Job ID = 10714474 sra ファイルのダウンロード中... Completed: 933379K bytes transferred in 16 seconds (473844K 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: PAIRED fastq に変換中... Read 15430972 spots for /home/okishinya/chipatlas/results/ce10/SRX4085390/SRR7167419.sra Written 15430972 spots for /home/okishinya/chipatlas/results/ce10/SRX4085390/SRR7167419.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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:37 15430972 reads; of these: 15430972 (100.00%) were paired; of these: 8920324 (57.81%) aligned concordantly 0 times 5617767 (36.41%) aligned concordantly exactly 1 time 892881 (5.79%) aligned concordantly >1 times ---- 8920324 pairs aligned concordantly 0 times; of these: 442444 (4.96%) aligned discordantly 1 time ---- 8477880 pairs aligned 0 times concordantly or discordantly; of these: 16955760 mates make up the pairs; of these: 12138208 (71.59%) aligned 0 times 4180062 (24.65%) aligned exactly 1 time 637490 (3.76%) aligned >1 times 60.67% overall alignment rate Time searching: 00:11:38 Overall time: 00:11:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 673785 / 6720988 = 0.1003 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, 03 Jun 2018 13:00:18: # Command line: callpeak -t SRX4085390.bam -f BAM -g ce -n SRX4085390.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085390.10 # format = BAM # ChIP-seq file = ['SRX4085390.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 03 Jun 2018 13:00:18: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:00:18: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:00:18: # Command line: callpeak -t SRX4085390.bam -f BAM -g ce -n SRX4085390.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085390.20 # format = BAM # ChIP-seq file = ['SRX4085390.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 03 Jun 2018 13:00:18: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:00:18: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:00:18: # Command line: callpeak -t SRX4085390.bam -f BAM -g ce -n SRX4085390.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085390.05 # format = BAM # ChIP-seq file = ['SRX4085390.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 03 Jun 2018 13:00:18: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:00:18: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:00:24: 1000000 INFO @ Sun, 03 Jun 2018 13:00:24: 1000000 INFO @ Sun, 03 Jun 2018 13:00:24: 1000000 INFO @ Sun, 03 Jun 2018 13:00:30: 2000000 INFO @ Sun, 03 Jun 2018 13:00:30: 2000000 INFO @ Sun, 03 Jun 2018 13:00:31: 2000000 INFO @ Sun, 03 Jun 2018 13:00:36: 3000000 INFO @ Sun, 03 Jun 2018 13:00:36: 3000000 INFO @ Sun, 03 Jun 2018 13:00:37: 3000000 INFO @ Sun, 03 Jun 2018 13:00:42: 4000000 INFO @ Sun, 03 Jun 2018 13:00:43: 4000000 INFO @ Sun, 03 Jun 2018 13:00:44: 4000000 INFO @ Sun, 03 Jun 2018 13:00:48: 5000000 INFO @ Sun, 03 Jun 2018 13:00:49: 5000000 INFO @ Sun, 03 Jun 2018 13:00:51: 5000000 INFO @ Sun, 03 Jun 2018 13:00:55: 6000000 INFO @ Sun, 03 Jun 2018 13:00:55: 6000000 INFO @ Sun, 03 Jun 2018 13:00:57: 6000000 INFO @ Sun, 03 Jun 2018 13:01:01: 7000000 INFO @ Sun, 03 Jun 2018 13:01:01: 7000000 INFO @ Sun, 03 Jun 2018 13:01:04: 7000000 INFO @ Sun, 03 Jun 2018 13:01:07: 8000000 INFO @ Sun, 03 Jun 2018 13:01:07: 8000000 INFO @ Sun, 03 Jun 2018 13:01:10: 8000000 INFO @ Sun, 03 Jun 2018 13:01:13: 9000000 INFO @ Sun, 03 Jun 2018 13:01:14: 9000000 INFO @ Sun, 03 Jun 2018 13:01:16: 9000000 INFO @ Sun, 03 Jun 2018 13:01:18: 10000000 INFO @ Sun, 03 Jun 2018 13:01:20: 10000000 INFO @ Sun, 03 Jun 2018 13:01:23: 10000000 INFO @ Sun, 03 Jun 2018 13:01:24: 11000000 INFO @ Sun, 03 Jun 2018 13:01:26: 11000000 INFO @ Sun, 03 Jun 2018 13:01:29: 11000000 INFO @ Sun, 03 Jun 2018 13:01:30: 12000000 INFO @ Sun, 03 Jun 2018 13:01:33: 12000000 INFO @ Sun, 03 Jun 2018 13:01:35: 12000000 INFO @ Sun, 03 Jun 2018 13:01:36: 13000000 INFO @ Sun, 03 Jun 2018 13:01:39: 13000000 INFO @ Sun, 03 Jun 2018 13:01:42: 13000000 INFO @ Sun, 03 Jun 2018 13:01:42: 14000000 INFO @ Sun, 03 Jun 2018 13:01:46: 14000000 INFO @ Sun, 03 Jun 2018 13:01:48: 15000000 INFO @ Sun, 03 Jun 2018 13:01:48: 14000000 INFO @ Sun, 03 Jun 2018 13:01:52: 15000000 INFO @ Sun, 03 Jun 2018 13:01:54: 16000000 INFO @ Sun, 03 Jun 2018 13:01:55: 15000000 INFO @ Sun, 03 Jun 2018 13:01:58: 16000000 INFO @ Sun, 03 Jun 2018 13:02:00: 17000000 INFO @ Sun, 03 Jun 2018 13:02:01: 16000000 INFO @ Sun, 03 Jun 2018 13:02:02: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:02:02: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:02:02: #1 total tags in treatment: 5857833 INFO @ Sun, 03 Jun 2018 13:02:02: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:02:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:02:02: #1 tags after filtering in treatment: 5471115 INFO @ Sun, 03 Jun 2018 13:02:02: #1 Redundant rate of treatment: 0.07 INFO @ Sun, 03 Jun 2018 13:02:02: #1 finished! INFO @ Sun, 03 Jun 2018 13:02:02: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:02:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:02:02: #2 number of paired peaks: 274 WARNING @ Sun, 03 Jun 2018 13:02:02: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Sun, 03 Jun 2018 13:02:02: start model_add_line... INFO @ Sun, 03 Jun 2018 13:02:02: start X-correlation... INFO @ Sun, 03 Jun 2018 13:02:02: end of X-cor INFO @ Sun, 03 Jun 2018 13:02:02: #2 finished! INFO @ Sun, 03 Jun 2018 13:02:02: #2 predicted fragment length is 142 bps INFO @ Sun, 03 Jun 2018 13:02:02: #2 alternative fragment length(s) may be 71,95,122,142,214 bps INFO @ Sun, 03 Jun 2018 13:02:02: #2.2 Generate R script for model : SRX4085390.10_model.r INFO @ Sun, 03 Jun 2018 13:02:02: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:02:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:02:05: 17000000 INFO @ Sun, 03 Jun 2018 13:02:07: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:02:07: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:02:07: #1 total tags in treatment: 5857833 INFO @ Sun, 03 Jun 2018 13:02:07: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:02:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:02:07: #1 tags after filtering in treatment: 5471115 INFO @ Sun, 03 Jun 2018 13:02:07: #1 Redundant rate of treatment: 0.07 INFO @ Sun, 03 Jun 2018 13:02:07: #1 finished! INFO @ Sun, 03 Jun 2018 13:02:07: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:02:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:02:07: 17000000 INFO @ Sun, 03 Jun 2018 13:02:08: #2 number of paired peaks: 274 WARNING @ Sun, 03 Jun 2018 13:02:08: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Sun, 03 Jun 2018 13:02:08: start model_add_line... INFO @ Sun, 03 Jun 2018 13:02:08: start X-correlation... INFO @ Sun, 03 Jun 2018 13:02:08: end of X-cor INFO @ Sun, 03 Jun 2018 13:02:08: #2 finished! INFO @ Sun, 03 Jun 2018 13:02:08: #2 predicted fragment length is 142 bps INFO @ Sun, 03 Jun 2018 13:02:08: #2 alternative fragment length(s) may be 71,95,122,142,214 bps INFO @ Sun, 03 Jun 2018 13:02:08: #2.2 Generate R script for model : SRX4085390.20_model.r INFO @ Sun, 03 Jun 2018 13:02:08: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:02:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:02:09: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:02:09: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:02:09: #1 total tags in treatment: 5857833 INFO @ Sun, 03 Jun 2018 13:02:09: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:02:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:02:10: #1 tags after filtering in treatment: 5471115 INFO @ Sun, 03 Jun 2018 13:02:10: #1 Redundant rate of treatment: 0.07 INFO @ Sun, 03 Jun 2018 13:02:10: #1 finished! INFO @ Sun, 03 Jun 2018 13:02:10: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:02:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:02:10: #2 number of paired peaks: 274 WARNING @ Sun, 03 Jun 2018 13:02:10: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Sun, 03 Jun 2018 13:02:10: start model_add_line... INFO @ Sun, 03 Jun 2018 13:02:10: start X-correlation... INFO @ Sun, 03 Jun 2018 13:02:10: end of X-cor INFO @ Sun, 03 Jun 2018 13:02:10: #2 finished! INFO @ Sun, 03 Jun 2018 13:02:10: #2 predicted fragment length is 142 bps INFO @ Sun, 03 Jun 2018 13:02:10: #2 alternative fragment length(s) may be 71,95,122,142,214 bps INFO @ Sun, 03 Jun 2018 13:02:10: #2.2 Generate R script for model : SRX4085390.05_model.r INFO @ Sun, 03 Jun 2018 13:02:10: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:02:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:02:15: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:02:20: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:02:22: #4 Write output xls file... SRX4085390.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:02:22: #4 Write peak in narrowPeak format file... SRX4085390.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:02:22: #4 Write summits bed file... SRX4085390.10_summits.bed INFO @ Sun, 03 Jun 2018 13:02:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (182 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:02:23: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:02:27: #4 Write output xls file... SRX4085390.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:02:27: #4 Write peak in narrowPeak format file... SRX4085390.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:02:27: #4 Write summits bed file... SRX4085390.20_summits.bed INFO @ Sun, 03 Jun 2018 13:02:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (104 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:02:29: #4 Write output xls file... SRX4085390.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:02:29: #4 Write peak in narrowPeak format file... SRX4085390.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:02:29: #4 Write summits bed file... SRX4085390.05_summits.bed INFO @ Sun, 03 Jun 2018 13:02:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (251 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。