Job ID = 10201982 sra ファイルのダウンロード中... Completed: 518182K bytes transferred in 16 seconds (256812K 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 29253295 spots for /home/okishinya/chipatlas/results/ce10/SRX2576651/SRR5272608.sra Written 29253295 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: 00:00:01 Multiseed full-index search: 00:06:07 29253295 reads; of these: 29253295 (100.00%) were unpaired; of these: 8704296 (29.75%) aligned 0 times 16755604 (57.28%) aligned exactly 1 time 3793395 (12.97%) aligned >1 times 70.25% overall alignment rate Time searching: 00:06:08 Overall time: 00:06:08 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 12 files... [bam_rmdupse_core] 13586714 / 20548999 = 0.6612 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 13:19:41: # Command line: callpeak -t SRX2576651.bam -f BAM -g ce -n SRX2576651.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576651.20 # format = BAM # ChIP-seq file = ['SRX2576651.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 13:19:41: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:19:41: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:19:41: # Command line: callpeak -t SRX2576651.bam -f BAM -g ce -n SRX2576651.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576651.10 # format = BAM # ChIP-seq file = ['SRX2576651.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 13:19:41: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:19:41: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:19:41: # Command line: callpeak -t SRX2576651.bam -f BAM -g ce -n SRX2576651.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576651.05 # format = BAM # ChIP-seq file = ['SRX2576651.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 13:19:41: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:19:41: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:19:48: 1000000 INFO @ Mon, 13 Nov 2017 13:19:48: 1000000 INFO @ Mon, 13 Nov 2017 13:19:48: 1000000 INFO @ Mon, 13 Nov 2017 13:19:55: 2000000 INFO @ Mon, 13 Nov 2017 13:19:55: 2000000 INFO @ Mon, 13 Nov 2017 13:19:55: 2000000 INFO @ Mon, 13 Nov 2017 13:20:02: 3000000 INFO @ Mon, 13 Nov 2017 13:20:02: 3000000 INFO @ Mon, 13 Nov 2017 13:20:03: 3000000 INFO @ Mon, 13 Nov 2017 13:20:08: 4000000 INFO @ Mon, 13 Nov 2017 13:20:09: 4000000 INFO @ Mon, 13 Nov 2017 13:20:10: 4000000 INFO @ Mon, 13 Nov 2017 13:20:15: 5000000 INFO @ Mon, 13 Nov 2017 13:20:16: 5000000 INFO @ Mon, 13 Nov 2017 13:20:17: 5000000 INFO @ Mon, 13 Nov 2017 13:20:22: 6000000 INFO @ Mon, 13 Nov 2017 13:20:23: 6000000 INFO @ Mon, 13 Nov 2017 13:20:25: 6000000 INFO @ Mon, 13 Nov 2017 13:20:28: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:20:28: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:20:28: #1 total tags in treatment: 6962285 INFO @ Mon, 13 Nov 2017 13:20:28: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:20:28: #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 13:20:29: #1 tags after filtering in treatment: 6962285 INFO @ Mon, 13 Nov 2017 13:20:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:20:29: #1 finished! INFO @ Mon, 13 Nov 2017 13:20:29: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:20:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:20:29: #2 number of paired peaks: 705 WARNING @ Mon, 13 Nov 2017 13:20:29: Fewer paired peaks (705) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 705 pairs to build model! INFO @ Mon, 13 Nov 2017 13:20:29: start model_add_line... INFO @ Mon, 13 Nov 2017 13:20:29: start X-correlation... INFO @ Mon, 13 Nov 2017 13:20:29: end of X-cor INFO @ Mon, 13 Nov 2017 13:20:29: #2 finished! INFO @ Mon, 13 Nov 2017 13:20:29: #2 predicted fragment length is 57 bps INFO @ Mon, 13 Nov 2017 13:20:29: #2 alternative fragment length(s) may be 57 bps INFO @ Mon, 13 Nov 2017 13:20:29: #2.2 Generate R script for model : SRX2576651.05_model.r WARNING @ Mon, 13 Nov 2017 13:20:29: #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 13:20:29: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Mon, 13 Nov 2017 13:20:29: #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 13:20:29: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:20:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:20:30: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:20:30: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:20:30: #1 total tags in treatment: 6962285 INFO @ Mon, 13 Nov 2017 13:20:30: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:20:30: #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 13:20:30: #1 tags after filtering in treatment: 6962285 INFO @ Mon, 13 Nov 2017 13:20:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:20:30: #1 finished! INFO @ Mon, 13 Nov 2017 13:20:30: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:20:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:20:30: #2 number of paired peaks: 705 WARNING @ Mon, 13 Nov 2017 13:20:30: Fewer paired peaks (705) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 705 pairs to build model! INFO @ Mon, 13 Nov 2017 13:20:30: start model_add_line... INFO @ Mon, 13 Nov 2017 13:20:31: start X-correlation... INFO @ Mon, 13 Nov 2017 13:20:31: end of X-cor INFO @ Mon, 13 Nov 2017 13:20:31: #2 finished! INFO @ Mon, 13 Nov 2017 13:20:31: #2 predicted fragment length is 57 bps INFO @ Mon, 13 Nov 2017 13:20:31: #2 alternative fragment length(s) may be 57 bps INFO @ Mon, 13 Nov 2017 13:20:31: #2.2 Generate R script for model : SRX2576651.20_model.r WARNING @ Mon, 13 Nov 2017 13:20:31: #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 13:20:31: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Mon, 13 Nov 2017 13:20:31: #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 13:20:31: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:20:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:20:32: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:20:32: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:20:32: #1 total tags in treatment: 6962285 INFO @ Mon, 13 Nov 2017 13:20:32: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:20:32: #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 13:20:32: #1 tags after filtering in treatment: 6962285 INFO @ Mon, 13 Nov 2017 13:20:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:20:32: #1 finished! INFO @ Mon, 13 Nov 2017 13:20:32: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:20:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:20:32: #2 number of paired peaks: 705 WARNING @ Mon, 13 Nov 2017 13:20:32: Fewer paired peaks (705) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 705 pairs to build model! INFO @ Mon, 13 Nov 2017 13:20:32: start model_add_line... INFO @ Mon, 13 Nov 2017 13:20:32: start X-correlation... INFO @ Mon, 13 Nov 2017 13:20:32: end of X-cor INFO @ Mon, 13 Nov 2017 13:20:32: #2 finished! INFO @ Mon, 13 Nov 2017 13:20:32: #2 predicted fragment length is 57 bps INFO @ Mon, 13 Nov 2017 13:20:32: #2 alternative fragment length(s) may be 57 bps INFO @ Mon, 13 Nov 2017 13:20:32: #2.2 Generate R script for model : SRX2576651.10_model.r WARNING @ Mon, 13 Nov 2017 13:20:32: #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 13:20:32: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Mon, 13 Nov 2017 13:20:32: #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 13:20:32: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:20:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:20:44: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:20:46: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:20:49: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:20:52: #4 Write output xls file... SRX2576651.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:20:52: #4 Write peak in narrowPeak format file... SRX2576651.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:20:52: #4 Write summits bed file... SRX2576651.05_summits.bed INFO @ Mon, 13 Nov 2017 13:20:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1444 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:20:54: #4 Write output xls file... SRX2576651.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:20:54: #4 Write peak in narrowPeak format file... SRX2576651.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:20:54: #4 Write summits bed file... SRX2576651.20_summits.bed INFO @ Mon, 13 Nov 2017 13:20:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (398 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:20:58: #4 Write output xls file... SRX2576651.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:20:58: #4 Write peak in narrowPeak format file... SRX2576651.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:20:58: #4 Write summits bed file... SRX2576651.10_summits.bed INFO @ Mon, 13 Nov 2017 13:20:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (892 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。