Job ID = 2590628 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,162,813 reads read : 25,162,813 reads written : 25,162,813 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1198780.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: 00:10:02 25162813 reads; of these: 25162813 (100.00%) were unpaired; of these: 1369133 (5.44%) aligned 0 times 16619024 (66.05%) aligned exactly 1 time 7174656 (28.51%) aligned >1 times 94.56% overall alignment rate Time searching: 00:10:02 Overall time: 00:10:02 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 12 files... [bam_rmdupse_core] 5651883 / 23793680 = 0.2375 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 23:03:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.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 23:03:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:03:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:03:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.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 23:03:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:03:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:03:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.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 23:03:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:03:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:03:59: 1000000 INFO @ Mon, 12 Aug 2019 23:03:59: 1000000 INFO @ Mon, 12 Aug 2019 23:04:01: 1000000 INFO @ Mon, 12 Aug 2019 23:04:06: 2000000 INFO @ Mon, 12 Aug 2019 23:04:07: 2000000 INFO @ Mon, 12 Aug 2019 23:04:09: 2000000 INFO @ Mon, 12 Aug 2019 23:04:14: 3000000 INFO @ Mon, 12 Aug 2019 23:04:15: 3000000 INFO @ Mon, 12 Aug 2019 23:04:17: 3000000 INFO @ Mon, 12 Aug 2019 23:04:21: 4000000 INFO @ Mon, 12 Aug 2019 23:04:23: 4000000 INFO @ Mon, 12 Aug 2019 23:04:25: 4000000 INFO @ Mon, 12 Aug 2019 23:04:28: 5000000 INFO @ Mon, 12 Aug 2019 23:04:31: 5000000 INFO @ Mon, 12 Aug 2019 23:04:33: 5000000 INFO @ Mon, 12 Aug 2019 23:04:35: 6000000 INFO @ Mon, 12 Aug 2019 23:04:39: 6000000 INFO @ Mon, 12 Aug 2019 23:04:41: 6000000 INFO @ Mon, 12 Aug 2019 23:04:43: 7000000 INFO @ Mon, 12 Aug 2019 23:04:47: 7000000 INFO @ Mon, 12 Aug 2019 23:04:48: 7000000 INFO @ Mon, 12 Aug 2019 23:04:50: 8000000 INFO @ Mon, 12 Aug 2019 23:04:55: 8000000 INFO @ Mon, 12 Aug 2019 23:04:56: 8000000 INFO @ Mon, 12 Aug 2019 23:04:57: 9000000 INFO @ Mon, 12 Aug 2019 23:05:03: 9000000 INFO @ Mon, 12 Aug 2019 23:05:04: 9000000 INFO @ Mon, 12 Aug 2019 23:05:04: 10000000 INFO @ Mon, 12 Aug 2019 23:05:11: 10000000 INFO @ Mon, 12 Aug 2019 23:05:12: 11000000 INFO @ Mon, 12 Aug 2019 23:05:12: 10000000 INFO @ Mon, 12 Aug 2019 23:05:19: 11000000 INFO @ Mon, 12 Aug 2019 23:05:19: 12000000 INFO @ Mon, 12 Aug 2019 23:05:20: 11000000 INFO @ Mon, 12 Aug 2019 23:05:26: 13000000 INFO @ Mon, 12 Aug 2019 23:05:27: 12000000 INFO @ Mon, 12 Aug 2019 23:05:28: 12000000 INFO @ Mon, 12 Aug 2019 23:05:33: 14000000 INFO @ Mon, 12 Aug 2019 23:05:34: 13000000 INFO @ Mon, 12 Aug 2019 23:05:36: 13000000 INFO @ Mon, 12 Aug 2019 23:05:41: 15000000 INFO @ Mon, 12 Aug 2019 23:05:42: 14000000 INFO @ Mon, 12 Aug 2019 23:05:44: 14000000 INFO @ Mon, 12 Aug 2019 23:05:48: 16000000 INFO @ Mon, 12 Aug 2019 23:05:50: 15000000 INFO @ Mon, 12 Aug 2019 23:05:52: 15000000 INFO @ Mon, 12 Aug 2019 23:05:55: 17000000 INFO @ Mon, 12 Aug 2019 23:05:58: 16000000 INFO @ Mon, 12 Aug 2019 23:06:00: 16000000 INFO @ Mon, 12 Aug 2019 23:06:02: 18000000 INFO @ Mon, 12 Aug 2019 23:06:04: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:06:04: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:06:04: #1 total tags in treatment: 18141797 INFO @ Mon, 12 Aug 2019 23:06:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:06:04: #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 23:06:04: #1 tags after filtering in treatment: 18141797 INFO @ Mon, 12 Aug 2019 23:06:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:06:04: #1 finished! INFO @ Mon, 12 Aug 2019 23:06:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:06:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:06:06: #2 number of paired peaks: 119 WARNING @ Mon, 12 Aug 2019 23:06:06: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Mon, 12 Aug 2019 23:06:06: start model_add_line... INFO @ Mon, 12 Aug 2019 23:06:06: start X-correlation... INFO @ Mon, 12 Aug 2019 23:06:06: end of X-cor INFO @ Mon, 12 Aug 2019 23:06:06: #2 finished! INFO @ Mon, 12 Aug 2019 23:06:06: #2 predicted fragment length is 51 bps INFO @ Mon, 12 Aug 2019 23:06:06: #2 alternative fragment length(s) may be 4,12,51,80,124,217,384,432,456,495,534,572,576 bps INFO @ Mon, 12 Aug 2019 23:06:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.10_model.r WARNING @ Mon, 12 Aug 2019 23:06:06: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:06:06: #2 You may need to consider one of the other alternative d(s): 4,12,51,80,124,217,384,432,456,495,534,572,576 WARNING @ Mon, 12 Aug 2019 23:06:06: #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 23:06:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:06:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:06:06: 17000000 INFO @ Mon, 12 Aug 2019 23:06:07: 17000000 INFO @ Mon, 12 Aug 2019 23:06:14: 18000000 INFO @ Mon, 12 Aug 2019 23:06:15: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:06:15: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:06:15: #1 total tags in treatment: 18141797 INFO @ Mon, 12 Aug 2019 23:06:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:06:15: #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 23:06:15: 18000000 INFO @ Mon, 12 Aug 2019 23:06:15: #1 tags after filtering in treatment: 18141797 INFO @ Mon, 12 Aug 2019 23:06:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:06:15: #1 finished! INFO @ Mon, 12 Aug 2019 23:06:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:06:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:06:16: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:06:16: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:06:16: #1 total tags in treatment: 18141797 INFO @ Mon, 12 Aug 2019 23:06:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:06:16: #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 23:06:17: #1 tags after filtering in treatment: 18141797 INFO @ Mon, 12 Aug 2019 23:06:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:06:17: #1 finished! INFO @ Mon, 12 Aug 2019 23:06:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:06:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:06:17: #2 number of paired peaks: 119 WARNING @ Mon, 12 Aug 2019 23:06:17: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Mon, 12 Aug 2019 23:06:17: start model_add_line... INFO @ Mon, 12 Aug 2019 23:06:17: start X-correlation... INFO @ Mon, 12 Aug 2019 23:06:17: end of X-cor INFO @ Mon, 12 Aug 2019 23:06:17: #2 finished! INFO @ Mon, 12 Aug 2019 23:06:17: #2 predicted fragment length is 51 bps INFO @ Mon, 12 Aug 2019 23:06:17: #2 alternative fragment length(s) may be 4,12,51,80,124,217,384,432,456,495,534,572,576 bps INFO @ Mon, 12 Aug 2019 23:06:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.05_model.r WARNING @ Mon, 12 Aug 2019 23:06:17: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:06:17: #2 You may need to consider one of the other alternative d(s): 4,12,51,80,124,217,384,432,456,495,534,572,576 WARNING @ Mon, 12 Aug 2019 23:06:17: #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 23:06:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:06:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:06:18: #2 number of paired peaks: 119 WARNING @ Mon, 12 Aug 2019 23:06:18: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Mon, 12 Aug 2019 23:06:18: start model_add_line... INFO @ Mon, 12 Aug 2019 23:06:18: start X-correlation... INFO @ Mon, 12 Aug 2019 23:06:18: end of X-cor INFO @ Mon, 12 Aug 2019 23:06:18: #2 finished! INFO @ Mon, 12 Aug 2019 23:06:18: #2 predicted fragment length is 51 bps INFO @ Mon, 12 Aug 2019 23:06:18: #2 alternative fragment length(s) may be 4,12,51,80,124,217,384,432,456,495,534,572,576 bps INFO @ Mon, 12 Aug 2019 23:06:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.20_model.r WARNING @ Mon, 12 Aug 2019 23:06:18: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:06:18: #2 You may need to consider one of the other alternative d(s): 4,12,51,80,124,217,384,432,456,495,534,572,576 WARNING @ Mon, 12 Aug 2019 23:06:18: #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 23:06:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:06:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:06:54: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:07:05: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:07:06: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:07:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:07:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:07:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.10_summits.bed INFO @ Mon, 12 Aug 2019 23:07:18: Done! pass1 - making usageList (10 chroms): 3 millis pass2 - checking and writing primary data (1146 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:07:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:07:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:07:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.05_summits.bed INFO @ Mon, 12 Aug 2019 23:07:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2359 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:07:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:07:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:07:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495275/SRX495275.20_summits.bed INFO @ Mon, 12 Aug 2019 23:07:30: Done! pass1 - making usageList (3 chroms): 2 millis pass2 - checking and writing primary data (165 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。