Job ID = 9029325 sra ファイルのダウンロード中... Completed: 801960K bytes transferred in 9 seconds (720114K 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 25902 0 25902 0 0 3325 0 --:--:-- 0:00:07 --:--:-- 19087 100 70719 0 70719 0 0 8206 0 --:--:-- 0:00:08 --:--:-- 32350 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 24752988 spots for /home/okishinya/chipatlas/results/dm3/SRX1561066/SRR3145068.sra Written 24752988 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: 00:05:23 24752988 reads; of these: 24752988 (100.00%) were unpaired; of these: 12135813 (49.03%) aligned 0 times 10217811 (41.28%) aligned exactly 1 time 2399364 (9.69%) aligned >1 times 50.97% overall alignment rate Time searching: 00:05:23 Overall time: 00:05:23 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] 4370582 / 12617175 = 0.3464 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 13:22:31: # Command line: callpeak -t SRX1561066.bam -f BAM -g dm -n SRX1561066.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1561066.05 # format = BAM # ChIP-seq file = ['SRX1561066.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 13:22:31: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:22:31: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:22:31: # Command line: callpeak -t SRX1561066.bam -f BAM -g dm -n SRX1561066.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1561066.20 # format = BAM # ChIP-seq file = ['SRX1561066.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 13:22:31: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:22:31: # Command line: callpeak -t SRX1561066.bam -f BAM -g dm -n SRX1561066.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1561066.10 # format = BAM # ChIP-seq file = ['SRX1561066.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 13:22:31: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:22:31: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:22:31: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:22:37: 1000000 INFO @ Sat, 03 Jun 2017 13:22:38: 1000000 INFO @ Sat, 03 Jun 2017 13:22:38: 1000000 INFO @ Sat, 03 Jun 2017 13:22:43: 2000000 INFO @ Sat, 03 Jun 2017 13:22:44: 2000000 INFO @ Sat, 03 Jun 2017 13:22:44: 2000000 INFO @ Sat, 03 Jun 2017 13:22:49: 3000000 INFO @ Sat, 03 Jun 2017 13:22:51: 3000000 INFO @ Sat, 03 Jun 2017 13:22:51: 3000000 INFO @ Sat, 03 Jun 2017 13:22:55: 4000000 INFO @ Sat, 03 Jun 2017 13:22:58: 4000000 INFO @ Sat, 03 Jun 2017 13:22:58: 4000000 INFO @ Sat, 03 Jun 2017 13:23:02: 5000000 INFO @ Sat, 03 Jun 2017 13:23:05: 5000000 INFO @ Sat, 03 Jun 2017 13:23:05: 5000000 INFO @ Sat, 03 Jun 2017 13:23:08: 6000000 INFO @ Sat, 03 Jun 2017 13:23:12: 6000000 INFO @ Sat, 03 Jun 2017 13:23:12: 6000000 INFO @ Sat, 03 Jun 2017 13:23:14: 7000000 INFO @ Sat, 03 Jun 2017 13:23:18: 7000000 INFO @ Sat, 03 Jun 2017 13:23:18: 7000000 INFO @ Sat, 03 Jun 2017 13:23:20: 8000000 INFO @ Sat, 03 Jun 2017 13:23:22: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:23:22: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:23:22: #1 total tags in treatment: 8246593 INFO @ Sat, 03 Jun 2017 13:23:22: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:23:22: #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 13:23:23: #1 tags after filtering in treatment: 8244080 INFO @ Sat, 03 Jun 2017 13:23:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:23:23: #1 finished! INFO @ Sat, 03 Jun 2017 13:23:23: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:23:25: #2 number of paired peaks: 111 WARNING @ Sat, 03 Jun 2017 13:23:25: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Sat, 03 Jun 2017 13:23:25: start model_add_line... INFO @ Sat, 03 Jun 2017 13:23:25: 8000000 INFO @ Sat, 03 Jun 2017 13:23:25: 8000000 INFO @ Sat, 03 Jun 2017 13:23:26: start X-correlation... INFO @ Sat, 03 Jun 2017 13:23:26: end of X-cor INFO @ Sat, 03 Jun 2017 13:23:26: #2 finished! INFO @ Sat, 03 Jun 2017 13:23:26: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Jun 2017 13:23:26: #2 alternative fragment length(s) may be 46 bps INFO @ Sat, 03 Jun 2017 13:23:26: #2.2 Generate R script for model : SRX1561066.20_model.r WARNING @ Sat, 03 Jun 2017 13:23:26: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:23:26: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Sat, 03 Jun 2017 13:23:26: #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 13:23:26: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:23:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:23:27: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:23:27: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:23:27: #1 total tags in treatment: 8246593 INFO @ Sat, 03 Jun 2017 13:23:27: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:23:27: #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 13:23:27: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:23:27: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:23:27: #1 total tags in treatment: 8246593 INFO @ Sat, 03 Jun 2017 13:23:27: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:23:27: #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 13:23:28: #1 tags after filtering in treatment: 8244080 INFO @ Sat, 03 Jun 2017 13:23:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:23:28: #1 finished! INFO @ Sat, 03 Jun 2017 13:23:28: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:23:29: #1 tags after filtering in treatment: 8244080 INFO @ Sat, 03 Jun 2017 13:23:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:23:29: #1 finished! INFO @ Sat, 03 Jun 2017 13:23:29: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:23:30: #2 number of paired peaks: 111 WARNING @ Sat, 03 Jun 2017 13:23:30: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Sat, 03 Jun 2017 13:23:30: start model_add_line... INFO @ Sat, 03 Jun 2017 13:23:30: #2 number of paired peaks: 111 WARNING @ Sat, 03 Jun 2017 13:23:30: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Sat, 03 Jun 2017 13:23:30: start model_add_line... INFO @ Sat, 03 Jun 2017 13:23:31: start X-correlation... INFO @ Sat, 03 Jun 2017 13:23:31: end of X-cor INFO @ Sat, 03 Jun 2017 13:23:31: #2 finished! INFO @ Sat, 03 Jun 2017 13:23:31: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Jun 2017 13:23:31: #2 alternative fragment length(s) may be 46 bps INFO @ Sat, 03 Jun 2017 13:23:31: #2.2 Generate R script for model : SRX1561066.05_model.r WARNING @ Sat, 03 Jun 2017 13:23:31: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:23:31: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Sat, 03 Jun 2017 13:23:31: #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 13:23:31: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:23:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:23:32: start X-correlation... INFO @ Sat, 03 Jun 2017 13:23:32: end of X-cor INFO @ Sat, 03 Jun 2017 13:23:32: #2 finished! INFO @ Sat, 03 Jun 2017 13:23:32: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Jun 2017 13:23:32: #2 alternative fragment length(s) may be 46 bps INFO @ Sat, 03 Jun 2017 13:23:32: #2.2 Generate R script for model : SRX1561066.10_model.r WARNING @ Sat, 03 Jun 2017 13:23:32: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:23:32: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Sat, 03 Jun 2017 13:23:32: #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 13:23:32: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:23:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:24:15: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:24:16: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:24:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:24:48: #4 Write output xls file... SRX1561066.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:24:48: #4 Write peak in narrowPeak format file... SRX1561066.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:24:48: #4 Write summits bed file... SRX1561066.10_summits.bed INFO @ Sat, 03 Jun 2017 13:24:48: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (638 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:24:49: #4 Write output xls file... SRX1561066.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:24:49: #4 Write peak in narrowPeak format file... SRX1561066.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:24:49: #4 Write summits bed file... SRX1561066.20_summits.bed INFO @ Sat, 03 Jun 2017 13:24:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (221 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:24:57: #4 Write output xls file... SRX1561066.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:24:57: #4 Write peak in narrowPeak format file... SRX1561066.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:24:57: #4 Write summits bed file... SRX1561066.05_summits.bed INFO @ Sat, 03 Jun 2017 13:24:57: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1156 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。