Job ID = 9028899 sra ファイルのダウンロード中... Completed: 380854K bytes transferred in 5 seconds (522471K 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 --:--:-- 0:00:07 --:--:-- 0 100 7663 0 7663 0 0 959 0 --:--:-- 0:00:07 --:--:-- 5573 100 30318 0 30318 0 0 3374 0 --:--:-- 0:00:08 --:--:-- 12787 100 51637 0 51637 0 0 5261 0 --:--:-- 0:00:09 --:--:-- 16141 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 11198348 spots for /home/okishinya/chipatlas/results/ce10/SRX982099/SRR1956586.sra Written 11198348 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: 00:03:31 11198348 reads; of these: 11198348 (100.00%) were unpaired; of these: 94227 (0.84%) aligned 0 times 9240538 (82.52%) aligned exactly 1 time 1863583 (16.64%) aligned >1 times 99.16% overall alignment rate Time searching: 00:03:31 Overall time: 00:03:31 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 890626 / 11104121 = 0.0802 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 12:22:07: # Command line: callpeak -t SRX982099.bam -f BAM -g ce -n SRX982099.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982099.05 # format = BAM # ChIP-seq file = ['SRX982099.bam'] # control file = None # effective genome size = 9.00e+07 # 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 12:22:07: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:22:07: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:22:07: # Command line: callpeak -t SRX982099.bam -f BAM -g ce -n SRX982099.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982099.10 # format = BAM # ChIP-seq file = ['SRX982099.bam'] # control file = None # effective genome size = 9.00e+07 # 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 12:22:07: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:22:07: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:22:07: # Command line: callpeak -t SRX982099.bam -f BAM -g ce -n SRX982099.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982099.20 # format = BAM # ChIP-seq file = ['SRX982099.bam'] # control file = None # effective genome size = 9.00e+07 # 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 12:22:07: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:22:07: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:22:14: 1000000 INFO @ Sat, 03 Jun 2017 12:22:14: 1000000 INFO @ Sat, 03 Jun 2017 12:22:14: 1000000 INFO @ Sat, 03 Jun 2017 12:22:20: 2000000 INFO @ Sat, 03 Jun 2017 12:22:20: 2000000 INFO @ Sat, 03 Jun 2017 12:22:20: 2000000 INFO @ Sat, 03 Jun 2017 12:22:27: 3000000 INFO @ Sat, 03 Jun 2017 12:22:27: 3000000 INFO @ Sat, 03 Jun 2017 12:22:27: 3000000 INFO @ Sat, 03 Jun 2017 12:22:34: 4000000 INFO @ Sat, 03 Jun 2017 12:22:34: 4000000 INFO @ Sat, 03 Jun 2017 12:22:34: 4000000 INFO @ Sat, 03 Jun 2017 12:22:41: 5000000 INFO @ Sat, 03 Jun 2017 12:22:41: 5000000 INFO @ Sat, 03 Jun 2017 12:22:41: 5000000 INFO @ Sat, 03 Jun 2017 12:22:47: 6000000 INFO @ Sat, 03 Jun 2017 12:22:48: 6000000 INFO @ Sat, 03 Jun 2017 12:22:48: 6000000 INFO @ Sat, 03 Jun 2017 12:22:54: 7000000 INFO @ Sat, 03 Jun 2017 12:22:54: 7000000 INFO @ Sat, 03 Jun 2017 12:22:55: 7000000 INFO @ Sat, 03 Jun 2017 12:23:01: 8000000 INFO @ Sat, 03 Jun 2017 12:23:01: 8000000 INFO @ Sat, 03 Jun 2017 12:23:02: 8000000 INFO @ Sat, 03 Jun 2017 12:23:08: 9000000 INFO @ Sat, 03 Jun 2017 12:23:08: 9000000 INFO @ Sat, 03 Jun 2017 12:23:10: 9000000 INFO @ Sat, 03 Jun 2017 12:23:16: 10000000 INFO @ Sat, 03 Jun 2017 12:23:16: 10000000 INFO @ Sat, 03 Jun 2017 12:23:17: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:23:17: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:23:17: #1 total tags in treatment: 10213495 INFO @ Sat, 03 Jun 2017 12:23:17: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:23:17: #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 12:23:17: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:23:17: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:23:17: #1 total tags in treatment: 10213495 INFO @ Sat, 03 Jun 2017 12:23:17: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:23:17: #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 12:23:18: 10000000 INFO @ Sat, 03 Jun 2017 12:23:19: #1 tags after filtering in treatment: 10212397 INFO @ Sat, 03 Jun 2017 12:23:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:23:19: #1 finished! INFO @ Sat, 03 Jun 2017 12:23:19: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:23:19: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:23:19: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:23:19: #1 total tags in treatment: 10213495 INFO @ Sat, 03 Jun 2017 12:23:19: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:23:19: #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 12:23:20: #1 tags after filtering in treatment: 10212397 INFO @ Sat, 03 Jun 2017 12:23:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:23:20: #1 finished! INFO @ Sat, 03 Jun 2017 12:23:20: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:23:21: #2 number of paired peaks: 320 WARNING @ Sat, 03 Jun 2017 12:23:21: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Sat, 03 Jun 2017 12:23:21: start model_add_line... INFO @ Sat, 03 Jun 2017 12:23:21: #1 tags after filtering in treatment: 10212397 INFO @ Sat, 03 Jun 2017 12:23:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:23:21: #1 finished! INFO @ Sat, 03 Jun 2017 12:23:21: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:23:22: #2 number of paired peaks: 320 WARNING @ Sat, 03 Jun 2017 12:23:22: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Sat, 03 Jun 2017 12:23:22: start model_add_line... INFO @ Sat, 03 Jun 2017 12:23:23: #2 number of paired peaks: 320 WARNING @ Sat, 03 Jun 2017 12:23:23: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Sat, 03 Jun 2017 12:23:23: start model_add_line... INFO @ Sat, 03 Jun 2017 12:23:26: start X-correlation... INFO @ Sat, 03 Jun 2017 12:23:26: end of X-cor INFO @ Sat, 03 Jun 2017 12:23:26: #2 finished! INFO @ Sat, 03 Jun 2017 12:23:26: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 12:23:26: #2 alternative fragment length(s) may be 3,51 bps INFO @ Sat, 03 Jun 2017 12:23:26: #2.2 Generate R script for model : SRX982099.10_model.r WARNING @ Sat, 03 Jun 2017 12:23:26: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:23:26: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Sat, 03 Jun 2017 12:23:26: #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 12:23:26: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:23:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:23:26: start X-correlation... INFO @ Sat, 03 Jun 2017 12:23:26: end of X-cor INFO @ Sat, 03 Jun 2017 12:23:26: #2 finished! INFO @ Sat, 03 Jun 2017 12:23:26: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 12:23:26: #2 alternative fragment length(s) may be 3,51 bps INFO @ Sat, 03 Jun 2017 12:23:26: #2.2 Generate R script for model : SRX982099.05_model.r WARNING @ Sat, 03 Jun 2017 12:23:26: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:23:26: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Sat, 03 Jun 2017 12:23:26: #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 12:23:26: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:23:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:23:28: start X-correlation... INFO @ Sat, 03 Jun 2017 12:23:28: end of X-cor INFO @ Sat, 03 Jun 2017 12:23:28: #2 finished! INFO @ Sat, 03 Jun 2017 12:23:28: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 12:23:28: #2 alternative fragment length(s) may be 3,51 bps INFO @ Sat, 03 Jun 2017 12:23:28: #2.2 Generate R script for model : SRX982099.20_model.r WARNING @ Sat, 03 Jun 2017 12:23:28: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:23:28: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Sat, 03 Jun 2017 12:23:28: #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 12:23:28: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:23:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:24:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:24:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:24:26: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:24:58: #4 Write output xls file... SRX982099.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:24:58: #4 Write peak in narrowPeak format file... SRX982099.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:24:58: #4 Write summits bed file... SRX982099.05_summits.bed INFO @ Sat, 03 Jun 2017 12:24:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (610 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:25:01: #4 Write output xls file... SRX982099.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:25:01: #4 Write peak in narrowPeak format file... SRX982099.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:25:01: #4 Write summits bed file... SRX982099.10_summits.bed INFO @ Sat, 03 Jun 2017 12:25:01: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (409 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:25:09: #4 Write output xls file... SRX982099.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:25:09: #4 Write peak in narrowPeak format file... SRX982099.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:25:09: #4 Write summits bed file... SRX982099.20_summits.bed INFO @ Sat, 03 Jun 2017 12:25:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (181 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。