Job ID = 9041088 sra ファイルのダウンロード中... Completed: 237643K bytes transferred in 5 seconds (371373K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 20110 0 20110 0 0 2575 0 --:--:-- 0:00:07 --:--:-- 15834 100 47284 0 47284 0 0 5370 0 --:--:-- 0:00:08 --:--:-- 20866 100 47284 0 47284 0 0 5369 0 --:--:-- 0:00:08 --:--:-- 20857 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 24763427 spots for /home/okishinya/chipatlas/results/dm3/SRX1166569/SRR2189037.sra Written 24763427 spots total rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:03:59 24763427 reads; of these: 24763427 (100.00%) were unpaired; of these: 1051241 (4.25%) aligned 0 times 18586030 (75.05%) aligned exactly 1 time 5126156 (20.70%) aligned >1 times 95.75% overall alignment rate Time searching: 00:03:59 Overall time: 00:03:59 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] 13913837 / 23712186 = 0.5868 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, 05 Jun 2017 00:41:50: # Command line: callpeak -t SRX1166569.bam -f BAM -g dm -n SRX1166569.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1166569.10 # format = BAM # ChIP-seq file = ['SRX1166569.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 INFO @ Mon, 05 Jun 2017 00:41:50: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:41:50: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:41:50: # Command line: callpeak -t SRX1166569.bam -f BAM -g dm -n SRX1166569.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1166569.05 # format = BAM # ChIP-seq file = ['SRX1166569.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 INFO @ Mon, 05 Jun 2017 00:41:50: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:41:50: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:41:50: # Command line: callpeak -t SRX1166569.bam -f BAM -g dm -n SRX1166569.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1166569.20 # format = BAM # ChIP-seq file = ['SRX1166569.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 INFO @ Mon, 05 Jun 2017 00:41:50: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:41:50: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:41:55: 1000000 INFO @ Mon, 05 Jun 2017 00:41:55: 1000000 INFO @ Mon, 05 Jun 2017 00:41:55: 1000000 INFO @ Mon, 05 Jun 2017 00:42:00: 2000000 INFO @ Mon, 05 Jun 2017 00:42:00: 2000000 INFO @ Mon, 05 Jun 2017 00:42:01: 2000000 INFO @ Mon, 05 Jun 2017 00:42:06: 3000000 INFO @ Mon, 05 Jun 2017 00:42:06: 3000000 INFO @ Mon, 05 Jun 2017 00:42:07: 3000000 INFO @ Mon, 05 Jun 2017 00:42:12: 4000000 INFO @ Mon, 05 Jun 2017 00:42:12: 4000000 INFO @ Mon, 05 Jun 2017 00:42:14: 4000000 INFO @ Mon, 05 Jun 2017 00:42:17: 5000000 INFO @ Mon, 05 Jun 2017 00:42:17: 5000000 INFO @ Mon, 05 Jun 2017 00:42:20: 5000000 INFO @ Mon, 05 Jun 2017 00:42:23: 6000000 INFO @ Mon, 05 Jun 2017 00:42:23: 6000000 INFO @ Mon, 05 Jun 2017 00:42:26: 6000000 INFO @ Mon, 05 Jun 2017 00:42:28: 7000000 INFO @ Mon, 05 Jun 2017 00:42:28: 7000000 INFO @ Mon, 05 Jun 2017 00:42:32: 7000000 INFO @ Mon, 05 Jun 2017 00:42:34: 8000000 INFO @ Mon, 05 Jun 2017 00:42:34: 8000000 INFO @ Mon, 05 Jun 2017 00:42:38: 8000000 INFO @ Mon, 05 Jun 2017 00:42:40: 9000000 INFO @ Mon, 05 Jun 2017 00:42:40: 9000000 INFO @ Mon, 05 Jun 2017 00:42:44: 9000000 INFO @ Mon, 05 Jun 2017 00:42:44: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 00:42:44: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 00:42:44: #1 total tags in treatment: 9798349 INFO @ Mon, 05 Jun 2017 00:42:44: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:42:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:42:44: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 00:42:44: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 00:42:44: #1 total tags in treatment: 9798349 INFO @ Mon, 05 Jun 2017 00:42:44: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:42:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:42:46: #1 tags after filtering in treatment: 9797294 INFO @ Mon, 05 Jun 2017 00:42:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:42:46: #1 finished! INFO @ Mon, 05 Jun 2017 00:42:46: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:42:46: #1 tags after filtering in treatment: 9797294 INFO @ Mon, 05 Jun 2017 00:42:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:42:46: #1 finished! INFO @ Mon, 05 Jun 2017 00:42:46: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:42:48: #2 number of paired peaks: 358 WARNING @ Mon, 05 Jun 2017 00:42:48: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Mon, 05 Jun 2017 00:42:48: start model_add_line... INFO @ Mon, 05 Jun 2017 00:42:48: #2 number of paired peaks: 358 WARNING @ Mon, 05 Jun 2017 00:42:48: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Mon, 05 Jun 2017 00:42:48: start model_add_line... INFO @ Mon, 05 Jun 2017 00:42:48: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 00:42:48: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 00:42:48: #1 total tags in treatment: 9798349 INFO @ Mon, 05 Jun 2017 00:42:48: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:42:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:42:50: #1 tags after filtering in treatment: 9797294 INFO @ Mon, 05 Jun 2017 00:42:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:42:50: #1 finished! INFO @ Mon, 05 Jun 2017 00:42:50: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:42:50: start X-correlation... INFO @ Mon, 05 Jun 2017 00:42:50: end of X-cor INFO @ Mon, 05 Jun 2017 00:42:50: #2 finished! INFO @ Mon, 05 Jun 2017 00:42:50: #2 predicted fragment length is 47 bps INFO @ Mon, 05 Jun 2017 00:42:50: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 05 Jun 2017 00:42:50: #2.2 Generate R script for model : SRX1166569.10_model.r WARNING @ Mon, 05 Jun 2017 00:42:50: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 00:42:50: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 05 Jun 2017 00:42:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 00:42:50: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:42:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:42:51: start X-correlation... INFO @ Mon, 05 Jun 2017 00:42:51: end of X-cor INFO @ Mon, 05 Jun 2017 00:42:51: #2 finished! INFO @ Mon, 05 Jun 2017 00:42:51: #2 predicted fragment length is 47 bps INFO @ Mon, 05 Jun 2017 00:42:51: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 05 Jun 2017 00:42:51: #2.2 Generate R script for model : SRX1166569.20_model.r WARNING @ Mon, 05 Jun 2017 00:42:51: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 00:42:51: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 05 Jun 2017 00:42:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 00:42:51: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:42:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:42:52: #2 number of paired peaks: 358 WARNING @ Mon, 05 Jun 2017 00:42:52: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Mon, 05 Jun 2017 00:42:52: start model_add_line... INFO @ Mon, 05 Jun 2017 00:42:54: start X-correlation... INFO @ Mon, 05 Jun 2017 00:42:54: end of X-cor INFO @ Mon, 05 Jun 2017 00:42:54: #2 finished! INFO @ Mon, 05 Jun 2017 00:42:54: #2 predicted fragment length is 47 bps INFO @ Mon, 05 Jun 2017 00:42:54: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 05 Jun 2017 00:42:54: #2.2 Generate R script for model : SRX1166569.05_model.r WARNING @ Mon, 05 Jun 2017 00:42:54: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 00:42:54: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 05 Jun 2017 00:42:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 00:42:54: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:42:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:43:41: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:43:43: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:43:46: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:44:22: #4 Write output xls file... SRX1166569.10_peaks.xls INFO @ Mon, 05 Jun 2017 00:44:22: #4 Write peak in narrowPeak format file... SRX1166569.10_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:44:22: #4 Write summits bed file... SRX1166569.10_summits.bed INFO @ Mon, 05 Jun 2017 00:44:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1269 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 00:44:23: #4 Write output xls file... SRX1166569.20_peaks.xls INFO @ Mon, 05 Jun 2017 00:44:23: #4 Write peak in narrowPeak format file... SRX1166569.20_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:44:23: #4 Write summits bed file... SRX1166569.20_summits.bed INFO @ Mon, 05 Jun 2017 00:44:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (792 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 00:44:27: #4 Write output xls file... SRX1166569.05_peaks.xls INFO @ Mon, 05 Jun 2017 00:44:27: #4 Write peak in narrowPeak format file... SRX1166569.05_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:44:27: #4 Write summits bed file... SRX1166569.05_summits.bed INFO @ Mon, 05 Jun 2017 00:44:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1884 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。