Job ID = 11240770 sra ファイルのダウンロード中... Completed: 516597K bytes transferred in 12 seconds (347277K 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 29123595 spots for /home/okishinya/chipatlas/results/dm3/SRX4669054/SRR7817579.sra Written 29123595 spots for /home/okishinya/chipatlas/results/dm3/SRX4669054/SRR7817579.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: 00:13:19 29123595 reads; of these: 29123595 (100.00%) were unpaired; of these: 1124946 (3.86%) aligned 0 times 18974676 (65.15%) aligned exactly 1 time 9023973 (30.99%) aligned >1 times 96.14% overall alignment rate Time searching: 00:13:19 Overall time: 00:13:19 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] 7242367 / 27998649 = 0.2587 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 20:50:42: # Command line: callpeak -t SRX4669054.bam -f BAM -g dm -n SRX4669054.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669054.10 # format = BAM # ChIP-seq file = ['SRX4669054.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 20:50:42: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:50:42: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:50:42: # Command line: callpeak -t SRX4669054.bam -f BAM -g dm -n SRX4669054.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669054.20 # format = BAM # ChIP-seq file = ['SRX4669054.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 20:50:42: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:50:42: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:50:42: # Command line: callpeak -t SRX4669054.bam -f BAM -g dm -n SRX4669054.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669054.05 # format = BAM # ChIP-seq file = ['SRX4669054.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 20:50:42: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:50:42: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:50:48: 1000000 INFO @ Sun, 07 Oct 2018 20:50:50: 1000000 INFO @ Sun, 07 Oct 2018 20:50:50: 1000000 INFO @ Sun, 07 Oct 2018 20:50:55: 2000000 INFO @ Sun, 07 Oct 2018 20:50:59: 2000000 INFO @ Sun, 07 Oct 2018 20:50:59: 2000000 INFO @ Sun, 07 Oct 2018 20:51:01: 3000000 INFO @ Sun, 07 Oct 2018 20:51:08: 3000000 INFO @ Sun, 07 Oct 2018 20:51:08: 3000000 INFO @ Sun, 07 Oct 2018 20:51:08: 4000000 INFO @ Sun, 07 Oct 2018 20:51:14: 5000000 INFO @ Sun, 07 Oct 2018 20:51:16: 4000000 INFO @ Sun, 07 Oct 2018 20:51:16: 4000000 INFO @ Sun, 07 Oct 2018 20:51:21: 6000000 INFO @ Sun, 07 Oct 2018 20:51:24: 5000000 INFO @ Sun, 07 Oct 2018 20:51:24: 5000000 INFO @ Sun, 07 Oct 2018 20:51:27: 7000000 INFO @ Sun, 07 Oct 2018 20:51:33: 6000000 INFO @ Sun, 07 Oct 2018 20:51:33: 6000000 INFO @ Sun, 07 Oct 2018 20:51:34: 8000000 INFO @ Sun, 07 Oct 2018 20:51:41: 9000000 INFO @ Sun, 07 Oct 2018 20:51:41: 7000000 INFO @ Sun, 07 Oct 2018 20:51:41: 7000000 INFO @ Sun, 07 Oct 2018 20:51:47: 10000000 INFO @ Sun, 07 Oct 2018 20:51:50: 8000000 INFO @ Sun, 07 Oct 2018 20:51:50: 8000000 INFO @ Sun, 07 Oct 2018 20:51:54: 11000000 INFO @ Sun, 07 Oct 2018 20:51:58: 9000000 INFO @ Sun, 07 Oct 2018 20:51:59: 9000000 INFO @ Sun, 07 Oct 2018 20:52:01: 12000000 INFO @ Sun, 07 Oct 2018 20:52:07: 10000000 INFO @ Sun, 07 Oct 2018 20:52:07: 10000000 INFO @ Sun, 07 Oct 2018 20:52:07: 13000000 INFO @ Sun, 07 Oct 2018 20:52:14: 14000000 INFO @ Sun, 07 Oct 2018 20:52:15: 11000000 INFO @ Sun, 07 Oct 2018 20:52:15: 11000000 INFO @ Sun, 07 Oct 2018 20:52:21: 15000000 INFO @ Sun, 07 Oct 2018 20:52:24: 12000000 INFO @ Sun, 07 Oct 2018 20:52:24: 12000000 INFO @ Sun, 07 Oct 2018 20:52:27: 16000000 INFO @ Sun, 07 Oct 2018 20:52:33: 13000000 INFO @ Sun, 07 Oct 2018 20:52:33: 13000000 INFO @ Sun, 07 Oct 2018 20:52:34: 17000000 INFO @ Sun, 07 Oct 2018 20:52:41: 18000000 INFO @ Sun, 07 Oct 2018 20:52:41: 14000000 INFO @ Sun, 07 Oct 2018 20:52:41: 14000000 INFO @ Sun, 07 Oct 2018 20:52:47: 19000000 INFO @ Sun, 07 Oct 2018 20:52:50: 15000000 INFO @ Sun, 07 Oct 2018 20:52:50: 15000000 INFO @ Sun, 07 Oct 2018 20:52:54: 20000000 INFO @ Sun, 07 Oct 2018 20:52:58: 16000000 INFO @ Sun, 07 Oct 2018 20:52:59: 16000000 INFO @ Sun, 07 Oct 2018 20:52:59: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:52:59: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:52:59: #1 total tags in treatment: 20756282 INFO @ Sun, 07 Oct 2018 20:52:59: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:52:59: #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 20:53:00: #1 tags after filtering in treatment: 20756282 INFO @ Sun, 07 Oct 2018 20:53:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:53:00: #1 finished! INFO @ Sun, 07 Oct 2018 20:53:00: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:53:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:53:01: #2 number of paired peaks: 132 WARNING @ Sun, 07 Oct 2018 20:53:01: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Sun, 07 Oct 2018 20:53:01: start model_add_line... INFO @ Sun, 07 Oct 2018 20:53:01: start X-correlation... INFO @ Sun, 07 Oct 2018 20:53:01: end of X-cor INFO @ Sun, 07 Oct 2018 20:53:01: #2 finished! INFO @ Sun, 07 Oct 2018 20:53:01: #2 predicted fragment length is 45 bps INFO @ Sun, 07 Oct 2018 20:53:01: #2 alternative fragment length(s) may be 45 bps INFO @ Sun, 07 Oct 2018 20:53:01: #2.2 Generate R script for model : SRX4669054.20_model.r WARNING @ Sun, 07 Oct 2018 20:53:01: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:53:01: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sun, 07 Oct 2018 20:53:01: #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 20:53:01: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:53:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:53:07: 17000000 INFO @ Sun, 07 Oct 2018 20:53:08: 17000000 INFO @ Sun, 07 Oct 2018 20:53:16: 18000000 INFO @ Sun, 07 Oct 2018 20:53:17: 18000000 INFO @ Sun, 07 Oct 2018 20:53:25: 19000000 INFO @ Sun, 07 Oct 2018 20:53:25: 19000000 INFO @ Sun, 07 Oct 2018 20:53:34: 20000000 INFO @ Sun, 07 Oct 2018 20:53:34: 20000000 INFO @ Sun, 07 Oct 2018 20:53:40: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:53:40: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:53:40: #1 total tags in treatment: 20756282 INFO @ Sun, 07 Oct 2018 20:53:40: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:53:40: #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 20:53:41: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:53:41: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:53:41: #1 total tags in treatment: 20756282 INFO @ Sun, 07 Oct 2018 20:53:41: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:53:41: #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 20:53:41: #1 tags after filtering in treatment: 20756282 INFO @ Sun, 07 Oct 2018 20:53:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:53:41: #1 finished! INFO @ Sun, 07 Oct 2018 20:53:41: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:53:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:53:41: #1 tags after filtering in treatment: 20756282 INFO @ Sun, 07 Oct 2018 20:53:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:53:41: #1 finished! INFO @ Sun, 07 Oct 2018 20:53:41: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:53:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:53:42: #2 number of paired peaks: 132 WARNING @ Sun, 07 Oct 2018 20:53:42: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Sun, 07 Oct 2018 20:53:42: start model_add_line... INFO @ Sun, 07 Oct 2018 20:53:42: start X-correlation... INFO @ Sun, 07 Oct 2018 20:53:42: end of X-cor INFO @ Sun, 07 Oct 2018 20:53:42: #2 finished! INFO @ Sun, 07 Oct 2018 20:53:42: #2 predicted fragment length is 45 bps INFO @ Sun, 07 Oct 2018 20:53:42: #2 alternative fragment length(s) may be 45 bps INFO @ Sun, 07 Oct 2018 20:53:42: #2.2 Generate R script for model : SRX4669054.10_model.r WARNING @ Sun, 07 Oct 2018 20:53:42: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:53:42: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sun, 07 Oct 2018 20:53:42: #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 20:53:42: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:53:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:53:42: #2 number of paired peaks: 132 WARNING @ Sun, 07 Oct 2018 20:53:42: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Sun, 07 Oct 2018 20:53:42: start model_add_line... INFO @ Sun, 07 Oct 2018 20:53:43: start X-correlation... INFO @ Sun, 07 Oct 2018 20:53:43: end of X-cor INFO @ Sun, 07 Oct 2018 20:53:43: #2 finished! INFO @ Sun, 07 Oct 2018 20:53:43: #2 predicted fragment length is 45 bps INFO @ Sun, 07 Oct 2018 20:53:43: #2 alternative fragment length(s) may be 45 bps INFO @ Sun, 07 Oct 2018 20:53:43: #2.2 Generate R script for model : SRX4669054.05_model.r WARNING @ Sun, 07 Oct 2018 20:53:43: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:53:43: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sun, 07 Oct 2018 20:53:43: #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 20:53:43: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:53:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:53:44: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:54:10: #4 Write output xls file... SRX4669054.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:54:10: #4 Write peak in narrowPeak format file... SRX4669054.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:54:10: #4 Write summits bed file... SRX4669054.20_summits.bed INFO @ Sun, 07 Oct 2018 20:54:10: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (1109 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:54:23: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:54:24: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:54:44: #4 Write output xls file... SRX4669054.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:54:44: #4 Write peak in narrowPeak format file... SRX4669054.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:54:44: #4 Write summits bed file... SRX4669054.05_summits.bed INFO @ Sun, 07 Oct 2018 20:54:44: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1946 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:54:46: #4 Write output xls file... SRX4669054.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:54:46: #4 Write peak in narrowPeak format file... SRX4669054.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:54:46: #4 Write summits bed file... SRX4669054.10_summits.bed INFO @ Sun, 07 Oct 2018 20:54:46: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1509 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。