Job ID = 11597972 sra ファイルのダウンロード中... Completed: 591265K bytes transferred in 9 seconds (503555K 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 24378022 spots for /home/okishinya/chipatlas/results/dm3/SRX4664640/SRR7813067.sra Written 24378022 spots for /home/okishinya/chipatlas/results/dm3/SRX4664640/SRR7813067.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: 00:10:07 24378022 reads; of these: 24378022 (100.00%) were unpaired; of these: 1056953 (4.34%) aligned 0 times 16129308 (66.16%) aligned exactly 1 time 7191761 (29.50%) aligned >1 times 95.66% overall alignment rate Time searching: 00:10:07 Overall time: 00:10:07 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] 6885945 / 23321069 = 0.2953 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 16:49:40: # Command line: callpeak -t SRX4664640.bam -f BAM -g dm -n SRX4664640.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4664640.20 # format = BAM # ChIP-seq file = ['SRX4664640.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 16:49:40: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:49:40: # Command line: callpeak -t SRX4664640.bam -f BAM -g dm -n SRX4664640.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4664640.05 # format = BAM # ChIP-seq file = ['SRX4664640.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 16:49:40: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:49:40: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:49:40: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:49:40: # Command line: callpeak -t SRX4664640.bam -f BAM -g dm -n SRX4664640.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4664640.10 # format = BAM # ChIP-seq file = ['SRX4664640.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 16:49:40: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:49:40: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:49:46: 1000000 INFO @ Wed, 30 Jan 2019 16:49:47: 1000000 INFO @ Wed, 30 Jan 2019 16:49:47: 1000000 INFO @ Wed, 30 Jan 2019 16:49:52: 2000000 INFO @ Wed, 30 Jan 2019 16:49:53: 2000000 INFO @ Wed, 30 Jan 2019 16:49:53: 2000000 INFO @ Wed, 30 Jan 2019 16:49:58: 3000000 INFO @ Wed, 30 Jan 2019 16:50:00: 3000000 INFO @ Wed, 30 Jan 2019 16:50:00: 3000000 INFO @ Wed, 30 Jan 2019 16:50:04: 4000000 INFO @ Wed, 30 Jan 2019 16:50:06: 4000000 INFO @ Wed, 30 Jan 2019 16:50:07: 4000000 INFO @ Wed, 30 Jan 2019 16:50:10: 5000000 INFO @ Wed, 30 Jan 2019 16:50:13: 5000000 INFO @ Wed, 30 Jan 2019 16:50:13: 5000000 INFO @ Wed, 30 Jan 2019 16:50:16: 6000000 INFO @ Wed, 30 Jan 2019 16:50:19: 6000000 INFO @ Wed, 30 Jan 2019 16:50:20: 6000000 INFO @ Wed, 30 Jan 2019 16:50:22: 7000000 INFO @ Wed, 30 Jan 2019 16:50:26: 7000000 INFO @ Wed, 30 Jan 2019 16:50:27: 7000000 INFO @ Wed, 30 Jan 2019 16:50:29: 8000000 INFO @ Wed, 30 Jan 2019 16:50:33: 8000000 INFO @ Wed, 30 Jan 2019 16:50:33: 8000000 INFO @ Wed, 30 Jan 2019 16:50:35: 9000000 INFO @ Wed, 30 Jan 2019 16:50:40: 9000000 INFO @ Wed, 30 Jan 2019 16:50:40: 9000000 INFO @ Wed, 30 Jan 2019 16:50:41: 10000000 INFO @ Wed, 30 Jan 2019 16:50:46: 10000000 INFO @ Wed, 30 Jan 2019 16:50:46: 10000000 INFO @ Wed, 30 Jan 2019 16:50:47: 11000000 INFO @ Wed, 30 Jan 2019 16:50:53: 11000000 INFO @ Wed, 30 Jan 2019 16:50:53: 11000000 INFO @ Wed, 30 Jan 2019 16:50:54: 12000000 INFO @ Wed, 30 Jan 2019 16:50:59: 12000000 INFO @ Wed, 30 Jan 2019 16:51:00: 12000000 INFO @ Wed, 30 Jan 2019 16:51:00: 13000000 INFO @ Wed, 30 Jan 2019 16:51:06: 14000000 INFO @ Wed, 30 Jan 2019 16:51:06: 13000000 INFO @ Wed, 30 Jan 2019 16:51:06: 13000000 INFO @ Wed, 30 Jan 2019 16:51:12: 15000000 INFO @ Wed, 30 Jan 2019 16:51:12: 14000000 INFO @ Wed, 30 Jan 2019 16:51:12: 14000000 INFO @ Wed, 30 Jan 2019 16:51:18: 16000000 INFO @ Wed, 30 Jan 2019 16:51:19: 15000000 INFO @ Wed, 30 Jan 2019 16:51:19: 15000000 INFO @ Wed, 30 Jan 2019 16:51:20: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:51:20: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:51:20: #1 total tags in treatment: 16435124 INFO @ Wed, 30 Jan 2019 16:51:20: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:51:20: #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 16:51:21: #1 tags after filtering in treatment: 16435124 INFO @ Wed, 30 Jan 2019 16:51:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:51:21: #1 finished! INFO @ Wed, 30 Jan 2019 16:51:21: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:51:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:51:22: #2 number of paired peaks: 1233 INFO @ Wed, 30 Jan 2019 16:51:22: start model_add_line... INFO @ Wed, 30 Jan 2019 16:51:22: start X-correlation... INFO @ Wed, 30 Jan 2019 16:51:22: end of X-cor INFO @ Wed, 30 Jan 2019 16:51:22: #2 finished! INFO @ Wed, 30 Jan 2019 16:51:22: #2 predicted fragment length is 96 bps INFO @ Wed, 30 Jan 2019 16:51:22: #2 alternative fragment length(s) may be 96 bps INFO @ Wed, 30 Jan 2019 16:51:22: #2.2 Generate R script for model : SRX4664640.10_model.r WARNING @ Wed, 30 Jan 2019 16:51:22: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 16:51:22: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Wed, 30 Jan 2019 16:51:22: #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 16:51:22: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:51:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:51:25: 16000000 INFO @ Wed, 30 Jan 2019 16:51:25: 16000000 INFO @ Wed, 30 Jan 2019 16:51:28: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:51:28: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:51:28: #1 total tags in treatment: 16435124 INFO @ Wed, 30 Jan 2019 16:51:28: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:51:28: #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 16:51:28: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:51:28: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:51:28: #1 total tags in treatment: 16435124 INFO @ Wed, 30 Jan 2019 16:51:28: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:51:28: #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 16:51:28: #1 tags after filtering in treatment: 16435124 INFO @ Wed, 30 Jan 2019 16:51:28: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:51:28: #1 finished! INFO @ Wed, 30 Jan 2019 16:51:28: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:51:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:51:29: #1 tags after filtering in treatment: 16435124 INFO @ Wed, 30 Jan 2019 16:51:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:51:29: #1 finished! INFO @ Wed, 30 Jan 2019 16:51:29: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:51:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:51:30: #2 number of paired peaks: 1233 INFO @ Wed, 30 Jan 2019 16:51:30: start model_add_line... INFO @ Wed, 30 Jan 2019 16:51:30: start X-correlation... INFO @ Wed, 30 Jan 2019 16:51:30: end of X-cor INFO @ Wed, 30 Jan 2019 16:51:30: #2 finished! INFO @ Wed, 30 Jan 2019 16:51:30: #2 predicted fragment length is 96 bps INFO @ Wed, 30 Jan 2019 16:51:30: #2 alternative fragment length(s) may be 96 bps INFO @ Wed, 30 Jan 2019 16:51:30: #2.2 Generate R script for model : SRX4664640.05_model.r WARNING @ Wed, 30 Jan 2019 16:51:30: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 16:51:30: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Wed, 30 Jan 2019 16:51:30: #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 16:51:30: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:51:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:51:30: #2 number of paired peaks: 1233 INFO @ Wed, 30 Jan 2019 16:51:30: start model_add_line... INFO @ Wed, 30 Jan 2019 16:51:30: start X-correlation... INFO @ Wed, 30 Jan 2019 16:51:30: end of X-cor INFO @ Wed, 30 Jan 2019 16:51:30: #2 finished! INFO @ Wed, 30 Jan 2019 16:51:30: #2 predicted fragment length is 96 bps INFO @ Wed, 30 Jan 2019 16:51:30: #2 alternative fragment length(s) may be 96 bps INFO @ Wed, 30 Jan 2019 16:51:30: #2.2 Generate R script for model : SRX4664640.20_model.r WARNING @ Wed, 30 Jan 2019 16:51:30: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 16:51:30: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Wed, 30 Jan 2019 16:51:30: #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 16:51:30: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:51:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:51:58: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:52:05: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:52:07: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:52:16: #4 Write output xls file... SRX4664640.10_peaks.xls INFO @ Wed, 30 Jan 2019 16:52:16: #4 Write peak in narrowPeak format file... SRX4664640.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:52:16: #4 Write summits bed file... SRX4664640.10_summits.bed INFO @ Wed, 30 Jan 2019 16:52:17: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5179 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:52:25: #4 Write output xls file... SRX4664640.20_peaks.xls INFO @ Wed, 30 Jan 2019 16:52:25: #4 Write peak in narrowPeak format file... SRX4664640.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:52:25: #4 Write summits bed file... SRX4664640.20_summits.bed INFO @ Wed, 30 Jan 2019 16:52:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2960 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:52:28: #4 Write output xls file... SRX4664640.05_peaks.xls INFO @ Wed, 30 Jan 2019 16:52:28: #4 Write peak in narrowPeak format file... SRX4664640.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:52:28: #4 Write summits bed file... SRX4664640.05_summits.bed INFO @ Wed, 30 Jan 2019 16:52:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7941 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。