Job ID = 10201965 sra ファイルのダウンロード中... Completed: 454672K bytes transferred in 13 seconds (267996K 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 14369137 spots for /home/okishinya/chipatlas/results/ce10/SRX2576634/SRR5272591.sra Written 14369137 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: 00:09:50 14369137 reads; of these: 14369137 (100.00%) were unpaired; of these: 593928 (4.13%) aligned 0 times 11397277 (79.32%) aligned exactly 1 time 2377932 (16.55%) aligned >1 times 95.87% overall alignment rate Time searching: 00:09:50 Overall time: 00:09:50 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] 4174011 / 13775209 = 0.3030 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 13:24:07: # Command line: callpeak -t SRX2576634.bam -f BAM -g ce -n SRX2576634.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576634.20 # format = BAM # ChIP-seq file = ['SRX2576634.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 13:24:07: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:24:07: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:24:07: # Command line: callpeak -t SRX2576634.bam -f BAM -g ce -n SRX2576634.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576634.05 # format = BAM # ChIP-seq file = ['SRX2576634.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 13:24:07: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:24:07: # Command line: callpeak -t SRX2576634.bam -f BAM -g ce -n SRX2576634.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576634.10 # format = BAM # ChIP-seq file = ['SRX2576634.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 13:24:07: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:24:07: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:24:07: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:24:24: 1000000 INFO @ Mon, 13 Nov 2017 13:24:26: 1000000 INFO @ Mon, 13 Nov 2017 13:24:29: 1000000 INFO @ Mon, 13 Nov 2017 13:24:40: 2000000 INFO @ Mon, 13 Nov 2017 13:24:44: 2000000 INFO @ Mon, 13 Nov 2017 13:24:50: 2000000 INFO @ Mon, 13 Nov 2017 13:24:58: 3000000 INFO @ Mon, 13 Nov 2017 13:25:03: 3000000 INFO @ Mon, 13 Nov 2017 13:25:13: 3000000 INFO @ Mon, 13 Nov 2017 13:25:19: 4000000 INFO @ Mon, 13 Nov 2017 13:25:22: 4000000 INFO @ Mon, 13 Nov 2017 13:25:36: 4000000 INFO @ Mon, 13 Nov 2017 13:25:40: 5000000 INFO @ Mon, 13 Nov 2017 13:25:41: 5000000 INFO @ Mon, 13 Nov 2017 13:25:55: 5000000 INFO @ Mon, 13 Nov 2017 13:25:58: 6000000 INFO @ Mon, 13 Nov 2017 13:25:58: 6000000 INFO @ Mon, 13 Nov 2017 13:26:13: 6000000 INFO @ Mon, 13 Nov 2017 13:26:14: 7000000 INFO @ Mon, 13 Nov 2017 13:26:15: 7000000 INFO @ Mon, 13 Nov 2017 13:26:29: 8000000 INFO @ Mon, 13 Nov 2017 13:26:30: 8000000 INFO @ Mon, 13 Nov 2017 13:26:31: 7000000 INFO @ Mon, 13 Nov 2017 13:26:40: 9000000 INFO @ Mon, 13 Nov 2017 13:26:46: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:26:46: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:26:46: #1 total tags in treatment: 9601198 INFO @ Mon, 13 Nov 2017 13:26:46: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:26:46: #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 13:26:47: #1 tags after filtering in treatment: 9601198 INFO @ Mon, 13 Nov 2017 13:26:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:26:47: #1 finished! INFO @ Mon, 13 Nov 2017 13:26:47: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:26:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:26:48: #2 number of paired peaks: 370 WARNING @ Mon, 13 Nov 2017 13:26:48: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Mon, 13 Nov 2017 13:26:48: start model_add_line... INFO @ Mon, 13 Nov 2017 13:26:48: start X-correlation... INFO @ Mon, 13 Nov 2017 13:26:48: end of X-cor INFO @ Mon, 13 Nov 2017 13:26:48: #2 finished! INFO @ Mon, 13 Nov 2017 13:26:48: #2 predicted fragment length is 46 bps INFO @ Mon, 13 Nov 2017 13:26:48: #2 alternative fragment length(s) may be 2,34,46 bps INFO @ Mon, 13 Nov 2017 13:26:48: #2.2 Generate R script for model : SRX2576634.10_model.r WARNING @ Mon, 13 Nov 2017 13:26:48: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:26:48: #2 You may need to consider one of the other alternative d(s): 2,34,46 WARNING @ Mon, 13 Nov 2017 13:26:48: #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 13:26:48: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:26:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:26:49: 8000000 INFO @ Mon, 13 Nov 2017 13:26:50: 9000000 INFO @ Mon, 13 Nov 2017 13:27:02: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:27:02: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:27:02: #1 total tags in treatment: 9601198 INFO @ Mon, 13 Nov 2017 13:27:02: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:27:02: #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 13:27:02: #1 tags after filtering in treatment: 9601198 INFO @ Mon, 13 Nov 2017 13:27:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:27:02: #1 finished! INFO @ Mon, 13 Nov 2017 13:27:02: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:27:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:27:03: #2 number of paired peaks: 370 WARNING @ Mon, 13 Nov 2017 13:27:03: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Mon, 13 Nov 2017 13:27:03: start model_add_line... INFO @ Mon, 13 Nov 2017 13:27:04: start X-correlation... INFO @ Mon, 13 Nov 2017 13:27:04: end of X-cor INFO @ Mon, 13 Nov 2017 13:27:04: #2 finished! INFO @ Mon, 13 Nov 2017 13:27:04: #2 predicted fragment length is 46 bps INFO @ Mon, 13 Nov 2017 13:27:04: #2 alternative fragment length(s) may be 2,34,46 bps INFO @ Mon, 13 Nov 2017 13:27:04: #2.2 Generate R script for model : SRX2576634.20_model.r WARNING @ Mon, 13 Nov 2017 13:27:04: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:27:04: #2 You may need to consider one of the other alternative d(s): 2,34,46 WARNING @ Mon, 13 Nov 2017 13:27:04: #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 13:27:04: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:27:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:27:08: 9000000 INFO @ Mon, 13 Nov 2017 13:27:15: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:27:19: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:27:19: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:27:19: #1 total tags in treatment: 9601198 INFO @ Mon, 13 Nov 2017 13:27:19: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:27:19: #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 13:27:20: #1 tags after filtering in treatment: 9601198 INFO @ Mon, 13 Nov 2017 13:27:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:27:20: #1 finished! INFO @ Mon, 13 Nov 2017 13:27:20: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:27:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:27:21: #2 number of paired peaks: 370 WARNING @ Mon, 13 Nov 2017 13:27:21: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Mon, 13 Nov 2017 13:27:21: start model_add_line... INFO @ Mon, 13 Nov 2017 13:27:21: start X-correlation... INFO @ Mon, 13 Nov 2017 13:27:21: end of X-cor INFO @ Mon, 13 Nov 2017 13:27:21: #2 finished! INFO @ Mon, 13 Nov 2017 13:27:21: #2 predicted fragment length is 46 bps INFO @ Mon, 13 Nov 2017 13:27:21: #2 alternative fragment length(s) may be 2,34,46 bps INFO @ Mon, 13 Nov 2017 13:27:21: #2.2 Generate R script for model : SRX2576634.05_model.r WARNING @ Mon, 13 Nov 2017 13:27:21: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:27:21: #2 You may need to consider one of the other alternative d(s): 2,34,46 WARNING @ Mon, 13 Nov 2017 13:27:21: #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 13:27:21: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:27:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:27:30: #4 Write output xls file... SRX2576634.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:27:30: #4 Write peak in narrowPeak format file... SRX2576634.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:27:30: #4 Write summits bed file... SRX2576634.10_summits.bed INFO @ Mon, 13 Nov 2017 13:27:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (438 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:27:30: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:27:45: #4 Write output xls file... SRX2576634.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:27:45: #4 Write peak in narrowPeak format file... SRX2576634.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:27:45: #4 Write summits bed file... SRX2576634.20_summits.bed INFO @ Mon, 13 Nov 2017 13:27:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (173 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:27:48: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:28:03: #4 Write output xls file... SRX2576634.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:28:03: #4 Write peak in narrowPeak format file... SRX2576634.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:28:03: #4 Write summits bed file... SRX2576634.05_summits.bed INFO @ Mon, 13 Nov 2017 13:28:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (693 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。