Job ID = 10175245 sra ファイルのダウンロード中... Completed: 580812K bytes transferred in 16 seconds (283455K 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 32781705 spots for /home/okishinya/chipatlas/results/dm3/SRX2804223/SRR5534651.sra Written 32781705 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: 00:00:00 Multiseed full-index search: 00:11:56 32781705 reads; of these: 32781705 (100.00%) were unpaired; of these: 9341855 (28.50%) aligned 0 times 16003658 (48.82%) aligned exactly 1 time 7436192 (22.68%) aligned >1 times 71.50% overall alignment rate Time searching: 00:11:56 Overall time: 00:11:56 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] 2885231 / 23439850 = 0.1231 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, 06 Nov 2017 12:06:06: # Command line: callpeak -t SRX2804223.bam -f BAM -g dm -n SRX2804223.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2804223.10 # format = BAM # ChIP-seq file = ['SRX2804223.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 @ Mon, 06 Nov 2017 12:06:06: # Command line: callpeak -t SRX2804223.bam -f BAM -g dm -n SRX2804223.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2804223.05 # format = BAM # ChIP-seq file = ['SRX2804223.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 @ Mon, 06 Nov 2017 12:06:06: # Command line: callpeak -t SRX2804223.bam -f BAM -g dm -n SRX2804223.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2804223.20 # format = BAM # ChIP-seq file = ['SRX2804223.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 @ Mon, 06 Nov 2017 12:06:06: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:06:06: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:06:06: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:06:06: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:06:06: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:06:06: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:06:13: 1000000 INFO @ Mon, 06 Nov 2017 12:06:13: 1000000 INFO @ Mon, 06 Nov 2017 12:06:13: 1000000 INFO @ Mon, 06 Nov 2017 12:06:21: 2000000 INFO @ Mon, 06 Nov 2017 12:06:21: 2000000 INFO @ Mon, 06 Nov 2017 12:06:21: 2000000 INFO @ Mon, 06 Nov 2017 12:06:28: 3000000 INFO @ Mon, 06 Nov 2017 12:06:29: 3000000 INFO @ Mon, 06 Nov 2017 12:06:29: 3000000 INFO @ Mon, 06 Nov 2017 12:06:36: 4000000 INFO @ Mon, 06 Nov 2017 12:06:36: 4000000 INFO @ Mon, 06 Nov 2017 12:06:36: 4000000 INFO @ Mon, 06 Nov 2017 12:06:43: 5000000 INFO @ Mon, 06 Nov 2017 12:06:44: 5000000 INFO @ Mon, 06 Nov 2017 12:06:44: 5000000 INFO @ Mon, 06 Nov 2017 12:06:50: 6000000 INFO @ Mon, 06 Nov 2017 12:06:51: 6000000 INFO @ Mon, 06 Nov 2017 12:06:51: 6000000 INFO @ Mon, 06 Nov 2017 12:06:58: 7000000 INFO @ Mon, 06 Nov 2017 12:06:59: 7000000 INFO @ Mon, 06 Nov 2017 12:06:59: 7000000 INFO @ Mon, 06 Nov 2017 12:07:05: 8000000 INFO @ Mon, 06 Nov 2017 12:07:06: 8000000 INFO @ Mon, 06 Nov 2017 12:07:06: 8000000 INFO @ Mon, 06 Nov 2017 12:07:12: 9000000 INFO @ Mon, 06 Nov 2017 12:07:13: 9000000 INFO @ Mon, 06 Nov 2017 12:07:14: 9000000 INFO @ Mon, 06 Nov 2017 12:07:20: 10000000 INFO @ Mon, 06 Nov 2017 12:07:21: 10000000 INFO @ Mon, 06 Nov 2017 12:07:21: 10000000 INFO @ Mon, 06 Nov 2017 12:07:27: 11000000 INFO @ Mon, 06 Nov 2017 12:07:28: 11000000 INFO @ Mon, 06 Nov 2017 12:07:30: 11000000 INFO @ Mon, 06 Nov 2017 12:07:34: 12000000 INFO @ Mon, 06 Nov 2017 12:07:36: 12000000 INFO @ Mon, 06 Nov 2017 12:07:38: 12000000 INFO @ Mon, 06 Nov 2017 12:07:41: 13000000 INFO @ Mon, 06 Nov 2017 12:07:44: 13000000 INFO @ Mon, 06 Nov 2017 12:07:46: 13000000 INFO @ Mon, 06 Nov 2017 12:07:49: 14000000 INFO @ Mon, 06 Nov 2017 12:07:51: 14000000 INFO @ Mon, 06 Nov 2017 12:07:53: 14000000 INFO @ Mon, 06 Nov 2017 12:07:56: 15000000 INFO @ Mon, 06 Nov 2017 12:07:59: 15000000 INFO @ Mon, 06 Nov 2017 12:08:01: 15000000 INFO @ Mon, 06 Nov 2017 12:08:03: 16000000 INFO @ Mon, 06 Nov 2017 12:08:07: 16000000 INFO @ Mon, 06 Nov 2017 12:08:09: 16000000 INFO @ Mon, 06 Nov 2017 12:08:11: 17000000 INFO @ Mon, 06 Nov 2017 12:08:14: 17000000 INFO @ Mon, 06 Nov 2017 12:08:17: 17000000 INFO @ Mon, 06 Nov 2017 12:08:18: 18000000 INFO @ Mon, 06 Nov 2017 12:08:22: 18000000 INFO @ Mon, 06 Nov 2017 12:08:24: 18000000 INFO @ Mon, 06 Nov 2017 12:08:25: 19000000 INFO @ Mon, 06 Nov 2017 12:08:31: 19000000 INFO @ Mon, 06 Nov 2017 12:08:33: 20000000 INFO @ Mon, 06 Nov 2017 12:08:34: 19000000 INFO @ Mon, 06 Nov 2017 12:08:37: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:08:37: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:08:37: #1 total tags in treatment: 20554619 INFO @ Mon, 06 Nov 2017 12:08:37: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:08:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:08:37: #1 tags after filtering in treatment: 20554619 INFO @ Mon, 06 Nov 2017 12:08:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:08:37: #1 finished! INFO @ Mon, 06 Nov 2017 12:08:37: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:08:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:08:39: #2 number of paired peaks: 120 WARNING @ Mon, 06 Nov 2017 12:08:39: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Mon, 06 Nov 2017 12:08:39: start model_add_line... INFO @ Mon, 06 Nov 2017 12:08:39: start X-correlation... INFO @ Mon, 06 Nov 2017 12:08:39: end of X-cor INFO @ Mon, 06 Nov 2017 12:08:39: #2 finished! INFO @ Mon, 06 Nov 2017 12:08:39: #2 predicted fragment length is 54 bps INFO @ Mon, 06 Nov 2017 12:08:39: #2 alternative fragment length(s) may be 4,54,508 bps INFO @ Mon, 06 Nov 2017 12:08:39: #2.2 Generate R script for model : SRX2804223.20_model.r WARNING @ Mon, 06 Nov 2017 12:08:39: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 12:08:39: #2 You may need to consider one of the other alternative d(s): 4,54,508 WARNING @ Mon, 06 Nov 2017 12:08:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 12:08:39: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:08:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:08:41: 20000000 INFO @ Mon, 06 Nov 2017 12:08:43: 20000000 INFO @ Mon, 06 Nov 2017 12:08:46: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:08:46: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:08:46: #1 total tags in treatment: 20554619 INFO @ Mon, 06 Nov 2017 12:08:46: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:08:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:08:46: #1 tags after filtering in treatment: 20554619 INFO @ Mon, 06 Nov 2017 12:08:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:08:46: #1 finished! INFO @ Mon, 06 Nov 2017 12:08:46: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:08:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:08:48: #2 number of paired peaks: 120 WARNING @ Mon, 06 Nov 2017 12:08:48: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Mon, 06 Nov 2017 12:08:48: start model_add_line... INFO @ Mon, 06 Nov 2017 12:08:48: start X-correlation... INFO @ Mon, 06 Nov 2017 12:08:48: end of X-cor INFO @ Mon, 06 Nov 2017 12:08:48: #2 finished! INFO @ Mon, 06 Nov 2017 12:08:48: #2 predicted fragment length is 54 bps INFO @ Mon, 06 Nov 2017 12:08:48: #2 alternative fragment length(s) may be 4,54,508 bps INFO @ Mon, 06 Nov 2017 12:08:48: #2.2 Generate R script for model : SRX2804223.05_model.r WARNING @ Mon, 06 Nov 2017 12:08:48: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 12:08:48: #2 You may need to consider one of the other alternative d(s): 4,54,508 WARNING @ Mon, 06 Nov 2017 12:08:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 12:08:48: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:08:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:08:48: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:08:48: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:08:48: #1 total tags in treatment: 20554619 INFO @ Mon, 06 Nov 2017 12:08:48: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:08:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:08:49: #1 tags after filtering in treatment: 20554619 INFO @ Mon, 06 Nov 2017 12:08:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:08:49: #1 finished! INFO @ Mon, 06 Nov 2017 12:08:49: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:08:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:08:50: #2 number of paired peaks: 120 WARNING @ Mon, 06 Nov 2017 12:08:50: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Mon, 06 Nov 2017 12:08:50: start model_add_line... INFO @ Mon, 06 Nov 2017 12:08:50: start X-correlation... INFO @ Mon, 06 Nov 2017 12:08:50: end of X-cor INFO @ Mon, 06 Nov 2017 12:08:50: #2 finished! INFO @ Mon, 06 Nov 2017 12:08:50: #2 predicted fragment length is 54 bps INFO @ Mon, 06 Nov 2017 12:08:50: #2 alternative fragment length(s) may be 4,54,508 bps INFO @ Mon, 06 Nov 2017 12:08:50: #2.2 Generate R script for model : SRX2804223.10_model.r WARNING @ Mon, 06 Nov 2017 12:08:50: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 12:08:50: #2 You may need to consider one of the other alternative d(s): 4,54,508 WARNING @ Mon, 06 Nov 2017 12:08:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 12:08:50: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:08:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:09:21: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:09:32: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:09:33: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:09:43: #4 Write output xls file... SRX2804223.20_peaks.xls INFO @ Mon, 06 Nov 2017 12:09:44: #4 Write peak in narrowPeak format file... SRX2804223.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:09:44: #4 Write summits bed file... SRX2804223.20_summits.bed INFO @ Mon, 06 Nov 2017 12:09:44: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1028 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:09:56: #4 Write output xls file... SRX2804223.10_peaks.xls INFO @ Mon, 06 Nov 2017 12:09:56: #4 Write peak in narrowPeak format file... SRX2804223.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:09:56: #4 Write summits bed file... SRX2804223.10_summits.bed INFO @ Mon, 06 Nov 2017 12:09:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2137 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:09:59: #4 Write output xls file... SRX2804223.05_peaks.xls INFO @ Mon, 06 Nov 2017 12:09:59: #4 Write peak in narrowPeak format file... SRX2804223.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:09:59: #4 Write summits bed file... SRX2804223.05_summits.bed INFO @ Mon, 06 Nov 2017 12:09:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4065 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。