Job ID = 9029328 sra ファイルのダウンロード中... Completed: 81400K bytes transferred in 3 seconds (180838K 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 --:--:-- 0 101 5455 0 5455 0 0 753 0 --:--:-- 0:00:07 --:--:-- 7693 100 27350 0 27350 0 0 3321 0 --:--:-- 0:00:08 --:--:-- 16050 100 53097 0 53097 0 0 5967 0 --:--:-- 0:00:08 --:--:-- 22422 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 2684317 spots for /home/okishinya/chipatlas/results/dm3/SRX1561069/SRR3145072.sra Written 2684317 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:48 2684317 reads; of these: 2684317 (100.00%) were unpaired; of these: 232406 (8.66%) aligned 0 times 2072608 (77.21%) aligned exactly 1 time 379303 (14.13%) aligned >1 times 91.34% overall alignment rate Time searching: 00:00:49 Overall time: 00:00:49 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_rmdupse_core] 180172 / 2451911 = 0.0735 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 @ Sat, 03 Jun 2017 13:15:03: # Command line: callpeak -t SRX1561069.bam -f BAM -g dm -n SRX1561069.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1561069.10 # format = BAM # ChIP-seq file = ['SRX1561069.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 @ Sat, 03 Jun 2017 13:15:03: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:15:03: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:15:03: # Command line: callpeak -t SRX1561069.bam -f BAM -g dm -n SRX1561069.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1561069.20 # format = BAM # ChIP-seq file = ['SRX1561069.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 @ Sat, 03 Jun 2017 13:15:03: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:15:03: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:15:03: # Command line: callpeak -t SRX1561069.bam -f BAM -g dm -n SRX1561069.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1561069.05 # format = BAM # ChIP-seq file = ['SRX1561069.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 @ Sat, 03 Jun 2017 13:15:03: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:15:03: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:15:09: 1000000 INFO @ Sat, 03 Jun 2017 13:15:10: 1000000 INFO @ Sat, 03 Jun 2017 13:15:10: 1000000 INFO @ Sat, 03 Jun 2017 13:15:16: 2000000 INFO @ Sat, 03 Jun 2017 13:15:16: 2000000 INFO @ Sat, 03 Jun 2017 13:15:16: 2000000 INFO @ Sat, 03 Jun 2017 13:15:18: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:15:18: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:15:18: #1 total tags in treatment: 2271739 INFO @ Sat, 03 Jun 2017 13:15:18: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:15:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:15:18: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:15:18: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:15:18: #1 total tags in treatment: 2271739 INFO @ Sat, 03 Jun 2017 13:15:18: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:15:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:15:18: #1 tags after filtering in treatment: 2271542 INFO @ Sat, 03 Jun 2017 13:15:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:15:18: #1 finished! INFO @ Sat, 03 Jun 2017 13:15:18: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:15:18: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:15:18: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:15:18: #1 total tags in treatment: 2271739 INFO @ Sat, 03 Jun 2017 13:15:18: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:15:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:15:18: #1 tags after filtering in treatment: 2271542 INFO @ Sat, 03 Jun 2017 13:15:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:15:18: #1 finished! INFO @ Sat, 03 Jun 2017 13:15:18: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:15:19: #2 number of paired peaks: 161 WARNING @ Sat, 03 Jun 2017 13:15:19: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 03 Jun 2017 13:15:19: start model_add_line... INFO @ Sat, 03 Jun 2017 13:15:19: #1 tags after filtering in treatment: 2271542 INFO @ Sat, 03 Jun 2017 13:15:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:15:19: #1 finished! INFO @ Sat, 03 Jun 2017 13:15:19: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:15:19: #2 number of paired peaks: 161 WARNING @ Sat, 03 Jun 2017 13:15:19: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 03 Jun 2017 13:15:19: start model_add_line... INFO @ Sat, 03 Jun 2017 13:15:19: start X-correlation... INFO @ Sat, 03 Jun 2017 13:15:19: end of X-cor INFO @ Sat, 03 Jun 2017 13:15:19: #2 finished! INFO @ Sat, 03 Jun 2017 13:15:19: #2 predicted fragment length is 54 bps INFO @ Sat, 03 Jun 2017 13:15:19: #2 alternative fragment length(s) may be 54 bps INFO @ Sat, 03 Jun 2017 13:15:19: #2.2 Generate R script for model : SRX1561069.05_model.r WARNING @ Sat, 03 Jun 2017 13:15:19: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:15:19: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sat, 03 Jun 2017 13:15:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:15:19: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:15:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:15:19: #2 number of paired peaks: 161 WARNING @ Sat, 03 Jun 2017 13:15:19: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 03 Jun 2017 13:15:19: start model_add_line... INFO @ Sat, 03 Jun 2017 13:15:20: start X-correlation... INFO @ Sat, 03 Jun 2017 13:15:20: end of X-cor INFO @ Sat, 03 Jun 2017 13:15:20: #2 finished! INFO @ Sat, 03 Jun 2017 13:15:20: #2 predicted fragment length is 54 bps INFO @ Sat, 03 Jun 2017 13:15:20: #2 alternative fragment length(s) may be 54 bps INFO @ Sat, 03 Jun 2017 13:15:20: #2.2 Generate R script for model : SRX1561069.10_model.r WARNING @ Sat, 03 Jun 2017 13:15:20: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:15:20: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sat, 03 Jun 2017 13:15:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:15:20: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:15:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:15:20: start X-correlation... INFO @ Sat, 03 Jun 2017 13:15:20: end of X-cor INFO @ Sat, 03 Jun 2017 13:15:20: #2 finished! INFO @ Sat, 03 Jun 2017 13:15:20: #2 predicted fragment length is 54 bps INFO @ Sat, 03 Jun 2017 13:15:20: #2 alternative fragment length(s) may be 54 bps INFO @ Sat, 03 Jun 2017 13:15:20: #2.2 Generate R script for model : SRX1561069.20_model.r WARNING @ Sat, 03 Jun 2017 13:15:20: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:15:20: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sat, 03 Jun 2017 13:15:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:15:20: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:15:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:15:33: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:15:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:15:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:15:43: #4 Write output xls file... SRX1561069.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:15:43: #4 Write peak in narrowPeak format file... SRX1561069.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:15:43: #4 Write summits bed file... SRX1561069.20_summits.bed INFO @ Sat, 03 Jun 2017 13:15:43: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (60 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:15:43: #4 Write output xls file... SRX1561069.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:15:43: #4 Write peak in narrowPeak format file... SRX1561069.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:15:43: #4 Write summits bed file... SRX1561069.05_summits.bed INFO @ Sat, 03 Jun 2017 13:15:43: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (302 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:15:44: #4 Write output xls file... SRX1561069.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:15:44: #4 Write peak in narrowPeak format file... SRX1561069.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:15:44: #4 Write summits bed file... SRX1561069.10_summits.bed INFO @ Sat, 03 Jun 2017 13:15:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (153 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。