Job ID = 9157405 sra ファイルのダウンロード中... Completed: 418825K bytes transferred in 5 seconds (576986K bits/sec), in 1 file, 2 directories. 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 12785509 spots for /home/okishinya/chipatlas/results/ce10/SRX208768/SRR628902.sra Written 12785509 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: 00:04:23 12785509 reads; of these: 12785509 (100.00%) were unpaired; of these: 1434946 (11.22%) aligned 0 times 9782658 (76.51%) aligned exactly 1 time 1567905 (12.26%) aligned >1 times 88.78% overall alignment rate Time searching: 00:04:23 Overall time: 00:04:23 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2859422 / 11350563 = 0.2519 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 @ Tue, 27 Jun 2017 11:53:28: # Command line: callpeak -t SRX208768.bam -f BAM -g ce -n SRX208768.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX208768.20 # format = BAM # ChIP-seq file = ['SRX208768.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 # Paired-End mode is off INFO @ Tue, 27 Jun 2017 11:53:28: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:53:28: # Command line: callpeak -t SRX208768.bam -f BAM -g ce -n SRX208768.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX208768.10 # format = BAM # ChIP-seq file = ['SRX208768.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 # Paired-End mode is off INFO @ Tue, 27 Jun 2017 11:53:28: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:53:28: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:53:28: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:53:28: # Command line: callpeak -t SRX208768.bam -f BAM -g ce -n SRX208768.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX208768.05 # format = BAM # ChIP-seq file = ['SRX208768.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 # Paired-End mode is off INFO @ Tue, 27 Jun 2017 11:53:28: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:53:28: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:53:37: 1000000 INFO @ Tue, 27 Jun 2017 11:53:38: 1000000 INFO @ Tue, 27 Jun 2017 11:53:38: 1000000 INFO @ Tue, 27 Jun 2017 11:53:45: 2000000 INFO @ Tue, 27 Jun 2017 11:53:49: 2000000 INFO @ Tue, 27 Jun 2017 11:53:49: 2000000 INFO @ Tue, 27 Jun 2017 11:53:54: 3000000 INFO @ Tue, 27 Jun 2017 11:54:00: 3000000 INFO @ Tue, 27 Jun 2017 11:54:00: 3000000 INFO @ Tue, 27 Jun 2017 11:54:03: 4000000 INFO @ Tue, 27 Jun 2017 11:54:10: 4000000 INFO @ Tue, 27 Jun 2017 11:54:10: 4000000 INFO @ Tue, 27 Jun 2017 11:54:12: 5000000 INFO @ Tue, 27 Jun 2017 11:54:21: 6000000 INFO @ Tue, 27 Jun 2017 11:54:21: 5000000 INFO @ Tue, 27 Jun 2017 11:54:21: 5000000 INFO @ Tue, 27 Jun 2017 11:54:29: 7000000 INFO @ Tue, 27 Jun 2017 11:54:32: 6000000 INFO @ Tue, 27 Jun 2017 11:54:32: 6000000 INFO @ Tue, 27 Jun 2017 11:54:38: 8000000 INFO @ Tue, 27 Jun 2017 11:54:42: 7000000 INFO @ Tue, 27 Jun 2017 11:54:42: 7000000 INFO @ Tue, 27 Jun 2017 11:54:42: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:54:42: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:54:42: #1 total tags in treatment: 8491141 INFO @ Tue, 27 Jun 2017 11:54:42: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:54:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:54:42: #1 tags after filtering in treatment: 8491141 INFO @ Tue, 27 Jun 2017 11:54:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:54:42: #1 finished! INFO @ Tue, 27 Jun 2017 11:54:42: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:54:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:54:43: #2 number of paired peaks: 102 WARNING @ Tue, 27 Jun 2017 11:54:43: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Tue, 27 Jun 2017 11:54:43: start model_add_line... INFO @ Tue, 27 Jun 2017 11:54:43: start X-correlation... INFO @ Tue, 27 Jun 2017 11:54:43: end of X-cor INFO @ Tue, 27 Jun 2017 11:54:43: #2 finished! INFO @ Tue, 27 Jun 2017 11:54:43: #2 predicted fragment length is 55 bps INFO @ Tue, 27 Jun 2017 11:54:43: #2 alternative fragment length(s) may be 2,55,124,154,478 bps INFO @ Tue, 27 Jun 2017 11:54:43: #2.2 Generate R script for model : SRX208768.20_model.r WARNING @ Tue, 27 Jun 2017 11:54:43: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:54:43: #2 You may need to consider one of the other alternative d(s): 2,55,124,154,478 WARNING @ Tue, 27 Jun 2017 11:54:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:54:43: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:54:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:54:53: 8000000 INFO @ Tue, 27 Jun 2017 11:54:53: 8000000 INFO @ Tue, 27 Jun 2017 11:54:58: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:54:58: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:54:58: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:54:58: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:54:58: #1 total tags in treatment: 8491141 INFO @ Tue, 27 Jun 2017 11:54:58: #1 total tags in treatment: 8491141 INFO @ Tue, 27 Jun 2017 11:54:58: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:54:58: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:54:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:54:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:54:58: #1 tags after filtering in treatment: 8491141 INFO @ Tue, 27 Jun 2017 11:54:58: #1 tags after filtering in treatment: 8491141 INFO @ Tue, 27 Jun 2017 11:54:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:54:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:54:58: #1 finished! INFO @ Tue, 27 Jun 2017 11:54:58: #1 finished! INFO @ Tue, 27 Jun 2017 11:54:58: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:54:58: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:54:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:54:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:54:59: #2 number of paired peaks: 102 WARNING @ Tue, 27 Jun 2017 11:54:59: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Tue, 27 Jun 2017 11:54:59: start model_add_line... INFO @ Tue, 27 Jun 2017 11:54:59: #2 number of paired peaks: 102 WARNING @ Tue, 27 Jun 2017 11:54:59: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Tue, 27 Jun 2017 11:54:59: start model_add_line... INFO @ Tue, 27 Jun 2017 11:54:59: start X-correlation... INFO @ Tue, 27 Jun 2017 11:54:59: end of X-cor INFO @ Tue, 27 Jun 2017 11:54:59: #2 finished! INFO @ Tue, 27 Jun 2017 11:54:59: #2 predicted fragment length is 55 bps INFO @ Tue, 27 Jun 2017 11:54:59: #2 alternative fragment length(s) may be 2,55,124,154,478 bps INFO @ Tue, 27 Jun 2017 11:54:59: #2.2 Generate R script for model : SRX208768.05_model.r INFO @ Tue, 27 Jun 2017 11:54:59: start X-correlation... INFO @ Tue, 27 Jun 2017 11:54:59: end of X-cor INFO @ Tue, 27 Jun 2017 11:54:59: #2 finished! INFO @ Tue, 27 Jun 2017 11:54:59: #2 predicted fragment length is 55 bps INFO @ Tue, 27 Jun 2017 11:54:59: #2 alternative fragment length(s) may be 2,55,124,154,478 bps INFO @ Tue, 27 Jun 2017 11:54:59: #2.2 Generate R script for model : SRX208768.10_model.r WARNING @ Tue, 27 Jun 2017 11:54:59: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:54:59: #2 You may need to consider one of the other alternative d(s): 2,55,124,154,478 WARNING @ Tue, 27 Jun 2017 11:54:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:54:59: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:54:59: #3 Pre-compute pvalue-qvalue table... WARNING @ Tue, 27 Jun 2017 11:54:59: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:54:59: #2 You may need to consider one of the other alternative d(s): 2,55,124,154,478 WARNING @ Tue, 27 Jun 2017 11:54:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:54:59: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:54:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:55:01: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:55:12: #4 Write output xls file... SRX208768.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:55:12: #4 Write peak in narrowPeak format file... SRX208768.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:55:12: #4 Write summits bed file... SRX208768.20_summits.bed INFO @ Tue, 27 Jun 2017 11:55:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (20 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:55:17: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:55:18: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:55:27: #4 Write output xls file... SRX208768.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:55:27: #4 Write peak in narrowPeak format file... SRX208768.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:55:27: #4 Write summits bed file... SRX208768.05_summits.bed INFO @ Tue, 27 Jun 2017 11:55:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (333 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:55:29: #4 Write output xls file... SRX208768.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:55:29: #4 Write peak in narrowPeak format file... SRX208768.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:55:29: #4 Write summits bed file... SRX208768.10_summits.bed INFO @ Tue, 27 Jun 2017 11:55:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (111 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。