Job ID = 10043504 sra ファイルのダウンロード中... Completed: 1476208K bytes transferred in 30 seconds (396849K bits/sec), in 2 files, 3 directories. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 17863221 spots for /home/okishinya/chipatlas/results/dm3/SRX2165286/SRR4244802.sra Written 17863221 spots total Written 21199238 spots for /home/okishinya/chipatlas/results/dm3/SRX2165286/SRR4244801.sra Written 21199238 spots total 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: 00:16:28 39062459 reads; of these: 39062459 (100.00%) were unpaired; of these: 5916453 (15.15%) aligned 0 times 23373381 (59.84%) aligned exactly 1 time 9772625 (25.02%) aligned >1 times 84.85% overall alignment rate Time searching: 00:16:28 Overall time: 00:16:28 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 16 files... [bam_rmdupse_core] 15336506 / 33146006 = 0.4627 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, 02 Oct 2017 03:54:43: # Command line: callpeak -t SRX2165286.bam -f BAM -g dm -n SRX2165286.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2165286.10 # format = BAM # ChIP-seq file = ['SRX2165286.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, 02 Oct 2017 03:54:43: # Command line: callpeak -t SRX2165286.bam -f BAM -g dm -n SRX2165286.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2165286.05 # format = BAM # ChIP-seq file = ['SRX2165286.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, 02 Oct 2017 03:54:43: # Command line: callpeak -t SRX2165286.bam -f BAM -g dm -n SRX2165286.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2165286.20 # format = BAM # ChIP-seq file = ['SRX2165286.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, 02 Oct 2017 03:54:43: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:54:43: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:54:43: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:54:43: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:54:43: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:54:43: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:54:51: 1000000 INFO @ Mon, 02 Oct 2017 03:54:51: 1000000 INFO @ Mon, 02 Oct 2017 03:54:52: 1000000 INFO @ Mon, 02 Oct 2017 03:54:59: 2000000 INFO @ Mon, 02 Oct 2017 03:54:59: 2000000 INFO @ Mon, 02 Oct 2017 03:55:00: 2000000 INFO @ Mon, 02 Oct 2017 03:55:07: 3000000 INFO @ Mon, 02 Oct 2017 03:55:08: 3000000 INFO @ Mon, 02 Oct 2017 03:55:08: 3000000 INFO @ Mon, 02 Oct 2017 03:55:14: 4000000 INFO @ Mon, 02 Oct 2017 03:55:16: 4000000 INFO @ Mon, 02 Oct 2017 03:55:16: 4000000 INFO @ Mon, 02 Oct 2017 03:55:22: 5000000 INFO @ Mon, 02 Oct 2017 03:55:25: 5000000 INFO @ Mon, 02 Oct 2017 03:55:25: 5000000 INFO @ Mon, 02 Oct 2017 03:55:29: 6000000 INFO @ Mon, 02 Oct 2017 03:55:33: 6000000 INFO @ Mon, 02 Oct 2017 03:55:34: 6000000 INFO @ Mon, 02 Oct 2017 03:55:36: 7000000 INFO @ Mon, 02 Oct 2017 03:55:42: 7000000 INFO @ Mon, 02 Oct 2017 03:55:42: 7000000 INFO @ Mon, 02 Oct 2017 03:55:43: 8000000 INFO @ Mon, 02 Oct 2017 03:55:51: 8000000 INFO @ Mon, 02 Oct 2017 03:55:51: 8000000 INFO @ Mon, 02 Oct 2017 03:55:51: 9000000 INFO @ Mon, 02 Oct 2017 03:55:58: 10000000 INFO @ Mon, 02 Oct 2017 03:55:59: 9000000 INFO @ Mon, 02 Oct 2017 03:55:59: 9000000 INFO @ Mon, 02 Oct 2017 03:56:05: 11000000 INFO @ Mon, 02 Oct 2017 03:56:08: 10000000 INFO @ Mon, 02 Oct 2017 03:56:08: 10000000 INFO @ Mon, 02 Oct 2017 03:56:12: 12000000 INFO @ Mon, 02 Oct 2017 03:56:16: 11000000 INFO @ Mon, 02 Oct 2017 03:56:17: 11000000 INFO @ Mon, 02 Oct 2017 03:56:20: 13000000 INFO @ Mon, 02 Oct 2017 03:56:25: 12000000 INFO @ Mon, 02 Oct 2017 03:56:25: 12000000 INFO @ Mon, 02 Oct 2017 03:56:27: 14000000 INFO @ Mon, 02 Oct 2017 03:56:34: 13000000 INFO @ Mon, 02 Oct 2017 03:56:34: 13000000 INFO @ Mon, 02 Oct 2017 03:56:34: 15000000 INFO @ Mon, 02 Oct 2017 03:56:42: 16000000 INFO @ Mon, 02 Oct 2017 03:56:42: 14000000 INFO @ Mon, 02 Oct 2017 03:56:43: 14000000 INFO @ Mon, 02 Oct 2017 03:56:50: 17000000 INFO @ Mon, 02 Oct 2017 03:56:52: 15000000 INFO @ Mon, 02 Oct 2017 03:56:53: 15000000 INFO @ Mon, 02 Oct 2017 03:56:56: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 03:56:56: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 03:56:56: #1 total tags in treatment: 17809500 INFO @ Mon, 02 Oct 2017 03:56:56: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:56:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 03:56:56: #1 tags after filtering in treatment: 17809500 INFO @ Mon, 02 Oct 2017 03:56:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:56:56: #1 finished! INFO @ Mon, 02 Oct 2017 03:56:56: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:56:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:56:57: #2 number of paired peaks: 241 WARNING @ Mon, 02 Oct 2017 03:56:57: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Mon, 02 Oct 2017 03:56:57: start model_add_line... INFO @ Mon, 02 Oct 2017 03:56:58: start X-correlation... INFO @ Mon, 02 Oct 2017 03:56:58: end of X-cor INFO @ Mon, 02 Oct 2017 03:56:58: #2 finished! INFO @ Mon, 02 Oct 2017 03:56:58: #2 predicted fragment length is 68 bps INFO @ Mon, 02 Oct 2017 03:56:58: #2 alternative fragment length(s) may be 68 bps INFO @ Mon, 02 Oct 2017 03:56:58: #2.2 Generate R script for model : SRX2165286.10_model.r WARNING @ Mon, 02 Oct 2017 03:56:58: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 03:56:58: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Mon, 02 Oct 2017 03:56:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 02 Oct 2017 03:56:58: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:56:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:57:01: 16000000 INFO @ Mon, 02 Oct 2017 03:57:02: 16000000 INFO @ Mon, 02 Oct 2017 03:57:10: 17000000 INFO @ Mon, 02 Oct 2017 03:57:12: 17000000 INFO @ Mon, 02 Oct 2017 03:57:18: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 03:57:18: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 03:57:18: #1 total tags in treatment: 17809500 INFO @ Mon, 02 Oct 2017 03:57:18: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:57:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 03:57:18: #1 tags after filtering in treatment: 17809500 INFO @ Mon, 02 Oct 2017 03:57:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:57:18: #1 finished! INFO @ Mon, 02 Oct 2017 03:57:18: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:57:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:57:19: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 03:57:19: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 03:57:19: #1 total tags in treatment: 17809500 INFO @ Mon, 02 Oct 2017 03:57:19: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:57:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 03:57:20: #1 tags after filtering in treatment: 17809500 INFO @ Mon, 02 Oct 2017 03:57:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:57:20: #1 finished! INFO @ Mon, 02 Oct 2017 03:57:20: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:57:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:57:20: #2 number of paired peaks: 241 WARNING @ Mon, 02 Oct 2017 03:57:20: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Mon, 02 Oct 2017 03:57:20: start model_add_line... INFO @ Mon, 02 Oct 2017 03:57:20: start X-correlation... INFO @ Mon, 02 Oct 2017 03:57:20: end of X-cor INFO @ Mon, 02 Oct 2017 03:57:20: #2 finished! INFO @ Mon, 02 Oct 2017 03:57:20: #2 predicted fragment length is 68 bps INFO @ Mon, 02 Oct 2017 03:57:20: #2 alternative fragment length(s) may be 68 bps INFO @ Mon, 02 Oct 2017 03:57:20: #2.2 Generate R script for model : SRX2165286.20_model.r WARNING @ Mon, 02 Oct 2017 03:57:20: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 03:57:20: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Mon, 02 Oct 2017 03:57:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 02 Oct 2017 03:57:20: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:57:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:57:21: #2 number of paired peaks: 241 WARNING @ Mon, 02 Oct 2017 03:57:21: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Mon, 02 Oct 2017 03:57:21: start model_add_line... INFO @ Mon, 02 Oct 2017 03:57:21: start X-correlation... INFO @ Mon, 02 Oct 2017 03:57:21: end of X-cor INFO @ Mon, 02 Oct 2017 03:57:21: #2 finished! INFO @ Mon, 02 Oct 2017 03:57:21: #2 predicted fragment length is 68 bps INFO @ Mon, 02 Oct 2017 03:57:21: #2 alternative fragment length(s) may be 68 bps INFO @ Mon, 02 Oct 2017 03:57:21: #2.2 Generate R script for model : SRX2165286.05_model.r WARNING @ Mon, 02 Oct 2017 03:57:21: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 03:57:21: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Mon, 02 Oct 2017 03:57:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 02 Oct 2017 03:57:21: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:57:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:57:34: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 03:57:54: #4 Write output xls file... SRX2165286.10_peaks.xls INFO @ Mon, 02 Oct 2017 03:57:54: #4 Write peak in narrowPeak format file... SRX2165286.10_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 03:57:54: #4 Write summits bed file... SRX2165286.10_summits.bed INFO @ Mon, 02 Oct 2017 03:57:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2100 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 02 Oct 2017 03:57:56: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 03:57:59: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 03:58:18: #4 Write output xls file... SRX2165286.05_peaks.xls INFO @ Mon, 02 Oct 2017 03:58:18: #4 Write peak in narrowPeak format file... SRX2165286.05_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 03:58:18: #4 Write summits bed file... SRX2165286.05_summits.bed INFO @ Mon, 02 Oct 2017 03:58:18: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3730 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 02 Oct 2017 03:58:20: #4 Write output xls file... SRX2165286.20_peaks.xls INFO @ Mon, 02 Oct 2017 03:58:20: #4 Write peak in narrowPeak format file... SRX2165286.20_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 03:58:20: #4 Write summits bed file... SRX2165286.20_summits.bed INFO @ Mon, 02 Oct 2017 03:58:20: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1199 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。