Job ID = 9029228 sra ファイルのダウンロード中... Completed: 510183K bytes transferred in 11 seconds (379039K 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 --:--:-- 0 100 7663 0 7663 0 0 1068 0 --:--:-- 0:00:07 --:--:-- 9345 100 30317 0 30317 0 0 3712 0 --:--:-- 0:00:08 --:--:-- 16694 100 54317 0 54317 0 0 6037 0 --:--:-- 0:00:08 --:--:-- 20520 100 88491 0 88491 0 0 9320 0 --:--:-- 0:00:09 --:--:-- 28145 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 23440045 spots for /home/okishinya/chipatlas/results/dm3/SRX1433368/SRR2919833.sra Written 23440045 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: 00:09:05 23440045 reads; of these: 23440045 (100.00%) were unpaired; of these: 1140583 (4.87%) aligned 0 times 16971211 (72.40%) aligned exactly 1 time 5328251 (22.73%) aligned >1 times 95.13% overall alignment rate Time searching: 00:09:05 Overall time: 00:09:05 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] 4827380 / 22299462 = 0.2165 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 13:07:43: # Command line: callpeak -t SRX1433368.bam -f BAM -g dm -n SRX1433368.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433368.05 # format = BAM # ChIP-seq file = ['SRX1433368.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 13:07:43: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:07:43: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:07:43: # Command line: callpeak -t SRX1433368.bam -f BAM -g dm -n SRX1433368.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433368.20 # format = BAM # ChIP-seq file = ['SRX1433368.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 13:07:43: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:07:43: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:07:43: # Command line: callpeak -t SRX1433368.bam -f BAM -g dm -n SRX1433368.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433368.10 # format = BAM # ChIP-seq file = ['SRX1433368.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 13:07:43: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:07:43: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:07:49: 1000000 INFO @ Sat, 03 Jun 2017 13:07:50: 1000000 INFO @ Sat, 03 Jun 2017 13:07:50: 1000000 INFO @ Sat, 03 Jun 2017 13:07:55: 2000000 INFO @ Sat, 03 Jun 2017 13:07:57: 2000000 INFO @ Sat, 03 Jun 2017 13:07:57: 2000000 INFO @ Sat, 03 Jun 2017 13:08:01: 3000000 INFO @ Sat, 03 Jun 2017 13:08:04: 3000000 INFO @ Sat, 03 Jun 2017 13:08:04: 3000000 INFO @ Sat, 03 Jun 2017 13:08:07: 4000000 INFO @ Sat, 03 Jun 2017 13:08:11: 4000000 INFO @ Sat, 03 Jun 2017 13:08:11: 4000000 INFO @ Sat, 03 Jun 2017 13:08:13: 5000000 INFO @ Sat, 03 Jun 2017 13:08:18: 5000000 INFO @ Sat, 03 Jun 2017 13:08:18: 5000000 INFO @ Sat, 03 Jun 2017 13:08:19: 6000000 INFO @ Sat, 03 Jun 2017 13:08:25: 7000000 INFO @ Sat, 03 Jun 2017 13:08:25: 6000000 INFO @ Sat, 03 Jun 2017 13:08:25: 6000000 INFO @ Sat, 03 Jun 2017 13:08:31: 8000000 INFO @ Sat, 03 Jun 2017 13:08:32: 7000000 INFO @ Sat, 03 Jun 2017 13:08:32: 7000000 INFO @ Sat, 03 Jun 2017 13:08:37: 9000000 INFO @ Sat, 03 Jun 2017 13:08:38: 8000000 INFO @ Sat, 03 Jun 2017 13:08:39: 8000000 INFO @ Sat, 03 Jun 2017 13:08:43: 10000000 INFO @ Sat, 03 Jun 2017 13:08:45: 9000000 INFO @ Sat, 03 Jun 2017 13:08:46: 9000000 INFO @ Sat, 03 Jun 2017 13:08:48: 11000000 INFO @ Sat, 03 Jun 2017 13:08:52: 10000000 INFO @ Sat, 03 Jun 2017 13:08:53: 10000000 INFO @ Sat, 03 Jun 2017 13:08:54: 12000000 INFO @ Sat, 03 Jun 2017 13:09:00: 11000000 INFO @ Sat, 03 Jun 2017 13:09:00: 11000000 INFO @ Sat, 03 Jun 2017 13:09:00: 13000000 INFO @ Sat, 03 Jun 2017 13:09:07: 14000000 INFO @ Sat, 03 Jun 2017 13:09:07: 12000000 INFO @ Sat, 03 Jun 2017 13:09:08: 12000000 INFO @ Sat, 03 Jun 2017 13:09:13: 15000000 INFO @ Sat, 03 Jun 2017 13:09:15: 13000000 INFO @ Sat, 03 Jun 2017 13:09:15: 13000000 INFO @ Sat, 03 Jun 2017 13:09:18: 16000000 INFO @ Sat, 03 Jun 2017 13:09:21: 14000000 INFO @ Sat, 03 Jun 2017 13:09:22: 14000000 INFO @ Sat, 03 Jun 2017 13:09:25: 17000000 INFO @ Sat, 03 Jun 2017 13:09:28: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:09:28: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:09:28: #1 total tags in treatment: 17472082 INFO @ Sat, 03 Jun 2017 13:09:28: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:09:28: #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 13:09:29: 15000000 INFO @ Sat, 03 Jun 2017 13:09:29: 15000000 INFO @ Sat, 03 Jun 2017 13:09:31: #1 tags after filtering in treatment: 17468464 INFO @ Sat, 03 Jun 2017 13:09:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:09:31: #1 finished! INFO @ Sat, 03 Jun 2017 13:09:31: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:09:35: #2 number of paired peaks: 196 WARNING @ Sat, 03 Jun 2017 13:09:35: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Sat, 03 Jun 2017 13:09:35: start model_add_line... INFO @ Sat, 03 Jun 2017 13:09:36: 16000000 INFO @ Sat, 03 Jun 2017 13:09:36: 16000000 INFO @ Sat, 03 Jun 2017 13:09:38: start X-correlation... INFO @ Sat, 03 Jun 2017 13:09:38: end of X-cor INFO @ Sat, 03 Jun 2017 13:09:38: #2 finished! INFO @ Sat, 03 Jun 2017 13:09:38: #2 predicted fragment length is 90 bps INFO @ Sat, 03 Jun 2017 13:09:38: #2 alternative fragment length(s) may be 90 bps INFO @ Sat, 03 Jun 2017 13:09:38: #2.2 Generate R script for model : SRX1433368.05_model.r WARNING @ Sat, 03 Jun 2017 13:09:38: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:09:38: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sat, 03 Jun 2017 13:09:38: #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 13:09:38: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:09:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:09:43: 17000000 INFO @ Sat, 03 Jun 2017 13:09:43: 17000000 INFO @ Sat, 03 Jun 2017 13:09:46: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:09:46: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:09:46: #1 total tags in treatment: 17472082 INFO @ Sat, 03 Jun 2017 13:09:46: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:09:46: #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 13:09:47: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:09:47: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:09:47: #1 total tags in treatment: 17472082 INFO @ Sat, 03 Jun 2017 13:09:47: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:09:47: #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 13:09:49: #1 tags after filtering in treatment: 17468464 INFO @ Sat, 03 Jun 2017 13:09:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:09:49: #1 finished! INFO @ Sat, 03 Jun 2017 13:09:49: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:09:50: #1 tags after filtering in treatment: 17468464 INFO @ Sat, 03 Jun 2017 13:09:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:09:50: #1 finished! INFO @ Sat, 03 Jun 2017 13:09:50: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:09:52: #2 number of paired peaks: 196 WARNING @ Sat, 03 Jun 2017 13:09:52: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Sat, 03 Jun 2017 13:09:52: start model_add_line... INFO @ Sat, 03 Jun 2017 13:09:53: #2 number of paired peaks: 196 WARNING @ Sat, 03 Jun 2017 13:09:53: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Sat, 03 Jun 2017 13:09:53: start model_add_line... INFO @ Sat, 03 Jun 2017 13:09:55: start X-correlation... INFO @ Sat, 03 Jun 2017 13:09:55: end of X-cor INFO @ Sat, 03 Jun 2017 13:09:55: #2 finished! INFO @ Sat, 03 Jun 2017 13:09:55: #2 predicted fragment length is 90 bps INFO @ Sat, 03 Jun 2017 13:09:55: #2 alternative fragment length(s) may be 90 bps INFO @ Sat, 03 Jun 2017 13:09:55: #2.2 Generate R script for model : SRX1433368.20_model.r WARNING @ Sat, 03 Jun 2017 13:09:55: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:09:55: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sat, 03 Jun 2017 13:09:55: #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 13:09:55: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:09:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:09:56: start X-correlation... INFO @ Sat, 03 Jun 2017 13:09:56: end of X-cor INFO @ Sat, 03 Jun 2017 13:09:56: #2 finished! INFO @ Sat, 03 Jun 2017 13:09:56: #2 predicted fragment length is 90 bps INFO @ Sat, 03 Jun 2017 13:09:56: #2 alternative fragment length(s) may be 90 bps INFO @ Sat, 03 Jun 2017 13:09:56: #2.2 Generate R script for model : SRX1433368.10_model.r WARNING @ Sat, 03 Jun 2017 13:09:56: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:09:56: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sat, 03 Jun 2017 13:09:56: #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 13:09:56: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:09:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:11:14: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:11:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:11:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:12:29: #4 Write output xls file... SRX1433368.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:12:29: #4 Write peak in narrowPeak format file... SRX1433368.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:12:29: #4 Write summits bed file... SRX1433368.05_summits.bed INFO @ Sat, 03 Jun 2017 13:12:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2965 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:12:39: #4 Write output xls file... SRX1433368.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:12:39: #4 Write peak in narrowPeak format file... SRX1433368.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:12:39: #4 Write summits bed file... SRX1433368.20_summits.bed INFO @ Sat, 03 Jun 2017 13:12:39: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1087 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:12:43: #4 Write output xls file... SRX1433368.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:12:43: #4 Write peak in narrowPeak format file... SRX1433368.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:12:43: #4 Write summits bed file... SRX1433368.10_summits.bed INFO @ Sat, 03 Jun 2017 13:12:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1893 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。