Job ID = 9158416 sra ファイルのダウンロード中... Completed: 1329537K bytes transferred in 13 seconds (820884K bits/sec), in 1 file, 2 directories. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Written 22183245 spots for /home/okishinya/chipatlas/results/dm3/SRX1179573/SRR2232434.sra Written 22183245 spots total 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:15:14 22183245 reads; of these: 22183245 (100.00%) were paired; of these: 821961 (3.71%) aligned concordantly 0 times 14576452 (65.71%) aligned concordantly exactly 1 time 6784832 (30.59%) aligned concordantly >1 times ---- 821961 pairs aligned concordantly 0 times; of these: 7779 (0.95%) aligned discordantly 1 time ---- 814182 pairs aligned 0 times concordantly or discordantly; of these: 1628364 mates make up the pairs; of these: 998659 (61.33%) aligned 0 times 438772 (26.95%) aligned exactly 1 time 190933 (11.73%) aligned >1 times 97.75% overall alignment rate Time searching: 01:15:15 Overall time: 01:15:15 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 20 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 7571933 / 21339213 = 0.3548 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 @ Tue, 27 Jun 2017 18:04:01: # Command line: callpeak -t SRX1179573.bam -f BAM -g dm -n SRX1179573.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1179573.20 # format = BAM # ChIP-seq file = ['SRX1179573.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 @ Tue, 27 Jun 2017 18:04:01: #1 read tag files... INFO @ Tue, 27 Jun 2017 18:04:01: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 18:04:01: # Command line: callpeak -t SRX1179573.bam -f BAM -g dm -n SRX1179573.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1179573.05 # format = BAM # ChIP-seq file = ['SRX1179573.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 @ Tue, 27 Jun 2017 18:04:01: #1 read tag files... INFO @ Tue, 27 Jun 2017 18:04:01: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 18:04:01: # Command line: callpeak -t SRX1179573.bam -f BAM -g dm -n SRX1179573.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1179573.10 # format = BAM # ChIP-seq file = ['SRX1179573.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 @ Tue, 27 Jun 2017 18:04:01: #1 read tag files... INFO @ Tue, 27 Jun 2017 18:04:01: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 18:04:09: 1000000 INFO @ Tue, 27 Jun 2017 18:04:10: 1000000 INFO @ Tue, 27 Jun 2017 18:04:10: 1000000 INFO @ Tue, 27 Jun 2017 18:04:17: 2000000 INFO @ Tue, 27 Jun 2017 18:04:18: 2000000 INFO @ Tue, 27 Jun 2017 18:04:18: 2000000 INFO @ Tue, 27 Jun 2017 18:04:25: 3000000 INFO @ Tue, 27 Jun 2017 18:04:27: 3000000 INFO @ Tue, 27 Jun 2017 18:04:27: 3000000 INFO @ Tue, 27 Jun 2017 18:04:33: 4000000 INFO @ Tue, 27 Jun 2017 18:04:37: 4000000 INFO @ Tue, 27 Jun 2017 18:04:37: 4000000 INFO @ Tue, 27 Jun 2017 18:04:40: 5000000 INFO @ Tue, 27 Jun 2017 18:04:45: 5000000 INFO @ Tue, 27 Jun 2017 18:04:45: 5000000 INFO @ Tue, 27 Jun 2017 18:04:48: 6000000 INFO @ Tue, 27 Jun 2017 18:04:54: 6000000 INFO @ Tue, 27 Jun 2017 18:04:54: 6000000 INFO @ Tue, 27 Jun 2017 18:04:56: 7000000 INFO @ Tue, 27 Jun 2017 18:05:03: 7000000 INFO @ Tue, 27 Jun 2017 18:05:03: 7000000 INFO @ Tue, 27 Jun 2017 18:05:03: 8000000 INFO @ Tue, 27 Jun 2017 18:05:11: 9000000 INFO @ Tue, 27 Jun 2017 18:05:12: 8000000 INFO @ Tue, 27 Jun 2017 18:05:12: 8000000 INFO @ Tue, 27 Jun 2017 18:05:19: 10000000 INFO @ Tue, 27 Jun 2017 18:05:21: 9000000 INFO @ Tue, 27 Jun 2017 18:05:21: 9000000 INFO @ Tue, 27 Jun 2017 18:05:27: 11000000 INFO @ Tue, 27 Jun 2017 18:05:29: 10000000 INFO @ Tue, 27 Jun 2017 18:05:29: 10000000 INFO @ Tue, 27 Jun 2017 18:05:35: 12000000 INFO @ Tue, 27 Jun 2017 18:05:38: 11000000 INFO @ Tue, 27 Jun 2017 18:05:38: 11000000 INFO @ Tue, 27 Jun 2017 18:05:43: 13000000 INFO @ Tue, 27 Jun 2017 18:05:47: 12000000 INFO @ Tue, 27 Jun 2017 18:05:47: 12000000 INFO @ Tue, 27 Jun 2017 18:05:51: 14000000 INFO @ Tue, 27 Jun 2017 18:05:55: 13000000 INFO @ Tue, 27 Jun 2017 18:05:55: 13000000 INFO @ Tue, 27 Jun 2017 18:06:00: 15000000 INFO @ Tue, 27 Jun 2017 18:06:04: 14000000 INFO @ Tue, 27 Jun 2017 18:06:04: 14000000 INFO @ Tue, 27 Jun 2017 18:06:07: 16000000 INFO @ Tue, 27 Jun 2017 18:06:13: 15000000 INFO @ Tue, 27 Jun 2017 18:06:13: 15000000 INFO @ Tue, 27 Jun 2017 18:06:15: 17000000 INFO @ Tue, 27 Jun 2017 18:06:22: 16000000 INFO @ Tue, 27 Jun 2017 18:06:22: 16000000 INFO @ Tue, 27 Jun 2017 18:06:23: 18000000 INFO @ Tue, 27 Jun 2017 18:06:31: 19000000 INFO @ Tue, 27 Jun 2017 18:06:31: 17000000 INFO @ Tue, 27 Jun 2017 18:06:31: 17000000 INFO @ Tue, 27 Jun 2017 18:06:39: 20000000 INFO @ Tue, 27 Jun 2017 18:06:39: 18000000 INFO @ Tue, 27 Jun 2017 18:06:39: 18000000 INFO @ Tue, 27 Jun 2017 18:06:47: 21000000 INFO @ Tue, 27 Jun 2017 18:06:48: 19000000 INFO @ Tue, 27 Jun 2017 18:06:48: 19000000 INFO @ Tue, 27 Jun 2017 18:06:55: 22000000 INFO @ Tue, 27 Jun 2017 18:06:57: 20000000 INFO @ Tue, 27 Jun 2017 18:06:57: 20000000 INFO @ Tue, 27 Jun 2017 18:07:02: 23000000 INFO @ Tue, 27 Jun 2017 18:07:06: 21000000 INFO @ Tue, 27 Jun 2017 18:07:06: 21000000 INFO @ Tue, 27 Jun 2017 18:07:10: 24000000 INFO @ Tue, 27 Jun 2017 18:07:14: 22000000 INFO @ Tue, 27 Jun 2017 18:07:14: 22000000 INFO @ Tue, 27 Jun 2017 18:07:18: 25000000 INFO @ Tue, 27 Jun 2017 18:07:23: 23000000 INFO @ Tue, 27 Jun 2017 18:07:23: 23000000 INFO @ Tue, 27 Jun 2017 18:07:26: 26000000 INFO @ Tue, 27 Jun 2017 18:07:32: 24000000 INFO @ Tue, 27 Jun 2017 18:07:32: 24000000 INFO @ Tue, 27 Jun 2017 18:07:35: 27000000 INFO @ Tue, 27 Jun 2017 18:07:41: 25000000 INFO @ Tue, 27 Jun 2017 18:07:41: 25000000 INFO @ Tue, 27 Jun 2017 18:07:43: 28000000 INFO @ Tue, 27 Jun 2017 18:07:45: #1 tag size is determined as 75 bps INFO @ Tue, 27 Jun 2017 18:07:45: #1 tag size = 75 INFO @ Tue, 27 Jun 2017 18:07:45: #1 total tags in treatment: 13791205 INFO @ Tue, 27 Jun 2017 18:07:45: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 18:07:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 18:07:45: #1 tags after filtering in treatment: 10912260 INFO @ Tue, 27 Jun 2017 18:07:45: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 27 Jun 2017 18:07:45: #1 finished! INFO @ Tue, 27 Jun 2017 18:07:45: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 18:07:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 18:07:46: #2 number of paired peaks: 1534 INFO @ Tue, 27 Jun 2017 18:07:46: start model_add_line... INFO @ Tue, 27 Jun 2017 18:07:46: start X-correlation... INFO @ Tue, 27 Jun 2017 18:07:46: end of X-cor INFO @ Tue, 27 Jun 2017 18:07:46: #2 finished! INFO @ Tue, 27 Jun 2017 18:07:46: #2 predicted fragment length is 149 bps INFO @ Tue, 27 Jun 2017 18:07:46: #2 alternative fragment length(s) may be 4,149 bps INFO @ Tue, 27 Jun 2017 18:07:46: #2.2 Generate R script for model : SRX1179573.10_model.r WARNING @ Tue, 27 Jun 2017 18:07:46: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 18:07:46: #2 You may need to consider one of the other alternative d(s): 4,149 WARNING @ Tue, 27 Jun 2017 18:07:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 18:07:46: #3 Call peaks... INFO @ Tue, 27 Jun 2017 18:07:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 18:07:50: 26000000 INFO @ Tue, 27 Jun 2017 18:07:50: 26000000 INFO @ Tue, 27 Jun 2017 18:07:58: 27000000 INFO @ Tue, 27 Jun 2017 18:07:58: 27000000 INFO @ Tue, 27 Jun 2017 18:08:07: 28000000 INFO @ Tue, 27 Jun 2017 18:08:07: 28000000 INFO @ Tue, 27 Jun 2017 18:08:09: #1 tag size is determined as 75 bps INFO @ Tue, 27 Jun 2017 18:08:09: #1 tag size is determined as 75 bps INFO @ Tue, 27 Jun 2017 18:08:09: #1 tag size = 75 INFO @ Tue, 27 Jun 2017 18:08:09: #1 tag size = 75 INFO @ Tue, 27 Jun 2017 18:08:09: #1 total tags in treatment: 13791205 INFO @ Tue, 27 Jun 2017 18:08:09: #1 total tags in treatment: 13791205 INFO @ Tue, 27 Jun 2017 18:08:09: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 18:08:09: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 18:08:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 18:08:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 18:08:09: #1 tags after filtering in treatment: 10912260 INFO @ Tue, 27 Jun 2017 18:08:09: #1 tags after filtering in treatment: 10912260 INFO @ Tue, 27 Jun 2017 18:08:09: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 27 Jun 2017 18:08:09: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 27 Jun 2017 18:08:09: #1 finished! INFO @ Tue, 27 Jun 2017 18:08:09: #1 finished! INFO @ Tue, 27 Jun 2017 18:08:09: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 18:08:09: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 18:08:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 18:08:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 18:08:10: #2 number of paired peaks: 1534 INFO @ Tue, 27 Jun 2017 18:08:10: start model_add_line... INFO @ Tue, 27 Jun 2017 18:08:10: #2 number of paired peaks: 1534 INFO @ Tue, 27 Jun 2017 18:08:10: start model_add_line... INFO @ Tue, 27 Jun 2017 18:08:10: start X-correlation... INFO @ Tue, 27 Jun 2017 18:08:10: end of X-cor INFO @ Tue, 27 Jun 2017 18:08:10: #2 finished! INFO @ Tue, 27 Jun 2017 18:08:10: #2 predicted fragment length is 149 bps INFO @ Tue, 27 Jun 2017 18:08:10: #2 alternative fragment length(s) may be 4,149 bps INFO @ Tue, 27 Jun 2017 18:08:10: #2.2 Generate R script for model : SRX1179573.20_model.r INFO @ Tue, 27 Jun 2017 18:08:10: start X-correlation... WARNING @ Tue, 27 Jun 2017 18:08:10: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 18:08:10: #2 You may need to consider one of the other alternative d(s): 4,149 WARNING @ Tue, 27 Jun 2017 18:08:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 18:08:10: end of X-cor INFO @ Tue, 27 Jun 2017 18:08:10: #3 Call peaks... INFO @ Tue, 27 Jun 2017 18:08:10: #2 finished! INFO @ Tue, 27 Jun 2017 18:08:10: #2 predicted fragment length is 149 bps INFO @ Tue, 27 Jun 2017 18:08:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 18:08:10: #2 alternative fragment length(s) may be 4,149 bps INFO @ Tue, 27 Jun 2017 18:08:10: #2.2 Generate R script for model : SRX1179573.05_model.r WARNING @ Tue, 27 Jun 2017 18:08:10: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 18:08:10: #2 You may need to consider one of the other alternative d(s): 4,149 WARNING @ Tue, 27 Jun 2017 18:08:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 18:08:10: #3 Call peaks... INFO @ Tue, 27 Jun 2017 18:08:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 18:08:13: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 18:08:27: #4 Write output xls file... SRX1179573.10_peaks.xls INFO @ Tue, 27 Jun 2017 18:08:27: #4 Write peak in narrowPeak format file... SRX1179573.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 18:08:27: #4 Write summits bed file... SRX1179573.10_summits.bed INFO @ Tue, 27 Jun 2017 18:08:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2472 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 18:08:36: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 18:08:37: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 18:08:51: #4 Write output xls file... SRX1179573.05_peaks.xls INFO @ Tue, 27 Jun 2017 18:08:51: #4 Write peak in narrowPeak format file... SRX1179573.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 18:08:51: #4 Write summits bed file... SRX1179573.05_summits.bed INFO @ Tue, 27 Jun 2017 18:08:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6410 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 18:08:52: #4 Write output xls file... SRX1179573.20_peaks.xls INFO @ Tue, 27 Jun 2017 18:08:52: #4 Write peak in narrowPeak format file... SRX1179573.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 18:08:52: #4 Write summits bed file... SRX1179573.20_summits.bed INFO @ Tue, 27 Jun 2017 18:08:52: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (976 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。