INFO @ Mon, 12 Aug 2019 22:58:06: 9000000 INFO @ Mon, 12 Aug 2019 22:58:08: 12000000 INFO @ Mon, 12 Aug 2019 22:58:11: 11000000 INFO @ Mon, 12 Aug 2019 22:58:15: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:58:15: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:58:15: #1 total tags in treatment: 12917169 INFO @ Mon, 12 Aug 2019 22:58:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:58:15: #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 22:58:15: #1 tags after filtering in treatment: 12917169 INFO @ Mon, 12 Aug 2019 22:58:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:58:15: #1 finished! INFO @ Mon, 12 Aug 2019 22:58:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:58:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:58:16: 10000000 INFO @ Mon, 12 Aug 2019 22:58:17: #2 number of paired peaks: 407 WARNING @ Mon, 12 Aug 2019 22:58:17: Fewer paired peaks (407) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 407 pairs to build model! INFO @ Mon, 12 Aug 2019 22:58:17: start model_add_line... INFO @ Mon, 12 Aug 2019 22:58:17: start X-correlation... INFO @ Mon, 12 Aug 2019 22:58:17: end of X-cor INFO @ Mon, 12 Aug 2019 22:58:17: #2 finished! INFO @ Mon, 12 Aug 2019 22:58:17: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 22:58:17: #2 alternative fragment length(s) may be 3,11,45,505,585 bps INFO @ Mon, 12 Aug 2019 22:58:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.05_model.r WARNING @ Mon, 12 Aug 2019 22:58:17: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:58:17: #2 You may need to consider one of the other alternative d(s): 3,11,45,505,585 WARNING @ Mon, 12 Aug 2019 22:58:17: #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 22:58:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:58:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:58:19: 12000000 INFO @ Mon, 12 Aug 2019 22:58:25: 11000000 INFO @ Mon, 12 Aug 2019 22:58:27: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:58:27: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:58:27: #1 total tags in treatment: 12917169 INFO @ Mon, 12 Aug 2019 22:58:27: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:58:27: #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 22:58:27: #1 tags after filtering in treatment: 12917169 INFO @ Mon, 12 Aug 2019 22:58:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:58:27: #1 finished! INFO @ Mon, 12 Aug 2019 22:58:27: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:58:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:58:28: #2 number of paired peaks: 407 WARNING @ Mon, 12 Aug 2019 22:58:28: Fewer paired peaks (407) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 407 pairs to build model! INFO @ Mon, 12 Aug 2019 22:58:28: start model_add_line... INFO @ Mon, 12 Aug 2019 22:58:28: start X-correlation... INFO @ Mon, 12 Aug 2019 22:58:28: end of X-cor INFO @ Mon, 12 Aug 2019 22:58:28: #2 finished! INFO @ Mon, 12 Aug 2019 22:58:28: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 22:58:28: #2 alternative fragment length(s) may be 3,11,45,505,585 bps INFO @ Mon, 12 Aug 2019 22:58:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.10_model.r WARNING @ Mon, 12 Aug 2019 22:58:28: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:58:28: #2 You may need to consider one of the other alternative d(s): 3,11,45,505,585 WARNING @ Mon, 12 Aug 2019 22:58:28: #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 22:58:28: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:58:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:58:34: 12000000 INFO @ Mon, 12 Aug 2019 22:58:42: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:58:42: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:58:42: #1 total tags in treatment: 12917169 INFO @ Mon, 12 Aug 2019 22:58:42: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:58:42: #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 22:58:43: #1 tags after filtering in treatment: 12917169 INFO @ Mon, 12 Aug 2019 22:58:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:58:43: #1 finished! INFO @ Mon, 12 Aug 2019 22:58:43: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:58:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:58:44: #2 number of paired peaks: 407 WARNING @ Mon, 12 Aug 2019 22:58:44: Fewer paired peaks (407) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 407 pairs to build model! INFO @ Mon, 12 Aug 2019 22:58:44: start model_add_line... INFO @ Mon, 12 Aug 2019 22:58:44: start X-correlation... INFO @ Mon, 12 Aug 2019 22:58:44: end of X-cor INFO @ Mon, 12 Aug 2019 22:58:44: #2 finished! INFO @ Mon, 12 Aug 2019 22:58:44: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 22:58:44: #2 alternative fragment length(s) may be 3,11,45,505,585 bps INFO @ Mon, 12 Aug 2019 22:58:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.20_model.r WARNING @ Mon, 12 Aug 2019 22:58:44: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:58:44: #2 You may need to consider one of the other alternative d(s): 3,11,45,505,585 WARNING @ Mon, 12 Aug 2019 22:58:44: #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 22:58:44: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:58:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:58:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:59:03: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:59:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:59:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:59:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.05_summits.bed INFO @ Mon, 12 Aug 2019 22:59:09: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2523 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:59:19: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:59:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:59:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:59:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.10_summits.bed INFO @ Mon, 12 Aug 2019 22:59:21: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1213 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:59:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:59:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:59:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495269/SRX495269.20_summits.bed INFO @ Mon, 12 Aug 2019 22:59:36: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (220 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。