Job ID = 10714442 sra ファイルのダウンロード中... Completed: 1752467K bytes transferred in 29 seconds (485077K 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 24365244 spots for /home/okishinya/chipatlas/results/ce10/SRX4085358/SRR7167387.sra Written 24365244 spots for /home/okishinya/chipatlas/results/ce10/SRX4085358/SRR7167387.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: 00:25:54 24365244 reads; of these: 24365244 (100.00%) were paired; of these: 859170 (3.53%) aligned concordantly 0 times 20471141 (84.02%) aligned concordantly exactly 1 time 3034933 (12.46%) aligned concordantly >1 times ---- 859170 pairs aligned concordantly 0 times; of these: 114210 (13.29%) aligned discordantly 1 time ---- 744960 pairs aligned 0 times concordantly or discordantly; of these: 1489920 mates make up the pairs; of these: 856769 (57.50%) aligned 0 times 494340 (33.18%) aligned exactly 1 time 138811 (9.32%) aligned >1 times 98.24% overall alignment rate Time searching: 00:25:54 Overall time: 00:25:54 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 20 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] 4139896 / 23570088 = 0.1756 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 13:19:02: # Command line: callpeak -t SRX4085358.bam -f BAM -g ce -n SRX4085358.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085358.05 # format = BAM # ChIP-seq file = ['SRX4085358.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 13:19:02: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:19:02: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:19:02: # Command line: callpeak -t SRX4085358.bam -f BAM -g ce -n SRX4085358.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085358.10 # format = BAM # ChIP-seq file = ['SRX4085358.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 13:19:02: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:19:02: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:19:02: # Command line: callpeak -t SRX4085358.bam -f BAM -g ce -n SRX4085358.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085358.20 # format = BAM # ChIP-seq file = ['SRX4085358.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 13:19:02: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:19:02: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:19:08: 1000000 INFO @ Sun, 03 Jun 2018 13:19:08: 1000000 INFO @ Sun, 03 Jun 2018 13:19:08: 1000000 INFO @ Sun, 03 Jun 2018 13:19:14: 2000000 INFO @ Sun, 03 Jun 2018 13:19:14: 2000000 INFO @ Sun, 03 Jun 2018 13:19:15: 2000000 INFO @ Sun, 03 Jun 2018 13:19:20: 3000000 INFO @ Sun, 03 Jun 2018 13:19:21: 3000000 INFO @ Sun, 03 Jun 2018 13:19:22: 3000000 INFO @ Sun, 03 Jun 2018 13:19:27: 4000000 INFO @ Sun, 03 Jun 2018 13:19:27: 4000000 INFO @ Sun, 03 Jun 2018 13:19:28: 4000000 INFO @ Sun, 03 Jun 2018 13:19:33: 5000000 INFO @ Sun, 03 Jun 2018 13:19:33: 5000000 INFO @ Sun, 03 Jun 2018 13:19:35: 5000000 INFO @ Sun, 03 Jun 2018 13:19:40: 6000000 INFO @ Sun, 03 Jun 2018 13:19:40: 6000000 INFO @ Sun, 03 Jun 2018 13:19:42: 6000000 INFO @ Sun, 03 Jun 2018 13:19:46: 7000000 INFO @ Sun, 03 Jun 2018 13:19:46: 7000000 INFO @ Sun, 03 Jun 2018 13:19:49: 7000000 INFO @ Sun, 03 Jun 2018 13:19:52: 8000000 INFO @ Sun, 03 Jun 2018 13:19:53: 8000000 INFO @ Sun, 03 Jun 2018 13:19:56: 8000000 INFO @ Sun, 03 Jun 2018 13:19:59: 9000000 INFO @ Sun, 03 Jun 2018 13:19:59: 9000000 INFO @ Sun, 03 Jun 2018 13:20:03: 9000000 INFO @ Sun, 03 Jun 2018 13:20:05: 10000000 INFO @ Sun, 03 Jun 2018 13:20:06: 10000000 INFO @ Sun, 03 Jun 2018 13:20:09: 10000000 INFO @ Sun, 03 Jun 2018 13:20:12: 11000000 INFO @ Sun, 03 Jun 2018 13:20:13: 11000000 INFO @ Sun, 03 Jun 2018 13:20:16: 11000000 INFO @ Sun, 03 Jun 2018 13:20:19: 12000000 INFO @ Sun, 03 Jun 2018 13:20:19: 12000000 INFO @ Sun, 03 Jun 2018 13:20:23: 12000000 INFO @ Sun, 03 Jun 2018 13:20:25: 13000000 INFO @ Sun, 03 Jun 2018 13:20:26: 13000000 INFO @ Sun, 03 Jun 2018 13:20:30: 13000000 INFO @ Sun, 03 Jun 2018 13:20:32: 14000000 INFO @ Sun, 03 Jun 2018 13:20:33: 14000000 INFO @ Sun, 03 Jun 2018 13:20:38: 14000000 INFO @ Sun, 03 Jun 2018 13:20:39: 15000000 INFO @ Sun, 03 Jun 2018 13:20:40: 15000000 INFO @ Sun, 03 Jun 2018 13:20:45: 15000000 INFO @ Sun, 03 Jun 2018 13:20:46: 16000000 INFO @ Sun, 03 Jun 2018 13:20:47: 16000000 INFO @ Sun, 03 Jun 2018 13:20:52: 16000000 INFO @ Sun, 03 Jun 2018 13:20:53: 17000000 INFO @ Sun, 03 Jun 2018 13:20:54: 17000000 INFO @ Sun, 03 Jun 2018 13:20:59: 17000000 INFO @ Sun, 03 Jun 2018 13:21:00: 18000000 INFO @ Sun, 03 Jun 2018 13:21:01: 18000000 INFO @ Sun, 03 Jun 2018 13:21:06: 18000000 INFO @ Sun, 03 Jun 2018 13:21:07: 19000000 INFO @ Sun, 03 Jun 2018 13:21:08: 19000000 INFO @ Sun, 03 Jun 2018 13:21:13: 19000000 INFO @ Sun, 03 Jun 2018 13:21:13: 20000000 INFO @ Sun, 03 Jun 2018 13:21:14: 20000000 INFO @ Sun, 03 Jun 2018 13:21:20: 21000000 INFO @ Sun, 03 Jun 2018 13:21:20: 20000000 INFO @ Sun, 03 Jun 2018 13:21:21: 21000000 INFO @ Sun, 03 Jun 2018 13:21:27: 22000000 INFO @ Sun, 03 Jun 2018 13:21:27: 21000000 INFO @ Sun, 03 Jun 2018 13:21:28: 22000000 INFO @ Sun, 03 Jun 2018 13:21:34: 23000000 INFO @ Sun, 03 Jun 2018 13:21:35: 22000000 INFO @ Sun, 03 Jun 2018 13:21:35: 23000000 INFO @ Sun, 03 Jun 2018 13:21:41: 24000000 INFO @ Sun, 03 Jun 2018 13:21:42: 23000000 INFO @ Sun, 03 Jun 2018 13:21:42: 24000000 INFO @ Sun, 03 Jun 2018 13:21:47: 25000000 INFO @ Sun, 03 Jun 2018 13:21:49: 24000000 INFO @ Sun, 03 Jun 2018 13:21:49: 25000000 INFO @ Sun, 03 Jun 2018 13:21:54: 26000000 INFO @ Sun, 03 Jun 2018 13:21:56: 25000000 INFO @ Sun, 03 Jun 2018 13:21:56: 26000000 INFO @ Sun, 03 Jun 2018 13:22:01: 27000000 INFO @ Sun, 03 Jun 2018 13:22:03: 27000000 INFO @ Sun, 03 Jun 2018 13:22:03: 26000000 INFO @ Sun, 03 Jun 2018 13:22:08: 28000000 INFO @ Sun, 03 Jun 2018 13:22:10: 28000000 INFO @ Sun, 03 Jun 2018 13:22:10: 27000000 INFO @ Sun, 03 Jun 2018 13:22:15: 29000000 INFO @ Sun, 03 Jun 2018 13:22:17: 29000000 INFO @ Sun, 03 Jun 2018 13:22:17: 28000000 INFO @ Sun, 03 Jun 2018 13:22:21: 30000000 INFO @ Sun, 03 Jun 2018 13:22:23: 30000000 INFO @ Sun, 03 Jun 2018 13:22:24: 29000000 INFO @ Sun, 03 Jun 2018 13:22:28: 31000000 INFO @ Sun, 03 Jun 2018 13:22:30: 31000000 INFO @ Sun, 03 Jun 2018 13:22:31: 30000000 INFO @ Sun, 03 Jun 2018 13:22:35: 32000000 INFO @ Sun, 03 Jun 2018 13:22:37: 32000000 INFO @ Sun, 03 Jun 2018 13:22:38: 31000000 INFO @ Sun, 03 Jun 2018 13:22:42: 33000000 INFO @ Sun, 03 Jun 2018 13:22:44: 33000000 INFO @ Sun, 03 Jun 2018 13:22:45: 32000000 INFO @ Sun, 03 Jun 2018 13:22:49: 34000000 INFO @ Sun, 03 Jun 2018 13:22:51: 34000000 INFO @ Sun, 03 Jun 2018 13:22:53: 33000000 INFO @ Sun, 03 Jun 2018 13:22:55: 35000000 INFO @ Sun, 03 Jun 2018 13:22:58: 35000000 INFO @ Sun, 03 Jun 2018 13:22:59: 34000000 INFO @ Sun, 03 Jun 2018 13:23:01: 36000000 INFO @ Sun, 03 Jun 2018 13:23:04: 36000000 INFO @ Sun, 03 Jun 2018 13:23:05: 35000000 INFO @ Sun, 03 Jun 2018 13:23:06: 37000000 INFO @ Sun, 03 Jun 2018 13:23:10: 37000000 INFO @ Sun, 03 Jun 2018 13:23:11: 38000000 INFO @ Sun, 03 Jun 2018 13:23:11: 36000000 INFO @ Sun, 03 Jun 2018 13:23:16: 38000000 INFO @ Sun, 03 Jun 2018 13:23:16: 39000000 INFO @ Sun, 03 Jun 2018 13:23:17: 37000000 INFO @ Sun, 03 Jun 2018 13:23:20: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:23:20: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:23:20: #1 total tags in treatment: 19377000 INFO @ Sun, 03 Jun 2018 13:23:20: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:23:20: #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 13:23:20: #1 tags after filtering in treatment: 15674884 INFO @ Sun, 03 Jun 2018 13:23:20: #1 Redundant rate of treatment: 0.19 INFO @ Sun, 03 Jun 2018 13:23:20: #1 finished! INFO @ Sun, 03 Jun 2018 13:23:20: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:23:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:23:21: #2 number of paired peaks: 204 WARNING @ Sun, 03 Jun 2018 13:23:21: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Sun, 03 Jun 2018 13:23:21: start model_add_line... INFO @ Sun, 03 Jun 2018 13:23:21: start X-correlation... INFO @ Sun, 03 Jun 2018 13:23:21: end of X-cor INFO @ Sun, 03 Jun 2018 13:23:21: #2 finished! INFO @ Sun, 03 Jun 2018 13:23:21: #2 predicted fragment length is 103 bps INFO @ Sun, 03 Jun 2018 13:23:21: #2 alternative fragment length(s) may be 2,103 bps INFO @ Sun, 03 Jun 2018 13:23:21: #2.2 Generate R script for model : SRX4085358.05_model.r INFO @ Sun, 03 Jun 2018 13:23:21: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:23:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:23:22: 39000000 INFO @ Sun, 03 Jun 2018 13:23:24: 38000000 INFO @ Sun, 03 Jun 2018 13:23:26: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:23:26: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:23:26: #1 total tags in treatment: 19377000 INFO @ Sun, 03 Jun 2018 13:23:26: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:23:26: #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 13:23:26: #1 tags after filtering in treatment: 15674884 INFO @ Sun, 03 Jun 2018 13:23:26: #1 Redundant rate of treatment: 0.19 INFO @ Sun, 03 Jun 2018 13:23:26: #1 finished! INFO @ Sun, 03 Jun 2018 13:23:26: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:23:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:23:27: #2 number of paired peaks: 204 WARNING @ Sun, 03 Jun 2018 13:23:27: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Sun, 03 Jun 2018 13:23:27: start model_add_line... INFO @ Sun, 03 Jun 2018 13:23:27: start X-correlation... INFO @ Sun, 03 Jun 2018 13:23:27: end of X-cor INFO @ Sun, 03 Jun 2018 13:23:27: #2 finished! INFO @ Sun, 03 Jun 2018 13:23:27: #2 predicted fragment length is 103 bps INFO @ Sun, 03 Jun 2018 13:23:27: #2 alternative fragment length(s) may be 2,103 bps INFO @ Sun, 03 Jun 2018 13:23:27: #2.2 Generate R script for model : SRX4085358.20_model.r INFO @ Sun, 03 Jun 2018 13:23:27: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:23:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:23:30: 39000000 INFO @ Sun, 03 Jun 2018 13:23:33: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:23:33: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:23:33: #1 total tags in treatment: 19377000 INFO @ Sun, 03 Jun 2018 13:23:33: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:23:33: #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 13:23:34: #1 tags after filtering in treatment: 15674884 INFO @ Sun, 03 Jun 2018 13:23:34: #1 Redundant rate of treatment: 0.19 INFO @ Sun, 03 Jun 2018 13:23:34: #1 finished! INFO @ Sun, 03 Jun 2018 13:23:34: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:23:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:23:35: #2 number of paired peaks: 204 WARNING @ Sun, 03 Jun 2018 13:23:35: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Sun, 03 Jun 2018 13:23:35: start model_add_line... INFO @ Sun, 03 Jun 2018 13:23:35: start X-correlation... INFO @ Sun, 03 Jun 2018 13:23:35: end of X-cor INFO @ Sun, 03 Jun 2018 13:23:35: #2 finished! INFO @ Sun, 03 Jun 2018 13:23:35: #2 predicted fragment length is 103 bps INFO @ Sun, 03 Jun 2018 13:23:35: #2 alternative fragment length(s) may be 2,103 bps INFO @ Sun, 03 Jun 2018 13:23:35: #2.2 Generate R script for model : SRX4085358.10_model.r INFO @ Sun, 03 Jun 2018 13:23:35: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:23:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:23:52: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:24:00: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:24:06: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:24:09: #4 Write output xls file... SRX4085358.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:24:09: #4 Write peak in narrowPeak format file... SRX4085358.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:24:09: #4 Write summits bed file... SRX4085358.05_summits.bed INFO @ Sun, 03 Jun 2018 13:24:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1952 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:24:16: #4 Write output xls file... SRX4085358.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:24:16: #4 Write peak in narrowPeak format file... SRX4085358.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:24:16: #4 Write summits bed file... SRX4085358.20_summits.bed INFO @ Sun, 03 Jun 2018 13:24:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (393 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:24:23: #4 Write output xls file... SRX4085358.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:24:23: #4 Write peak in narrowPeak format file... SRX4085358.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:24:23: #4 Write summits bed file... SRX4085358.10_summits.bed INFO @ Sun, 03 Jun 2018 13:24:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (990 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。