Job ID = 10201976 sra ファイルのダウンロード中... Completed: 349356K bytes transferred in 13 seconds (219438K bits/sec), in 1 file. 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 19611087 spots for /home/okishinya/chipatlas/results/ce10/SRX2576645/SRR5272602.sra Written 19611087 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:12:57 19611087 reads; of these: 19611087 (100.00%) were unpaired; of these: 1907319 (9.73%) aligned 0 times 14449388 (73.68%) aligned exactly 1 time 3254380 (16.59%) aligned >1 times 90.27% overall alignment rate Time searching: 00:12:57 Overall time: 00:12:57 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] 8891067 / 17703768 = 0.5022 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 @ Mon, 13 Nov 2017 13:27:51: # Command line: callpeak -t SRX2576645.bam -f BAM -g ce -n SRX2576645.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576645.05 # format = BAM # ChIP-seq file = ['SRX2576645.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 @ Mon, 13 Nov 2017 13:27:51: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:27:51: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:27:51: # Command line: callpeak -t SRX2576645.bam -f BAM -g ce -n SRX2576645.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576645.10 # format = BAM # ChIP-seq file = ['SRX2576645.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 @ Mon, 13 Nov 2017 13:27:51: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:27:51: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:27:51: # Command line: callpeak -t SRX2576645.bam -f BAM -g ce -n SRX2576645.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576645.20 # format = BAM # ChIP-seq file = ['SRX2576645.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 @ Mon, 13 Nov 2017 13:27:51: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:27:51: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:28:00: 1000000 INFO @ Mon, 13 Nov 2017 13:28:08: 1000000 INFO @ Mon, 13 Nov 2017 13:28:09: 2000000 INFO @ Mon, 13 Nov 2017 13:28:09: 1000000 INFO @ Mon, 13 Nov 2017 13:28:18: 3000000 INFO @ Mon, 13 Nov 2017 13:28:26: 2000000 INFO @ Mon, 13 Nov 2017 13:28:27: 4000000 INFO @ Mon, 13 Nov 2017 13:28:27: 2000000 INFO @ Mon, 13 Nov 2017 13:28:36: 5000000 INFO @ Mon, 13 Nov 2017 13:28:44: 3000000 INFO @ Mon, 13 Nov 2017 13:28:45: 6000000 INFO @ Mon, 13 Nov 2017 13:28:45: 3000000 INFO @ Mon, 13 Nov 2017 13:28:54: 7000000 INFO @ Mon, 13 Nov 2017 13:29:02: 4000000 INFO @ Mon, 13 Nov 2017 13:29:03: 4000000 INFO @ Mon, 13 Nov 2017 13:29:04: 8000000 INFO @ Mon, 13 Nov 2017 13:29:11: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:29:11: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:29:11: #1 total tags in treatment: 8812701 INFO @ Mon, 13 Nov 2017 13:29:11: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:29:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:29:11: #1 tags after filtering in treatment: 8812701 INFO @ Mon, 13 Nov 2017 13:29:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:29:11: #1 finished! INFO @ Mon, 13 Nov 2017 13:29:11: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:29:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:29:12: #2 number of paired peaks: 473 WARNING @ Mon, 13 Nov 2017 13:29:12: Fewer paired peaks (473) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 473 pairs to build model! INFO @ Mon, 13 Nov 2017 13:29:12: start model_add_line... INFO @ Mon, 13 Nov 2017 13:29:12: start X-correlation... INFO @ Mon, 13 Nov 2017 13:29:12: end of X-cor INFO @ Mon, 13 Nov 2017 13:29:12: #2 finished! INFO @ Mon, 13 Nov 2017 13:29:12: #2 predicted fragment length is 57 bps INFO @ Mon, 13 Nov 2017 13:29:12: #2 alternative fragment length(s) may be 4,57,575 bps INFO @ Mon, 13 Nov 2017 13:29:12: #2.2 Generate R script for model : SRX2576645.10_model.r WARNING @ Mon, 13 Nov 2017 13:29:12: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:29:12: #2 You may need to consider one of the other alternative d(s): 4,57,575 WARNING @ Mon, 13 Nov 2017 13:29:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:29:12: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:29:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:29:17: 5000000 INFO @ Mon, 13 Nov 2017 13:29:20: 5000000 INFO @ Mon, 13 Nov 2017 13:29:32: 6000000 INFO @ Mon, 13 Nov 2017 13:29:37: 6000000 INFO @ Mon, 13 Nov 2017 13:29:37: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:29:48: 7000000 INFO @ Mon, 13 Nov 2017 13:29:52: #4 Write output xls file... SRX2576645.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:29:52: #4 Write peak in narrowPeak format file... SRX2576645.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:29:52: #4 Write summits bed file... SRX2576645.10_summits.bed INFO @ Mon, 13 Nov 2017 13:29:52: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (736 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:29:52: 7000000 INFO @ Mon, 13 Nov 2017 13:30:02: 8000000 INFO @ Mon, 13 Nov 2017 13:30:07: 8000000 INFO @ Mon, 13 Nov 2017 13:30:14: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:30:14: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:30:14: #1 total tags in treatment: 8812701 INFO @ Mon, 13 Nov 2017 13:30:14: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:30:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:30:14: #1 tags after filtering in treatment: 8812701 INFO @ Mon, 13 Nov 2017 13:30:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:30:14: #1 finished! INFO @ Mon, 13 Nov 2017 13:30:14: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:30:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:30:15: #2 number of paired peaks: 473 WARNING @ Mon, 13 Nov 2017 13:30:15: Fewer paired peaks (473) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 473 pairs to build model! INFO @ Mon, 13 Nov 2017 13:30:15: start model_add_line... INFO @ Mon, 13 Nov 2017 13:30:15: start X-correlation... INFO @ Mon, 13 Nov 2017 13:30:15: end of X-cor INFO @ Mon, 13 Nov 2017 13:30:15: #2 finished! INFO @ Mon, 13 Nov 2017 13:30:15: #2 predicted fragment length is 57 bps INFO @ Mon, 13 Nov 2017 13:30:15: #2 alternative fragment length(s) may be 4,57,575 bps INFO @ Mon, 13 Nov 2017 13:30:15: #2.2 Generate R script for model : SRX2576645.20_model.r WARNING @ Mon, 13 Nov 2017 13:30:15: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:30:15: #2 You may need to consider one of the other alternative d(s): 4,57,575 WARNING @ Mon, 13 Nov 2017 13:30:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:30:15: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:30:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:30:18: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:30:18: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:30:18: #1 total tags in treatment: 8812701 INFO @ Mon, 13 Nov 2017 13:30:18: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:30:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:30:19: #1 tags after filtering in treatment: 8812701 INFO @ Mon, 13 Nov 2017 13:30:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:30:19: #1 finished! INFO @ Mon, 13 Nov 2017 13:30:19: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:30:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:30:20: #2 number of paired peaks: 473 WARNING @ Mon, 13 Nov 2017 13:30:20: Fewer paired peaks (473) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 473 pairs to build model! INFO @ Mon, 13 Nov 2017 13:30:20: start model_add_line... INFO @ Mon, 13 Nov 2017 13:30:20: start X-correlation... INFO @ Mon, 13 Nov 2017 13:30:20: end of X-cor INFO @ Mon, 13 Nov 2017 13:30:20: #2 finished! INFO @ Mon, 13 Nov 2017 13:30:20: #2 predicted fragment length is 57 bps INFO @ Mon, 13 Nov 2017 13:30:20: #2 alternative fragment length(s) may be 4,57,575 bps INFO @ Mon, 13 Nov 2017 13:30:20: #2.2 Generate R script for model : SRX2576645.05_model.r WARNING @ Mon, 13 Nov 2017 13:30:20: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:30:20: #2 You may need to consider one of the other alternative d(s): 4,57,575 WARNING @ Mon, 13 Nov 2017 13:30:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:30:20: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:30:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:30:40: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:30:44: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:30:54: #4 Write output xls file... SRX2576645.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:30:54: #4 Write peak in narrowPeak format file... SRX2576645.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:30:54: #4 Write summits bed file... SRX2576645.20_summits.bed INFO @ Mon, 13 Nov 2017 13:30:54: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (296 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:30:59: #4 Write output xls file... SRX2576645.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:30:59: #4 Write peak in narrowPeak format file... SRX2576645.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:30:59: #4 Write summits bed file... SRX2576645.05_summits.bed INFO @ Mon, 13 Nov 2017 13:30:59: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1178 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。