Job ID = 11240771 sra ファイルのダウンロード中... Completed: 146102K bytes transferred in 4 seconds (252514K 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... Read 8821570 spots for /home/okishinya/chipatlas/results/dm3/SRX4669055/SRR7817580.sra Written 8821570 spots for /home/okishinya/chipatlas/results/dm3/SRX4669055/SRR7817580.sra 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: 00:03:42 8821570 reads; of these: 8821570 (100.00%) were unpaired; of these: 304291 (3.45%) aligned 0 times 5913359 (67.03%) aligned exactly 1 time 2603920 (29.52%) aligned >1 times 96.55% overall alignment rate Time searching: 00:03:42 Overall time: 00:03:42 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 904260 / 8517279 = 0.1062 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 @ Sun, 07 Oct 2018 20:35:43: # Command line: callpeak -t SRX4669055.bam -f BAM -g dm -n SRX4669055.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669055.20 # format = BAM # ChIP-seq file = ['SRX4669055.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 07 Oct 2018 20:35:43: # Command line: callpeak -t SRX4669055.bam -f BAM -g dm -n SRX4669055.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669055.05 # format = BAM # ChIP-seq file = ['SRX4669055.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 07 Oct 2018 20:35:43: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:35:43: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:35:43: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:35:43: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:35:43: # Command line: callpeak -t SRX4669055.bam -f BAM -g dm -n SRX4669055.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669055.10 # format = BAM # ChIP-seq file = ['SRX4669055.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 07 Oct 2018 20:35:43: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:35:43: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:35:49: 1000000 INFO @ Sun, 07 Oct 2018 20:35:49: 1000000 INFO @ Sun, 07 Oct 2018 20:35:49: 1000000 INFO @ Sun, 07 Oct 2018 20:35:55: 2000000 INFO @ Sun, 07 Oct 2018 20:35:55: 2000000 INFO @ Sun, 07 Oct 2018 20:35:56: 2000000 INFO @ Sun, 07 Oct 2018 20:36:01: 3000000 INFO @ Sun, 07 Oct 2018 20:36:02: 3000000 INFO @ Sun, 07 Oct 2018 20:36:03: 3000000 INFO @ Sun, 07 Oct 2018 20:36:07: 4000000 INFO @ Sun, 07 Oct 2018 20:36:08: 4000000 INFO @ Sun, 07 Oct 2018 20:36:10: 4000000 INFO @ Sun, 07 Oct 2018 20:36:13: 5000000 INFO @ Sun, 07 Oct 2018 20:36:15: 5000000 INFO @ Sun, 07 Oct 2018 20:36:17: 5000000 INFO @ Sun, 07 Oct 2018 20:36:19: 6000000 INFO @ Sun, 07 Oct 2018 20:36:21: 6000000 INFO @ Sun, 07 Oct 2018 20:36:24: 6000000 INFO @ Sun, 07 Oct 2018 20:36:25: 7000000 INFO @ Sun, 07 Oct 2018 20:36:28: 7000000 INFO @ Sun, 07 Oct 2018 20:36:29: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:36:29: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:36:29: #1 total tags in treatment: 7613019 INFO @ Sun, 07 Oct 2018 20:36:29: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:36:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:36:29: #1 tags after filtering in treatment: 7613019 INFO @ Sun, 07 Oct 2018 20:36:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:36:29: #1 finished! INFO @ Sun, 07 Oct 2018 20:36:29: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:36:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:36:29: #2 number of paired peaks: 207 WARNING @ Sun, 07 Oct 2018 20:36:29: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sun, 07 Oct 2018 20:36:29: start model_add_line... INFO @ Sun, 07 Oct 2018 20:36:30: start X-correlation... INFO @ Sun, 07 Oct 2018 20:36:30: end of X-cor INFO @ Sun, 07 Oct 2018 20:36:30: #2 finished! INFO @ Sun, 07 Oct 2018 20:36:30: #2 predicted fragment length is 50 bps INFO @ Sun, 07 Oct 2018 20:36:30: #2 alternative fragment length(s) may be 50 bps INFO @ Sun, 07 Oct 2018 20:36:30: #2.2 Generate R script for model : SRX4669055.05_model.r WARNING @ Sun, 07 Oct 2018 20:36:30: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:36:30: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sun, 07 Oct 2018 20:36:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:36:30: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:36:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:36:30: 7000000 INFO @ Sun, 07 Oct 2018 20:36:32: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:36:32: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:36:32: #1 total tags in treatment: 7613019 INFO @ Sun, 07 Oct 2018 20:36:32: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:36:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:36:32: #1 tags after filtering in treatment: 7613019 INFO @ Sun, 07 Oct 2018 20:36:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:36:32: #1 finished! INFO @ Sun, 07 Oct 2018 20:36:32: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:36:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:36:33: #2 number of paired peaks: 207 WARNING @ Sun, 07 Oct 2018 20:36:33: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sun, 07 Oct 2018 20:36:33: start model_add_line... INFO @ Sun, 07 Oct 2018 20:36:33: start X-correlation... INFO @ Sun, 07 Oct 2018 20:36:33: end of X-cor INFO @ Sun, 07 Oct 2018 20:36:33: #2 finished! INFO @ Sun, 07 Oct 2018 20:36:33: #2 predicted fragment length is 50 bps INFO @ Sun, 07 Oct 2018 20:36:33: #2 alternative fragment length(s) may be 50 bps INFO @ Sun, 07 Oct 2018 20:36:33: #2.2 Generate R script for model : SRX4669055.10_model.r WARNING @ Sun, 07 Oct 2018 20:36:33: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:36:33: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sun, 07 Oct 2018 20:36:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:36:33: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:36:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:36:34: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:36:34: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:36:34: #1 total tags in treatment: 7613019 INFO @ Sun, 07 Oct 2018 20:36:34: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:36:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:36:34: #1 tags after filtering in treatment: 7613019 INFO @ Sun, 07 Oct 2018 20:36:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:36:34: #1 finished! INFO @ Sun, 07 Oct 2018 20:36:34: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:36:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:36:35: #2 number of paired peaks: 207 WARNING @ Sun, 07 Oct 2018 20:36:35: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sun, 07 Oct 2018 20:36:35: start model_add_line... INFO @ Sun, 07 Oct 2018 20:36:35: start X-correlation... INFO @ Sun, 07 Oct 2018 20:36:35: end of X-cor INFO @ Sun, 07 Oct 2018 20:36:35: #2 finished! INFO @ Sun, 07 Oct 2018 20:36:35: #2 predicted fragment length is 50 bps INFO @ Sun, 07 Oct 2018 20:36:35: #2 alternative fragment length(s) may be 50 bps INFO @ Sun, 07 Oct 2018 20:36:35: #2.2 Generate R script for model : SRX4669055.20_model.r WARNING @ Sun, 07 Oct 2018 20:36:35: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:36:35: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sun, 07 Oct 2018 20:36:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:36:35: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:36:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:36:46: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:36:50: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:36:52: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:36:55: #4 Write output xls file... SRX4669055.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:36:55: #4 Write peak in narrowPeak format file... SRX4669055.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:36:55: #4 Write summits bed file... SRX4669055.05_summits.bed INFO @ Sun, 07 Oct 2018 20:36:55: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1317 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:36:59: #4 Write output xls file... SRX4669055.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:36:59: #4 Write peak in narrowPeak format file... SRX4669055.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:36:59: #4 Write summits bed file... SRX4669055.10_summits.bed INFO @ Sun, 07 Oct 2018 20:36:59: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (936 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:37:02: #4 Write output xls file... SRX4669055.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:37:02: #4 Write peak in narrowPeak format file... SRX4669055.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:37:02: #4 Write summits bed file... SRX4669055.20_summits.bed INFO @ Sun, 07 Oct 2018 20:37:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (443 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。