Job ID = 11597975 sra ファイルのダウンロード中... Completed: 583909K bytes transferred in 9 seconds (530889K 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 24920281 spots for /home/okishinya/chipatlas/results/dm3/SRX4664642/SRR7813069.sra Written 24920281 spots for /home/okishinya/chipatlas/results/dm3/SRX4664642/SRR7813069.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: 00:10:19 24920281 reads; of these: 24920281 (100.00%) were unpaired; of these: 884044 (3.55%) aligned 0 times 16503031 (66.22%) aligned exactly 1 time 7533206 (30.23%) aligned >1 times 96.45% overall alignment rate Time searching: 00:10:19 Overall time: 00:10:19 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_sort_core] merging from 12 files... [bam_rmdupse_core] 3256706 / 24036237 = 0.1355 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 @ Wed, 30 Jan 2019 18:40:08: # Command line: callpeak -t SRX4664642.bam -f BAM -g dm -n SRX4664642.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4664642.05 # format = BAM # ChIP-seq file = ['SRX4664642.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 @ Wed, 30 Jan 2019 18:40:08: #1 read tag files... INFO @ Wed, 30 Jan 2019 18:40:08: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 18:40:08: # Command line: callpeak -t SRX4664642.bam -f BAM -g dm -n SRX4664642.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4664642.10 # format = BAM # ChIP-seq file = ['SRX4664642.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 @ Wed, 30 Jan 2019 18:40:08: #1 read tag files... INFO @ Wed, 30 Jan 2019 18:40:08: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 18:40:08: # Command line: callpeak -t SRX4664642.bam -f BAM -g dm -n SRX4664642.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4664642.20 # format = BAM # ChIP-seq file = ['SRX4664642.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 @ Wed, 30 Jan 2019 18:40:08: #1 read tag files... INFO @ Wed, 30 Jan 2019 18:40:08: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 18:40:14: 1000000 INFO @ Wed, 30 Jan 2019 18:40:14: 1000000 INFO @ Wed, 30 Jan 2019 18:40:14: 1000000 INFO @ Wed, 30 Jan 2019 18:40:21: 2000000 INFO @ Wed, 30 Jan 2019 18:40:21: 2000000 INFO @ Wed, 30 Jan 2019 18:40:21: 2000000 INFO @ Wed, 30 Jan 2019 18:40:27: 3000000 INFO @ Wed, 30 Jan 2019 18:40:27: 3000000 INFO @ Wed, 30 Jan 2019 18:40:28: 3000000 INFO @ Wed, 30 Jan 2019 18:40:34: 4000000 INFO @ Wed, 30 Jan 2019 18:40:34: 4000000 INFO @ Wed, 30 Jan 2019 18:40:36: 4000000 INFO @ Wed, 30 Jan 2019 18:40:41: 5000000 INFO @ Wed, 30 Jan 2019 18:40:41: 5000000 INFO @ Wed, 30 Jan 2019 18:40:43: 5000000 INFO @ Wed, 30 Jan 2019 18:40:48: 6000000 INFO @ Wed, 30 Jan 2019 18:40:48: 6000000 INFO @ Wed, 30 Jan 2019 18:40:51: 6000000 INFO @ Wed, 30 Jan 2019 18:40:55: 7000000 INFO @ Wed, 30 Jan 2019 18:40:55: 7000000 INFO @ Wed, 30 Jan 2019 18:40:58: 7000000 INFO @ Wed, 30 Jan 2019 18:41:02: 8000000 INFO @ Wed, 30 Jan 2019 18:41:02: 8000000 INFO @ Wed, 30 Jan 2019 18:41:06: 8000000 INFO @ Wed, 30 Jan 2019 18:41:09: 9000000 INFO @ Wed, 30 Jan 2019 18:41:09: 9000000 INFO @ Wed, 30 Jan 2019 18:41:13: 9000000 INFO @ Wed, 30 Jan 2019 18:41:16: 10000000 INFO @ Wed, 30 Jan 2019 18:41:16: 10000000 INFO @ Wed, 30 Jan 2019 18:41:21: 10000000 INFO @ Wed, 30 Jan 2019 18:41:23: 11000000 INFO @ Wed, 30 Jan 2019 18:41:23: 11000000 INFO @ Wed, 30 Jan 2019 18:41:28: 11000000 INFO @ Wed, 30 Jan 2019 18:41:30: 12000000 INFO @ Wed, 30 Jan 2019 18:41:30: 12000000 INFO @ Wed, 30 Jan 2019 18:41:36: 12000000 INFO @ Wed, 30 Jan 2019 18:41:37: 13000000 INFO @ Wed, 30 Jan 2019 18:41:37: 13000000 INFO @ Wed, 30 Jan 2019 18:41:43: 13000000 INFO @ Wed, 30 Jan 2019 18:41:44: 14000000 INFO @ Wed, 30 Jan 2019 18:41:44: 14000000 INFO @ Wed, 30 Jan 2019 18:41:51: 14000000 INFO @ Wed, 30 Jan 2019 18:41:51: 15000000 INFO @ Wed, 30 Jan 2019 18:41:51: 15000000 INFO @ Wed, 30 Jan 2019 18:41:58: 16000000 INFO @ Wed, 30 Jan 2019 18:41:58: 16000000 INFO @ Wed, 30 Jan 2019 18:41:58: 15000000 INFO @ Wed, 30 Jan 2019 18:42:05: 17000000 INFO @ Wed, 30 Jan 2019 18:42:05: 17000000 INFO @ Wed, 30 Jan 2019 18:42:06: 16000000 INFO @ Wed, 30 Jan 2019 18:42:12: 18000000 INFO @ Wed, 30 Jan 2019 18:42:12: 18000000 INFO @ Wed, 30 Jan 2019 18:42:13: 17000000 INFO @ Wed, 30 Jan 2019 18:42:19: 19000000 INFO @ Wed, 30 Jan 2019 18:42:19: 19000000 INFO @ Wed, 30 Jan 2019 18:42:21: 18000000 INFO @ Wed, 30 Jan 2019 18:42:26: 20000000 INFO @ Wed, 30 Jan 2019 18:42:26: 20000000 INFO @ Wed, 30 Jan 2019 18:42:28: 19000000 INFO @ Wed, 30 Jan 2019 18:42:31: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 18:42:31: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 18:42:31: #1 total tags in treatment: 20779531 INFO @ Wed, 30 Jan 2019 18:42:31: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 18:42:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 18:42:31: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 18:42:31: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 18:42:31: #1 total tags in treatment: 20779531 INFO @ Wed, 30 Jan 2019 18:42:31: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 18:42:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 18:42:32: #1 tags after filtering in treatment: 20779531 INFO @ Wed, 30 Jan 2019 18:42:32: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 18:42:32: #1 finished! INFO @ Wed, 30 Jan 2019 18:42:32: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 18:42:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 18:42:32: #1 tags after filtering in treatment: 20779531 INFO @ Wed, 30 Jan 2019 18:42:32: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 18:42:32: #1 finished! INFO @ Wed, 30 Jan 2019 18:42:32: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 18:42:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 18:42:33: #2 number of paired peaks: 600 WARNING @ Wed, 30 Jan 2019 18:42:33: Fewer paired peaks (600) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 600 pairs to build model! INFO @ Wed, 30 Jan 2019 18:42:33: start model_add_line... INFO @ Wed, 30 Jan 2019 18:42:33: #2 number of paired peaks: 600 WARNING @ Wed, 30 Jan 2019 18:42:33: Fewer paired peaks (600) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 600 pairs to build model! INFO @ Wed, 30 Jan 2019 18:42:33: start model_add_line... INFO @ Wed, 30 Jan 2019 18:42:33: start X-correlation... INFO @ Wed, 30 Jan 2019 18:42:33: end of X-cor INFO @ Wed, 30 Jan 2019 18:42:33: #2 finished! INFO @ Wed, 30 Jan 2019 18:42:33: #2 predicted fragment length is 66 bps INFO @ Wed, 30 Jan 2019 18:42:33: #2 alternative fragment length(s) may be 4,66 bps INFO @ Wed, 30 Jan 2019 18:42:33: #2.2 Generate R script for model : SRX4664642.10_model.r WARNING @ Wed, 30 Jan 2019 18:42:33: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 18:42:33: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Wed, 30 Jan 2019 18:42:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 18:42:33: #3 Call peaks... INFO @ Wed, 30 Jan 2019 18:42:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 18:42:33: start X-correlation... INFO @ Wed, 30 Jan 2019 18:42:33: end of X-cor INFO @ Wed, 30 Jan 2019 18:42:33: #2 finished! INFO @ Wed, 30 Jan 2019 18:42:33: #2 predicted fragment length is 66 bps INFO @ Wed, 30 Jan 2019 18:42:33: #2 alternative fragment length(s) may be 4,66 bps INFO @ Wed, 30 Jan 2019 18:42:33: #2.2 Generate R script for model : SRX4664642.20_model.r WARNING @ Wed, 30 Jan 2019 18:42:33: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 18:42:33: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Wed, 30 Jan 2019 18:42:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 18:42:33: #3 Call peaks... INFO @ Wed, 30 Jan 2019 18:42:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 18:42:35: 20000000 INFO @ Wed, 30 Jan 2019 18:42:40: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 18:42:40: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 18:42:40: #1 total tags in treatment: 20779531 INFO @ Wed, 30 Jan 2019 18:42:40: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 18:42:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 18:42:41: #1 tags after filtering in treatment: 20779531 INFO @ Wed, 30 Jan 2019 18:42:41: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 18:42:41: #1 finished! INFO @ Wed, 30 Jan 2019 18:42:41: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 18:42:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 18:42:42: #2 number of paired peaks: 600 WARNING @ Wed, 30 Jan 2019 18:42:42: Fewer paired peaks (600) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 600 pairs to build model! INFO @ Wed, 30 Jan 2019 18:42:42: start model_add_line... INFO @ Wed, 30 Jan 2019 18:42:42: start X-correlation... INFO @ Wed, 30 Jan 2019 18:42:42: end of X-cor INFO @ Wed, 30 Jan 2019 18:42:42: #2 finished! INFO @ Wed, 30 Jan 2019 18:42:42: #2 predicted fragment length is 66 bps INFO @ Wed, 30 Jan 2019 18:42:42: #2 alternative fragment length(s) may be 4,66 bps INFO @ Wed, 30 Jan 2019 18:42:42: #2.2 Generate R script for model : SRX4664642.05_model.r WARNING @ Wed, 30 Jan 2019 18:42:42: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 18:42:42: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Wed, 30 Jan 2019 18:42:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 18:42:42: #3 Call peaks... INFO @ Wed, 30 Jan 2019 18:42:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 18:43:15: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 18:43:15: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 18:43:26: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 18:43:38: #4 Write output xls file... SRX4664642.20_peaks.xls INFO @ Wed, 30 Jan 2019 18:43:38: #4 Write output xls file... SRX4664642.10_peaks.xls INFO @ Wed, 30 Jan 2019 18:43:38: #4 Write peak in narrowPeak format file... SRX4664642.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 18:43:38: #4 Write summits bed file... SRX4664642.20_summits.bed INFO @ Wed, 30 Jan 2019 18:43:38: #4 Write peak in narrowPeak format file... SRX4664642.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 18:43:38: Done! INFO @ Wed, 30 Jan 2019 18:43:38: #4 Write summits bed file... SRX4664642.10_summits.bed INFO @ Wed, 30 Jan 2019 18:43:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2255 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3996 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 18:43:51: #4 Write output xls file... SRX4664642.05_peaks.xls INFO @ Wed, 30 Jan 2019 18:43:51: #4 Write peak in narrowPeak format file... SRX4664642.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 18:43:51: #4 Write summits bed file... SRX4664642.05_summits.bed INFO @ Wed, 30 Jan 2019 18:43:51: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6527 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。