Job ID = 10201993 sra ファイルのダウンロード中... Completed: 303222K bytes transferred in 11 seconds (215276K 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 16607128 spots for /home/okishinya/chipatlas/results/ce10/SRX2576662/SRR5272619.sra Written 16607128 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: 00:04:25 16607128 reads; of these: 16607128 (100.00%) were unpaired; of these: 192157 (1.16%) aligned 0 times 13231285 (79.67%) aligned exactly 1 time 3183686 (19.17%) aligned >1 times 98.84% overall alignment rate Time searching: 00:04:25 Overall time: 00:04:25 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] 4125941 / 16414971 = 0.2514 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 13:17:15: # Command line: callpeak -t SRX2576662.bam -f BAM -g ce -n SRX2576662.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576662.10 # format = BAM # ChIP-seq file = ['SRX2576662.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 13:17:15: # Command line: callpeak -t SRX2576662.bam -f BAM -g ce -n SRX2576662.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576662.20 # format = BAM # ChIP-seq file = ['SRX2576662.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 13:17:15: # Command line: callpeak -t SRX2576662.bam -f BAM -g ce -n SRX2576662.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576662.05 # format = BAM # ChIP-seq file = ['SRX2576662.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 13:17:15: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:17:15: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:17:15: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:17:15: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:17:15: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:17:15: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:17:23: 1000000 INFO @ Mon, 13 Nov 2017 13:17:23: 1000000 INFO @ Mon, 13 Nov 2017 13:17:23: 1000000 INFO @ Mon, 13 Nov 2017 13:17:30: 2000000 INFO @ Mon, 13 Nov 2017 13:17:31: 2000000 INFO @ Mon, 13 Nov 2017 13:17:31: 2000000 INFO @ Mon, 13 Nov 2017 13:17:37: 3000000 INFO @ Mon, 13 Nov 2017 13:17:38: 3000000 INFO @ Mon, 13 Nov 2017 13:17:38: 3000000 INFO @ Mon, 13 Nov 2017 13:17:45: 4000000 INFO @ Mon, 13 Nov 2017 13:17:46: 4000000 INFO @ Mon, 13 Nov 2017 13:17:46: 4000000 INFO @ Mon, 13 Nov 2017 13:17:52: 5000000 INFO @ Mon, 13 Nov 2017 13:17:54: 5000000 INFO @ Mon, 13 Nov 2017 13:17:54: 5000000 INFO @ Mon, 13 Nov 2017 13:17:59: 6000000 INFO @ Mon, 13 Nov 2017 13:18:02: 6000000 INFO @ Mon, 13 Nov 2017 13:18:02: 6000000 INFO @ Mon, 13 Nov 2017 13:18:06: 7000000 INFO @ Mon, 13 Nov 2017 13:18:09: 7000000 INFO @ Mon, 13 Nov 2017 13:18:09: 7000000 INFO @ Mon, 13 Nov 2017 13:18:14: 8000000 INFO @ Mon, 13 Nov 2017 13:18:17: 8000000 INFO @ Mon, 13 Nov 2017 13:18:17: 8000000 INFO @ Mon, 13 Nov 2017 13:18:21: 9000000 INFO @ Mon, 13 Nov 2017 13:18:25: 9000000 INFO @ Mon, 13 Nov 2017 13:18:25: 9000000 INFO @ Mon, 13 Nov 2017 13:18:28: 10000000 INFO @ Mon, 13 Nov 2017 13:18:33: 10000000 INFO @ Mon, 13 Nov 2017 13:18:33: 10000000 INFO @ Mon, 13 Nov 2017 13:18:35: 11000000 INFO @ Mon, 13 Nov 2017 13:18:40: 11000000 INFO @ Mon, 13 Nov 2017 13:18:40: 11000000 INFO @ Mon, 13 Nov 2017 13:18:43: 12000000 INFO @ Mon, 13 Nov 2017 13:18:45: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:18:45: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:18:45: #1 total tags in treatment: 12289030 INFO @ Mon, 13 Nov 2017 13:18:45: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:18:45: #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 13:18:45: #1 tags after filtering in treatment: 12289030 INFO @ Mon, 13 Nov 2017 13:18:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:18:45: #1 finished! INFO @ Mon, 13 Nov 2017 13:18:45: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:18:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:18:46: #2 number of paired peaks: 327 WARNING @ Mon, 13 Nov 2017 13:18:46: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Mon, 13 Nov 2017 13:18:46: start model_add_line... INFO @ Mon, 13 Nov 2017 13:18:46: start X-correlation... INFO @ Mon, 13 Nov 2017 13:18:46: end of X-cor INFO @ Mon, 13 Nov 2017 13:18:46: #2 finished! INFO @ Mon, 13 Nov 2017 13:18:46: #2 predicted fragment length is 49 bps INFO @ Mon, 13 Nov 2017 13:18:46: #2 alternative fragment length(s) may be 2,49 bps INFO @ Mon, 13 Nov 2017 13:18:46: #2.2 Generate R script for model : SRX2576662.05_model.r WARNING @ Mon, 13 Nov 2017 13:18:46: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:18:46: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Mon, 13 Nov 2017 13:18:46: #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 13:18:46: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:18:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:18:48: 12000000 INFO @ Mon, 13 Nov 2017 13:18:48: 12000000 INFO @ Mon, 13 Nov 2017 13:18:50: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:18:50: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:18:50: #1 total tags in treatment: 12289030 INFO @ Mon, 13 Nov 2017 13:18:50: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:18:50: #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 13:18:50: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:18:50: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:18:50: #1 total tags in treatment: 12289030 INFO @ Mon, 13 Nov 2017 13:18:50: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:18:50: #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 13:18:50: #1 tags after filtering in treatment: 12289030 INFO @ Mon, 13 Nov 2017 13:18:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:18:50: #1 finished! INFO @ Mon, 13 Nov 2017 13:18:50: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:18:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:18:50: #1 tags after filtering in treatment: 12289030 INFO @ Mon, 13 Nov 2017 13:18:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:18:50: #1 finished! INFO @ Mon, 13 Nov 2017 13:18:50: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:18:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:18:51: #2 number of paired peaks: 327 WARNING @ Mon, 13 Nov 2017 13:18:51: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Mon, 13 Nov 2017 13:18:51: start model_add_line... INFO @ Mon, 13 Nov 2017 13:18:51: #2 number of paired peaks: 327 WARNING @ Mon, 13 Nov 2017 13:18:51: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Mon, 13 Nov 2017 13:18:51: start model_add_line... INFO @ Mon, 13 Nov 2017 13:18:51: start X-correlation... INFO @ Mon, 13 Nov 2017 13:18:51: end of X-cor INFO @ Mon, 13 Nov 2017 13:18:51: #2 finished! INFO @ Mon, 13 Nov 2017 13:18:51: #2 predicted fragment length is 49 bps INFO @ Mon, 13 Nov 2017 13:18:51: #2 alternative fragment length(s) may be 2,49 bps INFO @ Mon, 13 Nov 2017 13:18:51: #2.2 Generate R script for model : SRX2576662.20_model.r WARNING @ Mon, 13 Nov 2017 13:18:51: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:18:51: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Mon, 13 Nov 2017 13:18:51: #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 13:18:51: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:18:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:18:51: start X-correlation... INFO @ Mon, 13 Nov 2017 13:18:51: end of X-cor INFO @ Mon, 13 Nov 2017 13:18:51: #2 finished! INFO @ Mon, 13 Nov 2017 13:18:51: #2 predicted fragment length is 49 bps INFO @ Mon, 13 Nov 2017 13:18:51: #2 alternative fragment length(s) may be 2,49 bps INFO @ Mon, 13 Nov 2017 13:18:51: #2.2 Generate R script for model : SRX2576662.10_model.r WARNING @ Mon, 13 Nov 2017 13:18:51: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:18:51: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Mon, 13 Nov 2017 13:18:51: #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 13:18:51: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:18:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:19:11: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:19:15: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:19:16: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:19:24: #4 Write output xls file... SRX2576662.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:19:24: #4 Write peak in narrowPeak format file... SRX2576662.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:19:24: #4 Write summits bed file... SRX2576662.05_summits.bed INFO @ Mon, 13 Nov 2017 13:19:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1236 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:19:29: #4 Write output xls file... SRX2576662.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:19:29: #4 Write peak in narrowPeak format file... SRX2576662.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:19:29: #4 Write summits bed file... SRX2576662.10_summits.bed INFO @ Mon, 13 Nov 2017 13:19:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (458 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:19:30: #4 Write output xls file... SRX2576662.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:19:30: #4 Write peak in narrowPeak format file... SRX2576662.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:19:30: #4 Write summits bed file... SRX2576662.20_summits.bed INFO @ Mon, 13 Nov 2017 13:19:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (176 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。