Job ID = 10714511 sra ファイルのダウンロード中... Completed: 2172166K bytes transferred in 23 seconds (751279K 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 31721561 spots for /home/okishinya/chipatlas/results/ce10/SRX4085427/SRR7167456.sra Written 31721561 spots for /home/okishinya/chipatlas/results/ce10/SRX4085427/SRR7167456.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: 00:31:11 31721561 reads; of these: 31721561 (100.00%) were paired; of these: 2560664 (8.07%) aligned concordantly 0 times 25226861 (79.53%) aligned concordantly exactly 1 time 3934036 (12.40%) aligned concordantly >1 times ---- 2560664 pairs aligned concordantly 0 times; of these: 141267 (5.52%) aligned discordantly 1 time ---- 2419397 pairs aligned 0 times concordantly or discordantly; of these: 4838794 mates make up the pairs; of these: 4158908 (85.95%) aligned 0 times 527753 (10.91%) aligned exactly 1 time 152133 (3.14%) aligned >1 times 93.44% overall alignment rate Time searching: 00:31:11 Overall time: 00:31:11 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 28 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] 12926768 / 29256357 = 0.4418 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 13:52:16: # Command line: callpeak -t SRX4085427.bam -f BAM -g ce -n SRX4085427.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085427.05 # format = BAM # ChIP-seq file = ['SRX4085427.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 13:52:16: # Command line: callpeak -t SRX4085427.bam -f BAM -g ce -n SRX4085427.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085427.20 # format = BAM # ChIP-seq file = ['SRX4085427.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 13:52:16: # Command line: callpeak -t SRX4085427.bam -f BAM -g ce -n SRX4085427.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085427.10 # format = BAM # ChIP-seq file = ['SRX4085427.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 13:52:16: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:52:16: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:52:16: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:52:16: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:52:16: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:52:16: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:52:22: 1000000 INFO @ Sun, 03 Jun 2018 13:52:22: 1000000 INFO @ Sun, 03 Jun 2018 13:52:22: 1000000 INFO @ Sun, 03 Jun 2018 13:52:28: 2000000 INFO @ Sun, 03 Jun 2018 13:52:28: 2000000 INFO @ Sun, 03 Jun 2018 13:52:28: 2000000 INFO @ Sun, 03 Jun 2018 13:52:34: 3000000 INFO @ Sun, 03 Jun 2018 13:52:35: 3000000 INFO @ Sun, 03 Jun 2018 13:52:35: 3000000 INFO @ Sun, 03 Jun 2018 13:52:40: 4000000 INFO @ Sun, 03 Jun 2018 13:52:41: 4000000 INFO @ Sun, 03 Jun 2018 13:52:41: 4000000 INFO @ Sun, 03 Jun 2018 13:52:46: 5000000 INFO @ Sun, 03 Jun 2018 13:52:47: 5000000 INFO @ Sun, 03 Jun 2018 13:52:47: 5000000 INFO @ Sun, 03 Jun 2018 13:52:52: 6000000 INFO @ Sun, 03 Jun 2018 13:52:54: 6000000 INFO @ Sun, 03 Jun 2018 13:52:54: 6000000 INFO @ Sun, 03 Jun 2018 13:52:58: 7000000 INFO @ Sun, 03 Jun 2018 13:53:00: 7000000 INFO @ Sun, 03 Jun 2018 13:53:00: 7000000 INFO @ Sun, 03 Jun 2018 13:53:04: 8000000 INFO @ Sun, 03 Jun 2018 13:53:07: 8000000 INFO @ Sun, 03 Jun 2018 13:53:07: 8000000 INFO @ Sun, 03 Jun 2018 13:53:10: 9000000 INFO @ Sun, 03 Jun 2018 13:53:13: 9000000 INFO @ Sun, 03 Jun 2018 13:53:13: 9000000 INFO @ Sun, 03 Jun 2018 13:53:16: 10000000 INFO @ Sun, 03 Jun 2018 13:53:19: 10000000 INFO @ Sun, 03 Jun 2018 13:53:19: 10000000 INFO @ Sun, 03 Jun 2018 13:53:22: 11000000 INFO @ Sun, 03 Jun 2018 13:53:26: 11000000 INFO @ Sun, 03 Jun 2018 13:53:26: 11000000 INFO @ Sun, 03 Jun 2018 13:53:28: 12000000 INFO @ Sun, 03 Jun 2018 13:53:32: 12000000 INFO @ Sun, 03 Jun 2018 13:53:32: 12000000 INFO @ Sun, 03 Jun 2018 13:53:34: 13000000 INFO @ Sun, 03 Jun 2018 13:53:38: 13000000 INFO @ Sun, 03 Jun 2018 13:53:38: 13000000 INFO @ Sun, 03 Jun 2018 13:53:40: 14000000 INFO @ Sun, 03 Jun 2018 13:53:45: 14000000 INFO @ Sun, 03 Jun 2018 13:53:45: 14000000 INFO @ Sun, 03 Jun 2018 13:53:47: 15000000 INFO @ Sun, 03 Jun 2018 13:53:51: 15000000 INFO @ Sun, 03 Jun 2018 13:53:51: 15000000 INFO @ Sun, 03 Jun 2018 13:53:53: 16000000 INFO @ Sun, 03 Jun 2018 13:53:58: 16000000 INFO @ Sun, 03 Jun 2018 13:53:58: 16000000 INFO @ Sun, 03 Jun 2018 13:53:59: 17000000 INFO @ Sun, 03 Jun 2018 13:54:05: 17000000 INFO @ Sun, 03 Jun 2018 13:54:05: 17000000 INFO @ Sun, 03 Jun 2018 13:54:05: 18000000 INFO @ Sun, 03 Jun 2018 13:54:12: 18000000 INFO @ Sun, 03 Jun 2018 13:54:12: 18000000 INFO @ Sun, 03 Jun 2018 13:54:12: 19000000 INFO @ Sun, 03 Jun 2018 13:54:18: 20000000 INFO @ Sun, 03 Jun 2018 13:54:18: 19000000 INFO @ Sun, 03 Jun 2018 13:54:18: 19000000 INFO @ Sun, 03 Jun 2018 13:54:24: 21000000 INFO @ Sun, 03 Jun 2018 13:54:25: 20000000 INFO @ Sun, 03 Jun 2018 13:54:25: 20000000 INFO @ Sun, 03 Jun 2018 13:54:30: 22000000 INFO @ Sun, 03 Jun 2018 13:54:31: 21000000 INFO @ Sun, 03 Jun 2018 13:54:31: 21000000 INFO @ Sun, 03 Jun 2018 13:54:37: 23000000 INFO @ Sun, 03 Jun 2018 13:54:38: 22000000 INFO @ Sun, 03 Jun 2018 13:54:38: 22000000 INFO @ Sun, 03 Jun 2018 13:54:43: 24000000 INFO @ Sun, 03 Jun 2018 13:54:45: 23000000 INFO @ Sun, 03 Jun 2018 13:54:45: 23000000 INFO @ Sun, 03 Jun 2018 13:54:49: 25000000 INFO @ Sun, 03 Jun 2018 13:54:51: 24000000 INFO @ Sun, 03 Jun 2018 13:54:51: 24000000 INFO @ Sun, 03 Jun 2018 13:54:55: 26000000 INFO @ Sun, 03 Jun 2018 13:54:58: 25000000 INFO @ Sun, 03 Jun 2018 13:54:58: 25000000 INFO @ Sun, 03 Jun 2018 13:55:02: 27000000 INFO @ Sun, 03 Jun 2018 13:55:04: 26000000 INFO @ Sun, 03 Jun 2018 13:55:04: 26000000 INFO @ Sun, 03 Jun 2018 13:55:08: 28000000 INFO @ Sun, 03 Jun 2018 13:55:11: 27000000 INFO @ Sun, 03 Jun 2018 13:55:11: 27000000 INFO @ Sun, 03 Jun 2018 13:55:14: 29000000 INFO @ Sun, 03 Jun 2018 13:55:17: 28000000 INFO @ Sun, 03 Jun 2018 13:55:17: 28000000 INFO @ Sun, 03 Jun 2018 13:55:20: 30000000 INFO @ Sun, 03 Jun 2018 13:55:23: 29000000 INFO @ Sun, 03 Jun 2018 13:55:23: 29000000 INFO @ Sun, 03 Jun 2018 13:55:27: 31000000 INFO @ Sun, 03 Jun 2018 13:55:29: 30000000 INFO @ Sun, 03 Jun 2018 13:55:29: 30000000 INFO @ Sun, 03 Jun 2018 13:55:33: 32000000 INFO @ Sun, 03 Jun 2018 13:55:36: 31000000 INFO @ Sun, 03 Jun 2018 13:55:36: 31000000 INFO @ Sun, 03 Jun 2018 13:55:39: 33000000 INFO @ Sun, 03 Jun 2018 13:55:42: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:55:42: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:55:42: #1 total tags in treatment: 16274616 INFO @ Sun, 03 Jun 2018 13:55:42: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:55:42: #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 13:55:42: #1 tags after filtering in treatment: 12949221 INFO @ Sun, 03 Jun 2018 13:55:42: #1 Redundant rate of treatment: 0.20 INFO @ Sun, 03 Jun 2018 13:55:42: #1 finished! INFO @ Sun, 03 Jun 2018 13:55:42: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:55:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:55:42: 32000000 INFO @ Sun, 03 Jun 2018 13:55:42: 32000000 INFO @ Sun, 03 Jun 2018 13:55:43: #2 number of paired peaks: 244 WARNING @ Sun, 03 Jun 2018 13:55:43: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Sun, 03 Jun 2018 13:55:43: start model_add_line... INFO @ Sun, 03 Jun 2018 13:55:43: start X-correlation... INFO @ Sun, 03 Jun 2018 13:55:43: end of X-cor INFO @ Sun, 03 Jun 2018 13:55:43: #2 finished! INFO @ Sun, 03 Jun 2018 13:55:43: #2 predicted fragment length is 125 bps INFO @ Sun, 03 Jun 2018 13:55:43: #2 alternative fragment length(s) may be 3,125 bps INFO @ Sun, 03 Jun 2018 13:55:43: #2.2 Generate R script for model : SRX4085427.10_model.r INFO @ Sun, 03 Jun 2018 13:55:43: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:55:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:55:48: 33000000 INFO @ Sun, 03 Jun 2018 13:55:48: 33000000 INFO @ Sun, 03 Jun 2018 13:55:51: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:55:51: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:55:51: #1 total tags in treatment: 16274616 INFO @ Sun, 03 Jun 2018 13:55:51: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:55:51: #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 13:55:51: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:55:51: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:55:51: #1 total tags in treatment: 16274616 INFO @ Sun, 03 Jun 2018 13:55:51: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:55:51: #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 13:55:51: #1 tags after filtering in treatment: 12949221 INFO @ Sun, 03 Jun 2018 13:55:51: #1 Redundant rate of treatment: 0.20 INFO @ Sun, 03 Jun 2018 13:55:51: #1 finished! INFO @ Sun, 03 Jun 2018 13:55:51: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:55:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:55:51: #1 tags after filtering in treatment: 12949221 INFO @ Sun, 03 Jun 2018 13:55:51: #1 Redundant rate of treatment: 0.20 INFO @ Sun, 03 Jun 2018 13:55:51: #1 finished! INFO @ Sun, 03 Jun 2018 13:55:51: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:55:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:55:52: #2 number of paired peaks: 244 WARNING @ Sun, 03 Jun 2018 13:55:52: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Sun, 03 Jun 2018 13:55:52: start model_add_line... INFO @ Sun, 03 Jun 2018 13:55:52: #2 number of paired peaks: 244 WARNING @ Sun, 03 Jun 2018 13:55:52: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Sun, 03 Jun 2018 13:55:52: start model_add_line... INFO @ Sun, 03 Jun 2018 13:55:52: start X-correlation... INFO @ Sun, 03 Jun 2018 13:55:52: end of X-cor INFO @ Sun, 03 Jun 2018 13:55:52: #2 finished! INFO @ Sun, 03 Jun 2018 13:55:52: #2 predicted fragment length is 125 bps INFO @ Sun, 03 Jun 2018 13:55:52: #2 alternative fragment length(s) may be 3,125 bps INFO @ Sun, 03 Jun 2018 13:55:52: #2.2 Generate R script for model : SRX4085427.20_model.r INFO @ Sun, 03 Jun 2018 13:55:52: start X-correlation... INFO @ Sun, 03 Jun 2018 13:55:52: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:55:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:55:52: end of X-cor INFO @ Sun, 03 Jun 2018 13:55:52: #2 finished! INFO @ Sun, 03 Jun 2018 13:55:52: #2 predicted fragment length is 125 bps INFO @ Sun, 03 Jun 2018 13:55:52: #2 alternative fragment length(s) may be 3,125 bps INFO @ Sun, 03 Jun 2018 13:55:52: #2.2 Generate R script for model : SRX4085427.05_model.r INFO @ Sun, 03 Jun 2018 13:55:52: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:55:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:56:10: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:56:18: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:56:20: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:56:26: #4 Write output xls file... SRX4085427.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:56:26: #4 Write peak in narrowPeak format file... SRX4085427.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:56:26: #4 Write summits bed file... SRX4085427.10_summits.bed INFO @ Sun, 03 Jun 2018 13:56:26: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (665 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:56:32: #4 Write output xls file... SRX4085427.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:56:32: #4 Write peak in narrowPeak format file... SRX4085427.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:56:32: #4 Write summits bed file... SRX4085427.20_summits.bed INFO @ Sun, 03 Jun 2018 13:56:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (289 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:56:35: #4 Write output xls file... SRX4085427.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:56:35: #4 Write peak in narrowPeak format file... SRX4085427.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:56:35: #4 Write summits bed file... SRX4085427.05_summits.bed INFO @ Sun, 03 Jun 2018 13:56:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1318 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。