Job ID = 9732043 sra ファイルのダウンロード中... Completed: 451952K bytes transferred in 14 seconds (260083K 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 20459447 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675847/SRR5380623.sra Written 20459447 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:23 20459447 reads; of these: 20459447 (100.00%) were paired; of these: 4360045 (21.31%) aligned concordantly 0 times 14913880 (72.89%) aligned concordantly exactly 1 time 1185522 (5.79%) aligned concordantly >1 times ---- 4360045 pairs aligned concordantly 0 times; of these: 1195839 (27.43%) aligned discordantly 1 time ---- 3164206 pairs aligned 0 times concordantly or discordantly; of these: 6328412 mates make up the pairs; of these: 5520930 (87.24%) aligned 0 times 549451 (8.68%) aligned exactly 1 time 258031 (4.08%) aligned >1 times 86.51% overall alignment rate Time searching: 00:09:23 Overall time: 00:09:23 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 12 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 chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 2304278 / 17121395 = 0.1346 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 Sep 2017 19:28:17: # Command line: callpeak -t SRX2675847.bam -f BAM -g 12100000 -n SRX2675847.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675847.05 # format = BAM # ChIP-seq file = ['SRX2675847.bam'] # control file = None # effective genome size = 1.21e+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 Sep 2017 19:28:17: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:28:17: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:28:17: # Command line: callpeak -t SRX2675847.bam -f BAM -g 12100000 -n SRX2675847.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675847.10 # format = BAM # ChIP-seq file = ['SRX2675847.bam'] # control file = None # effective genome size = 1.21e+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 Sep 2017 19:28:17: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:28:17: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:28:17: # Command line: callpeak -t SRX2675847.bam -f BAM -g 12100000 -n SRX2675847.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675847.20 # format = BAM # ChIP-seq file = ['SRX2675847.bam'] # control file = None # effective genome size = 1.21e+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 Sep 2017 19:28:17: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:28:17: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:28:22: 1000000 INFO @ Sun, 03 Sep 2017 19:28:22: 1000000 INFO @ Sun, 03 Sep 2017 19:28:22: 1000000 INFO @ Sun, 03 Sep 2017 19:28:27: 2000000 INFO @ Sun, 03 Sep 2017 19:28:27: 2000000 INFO @ Sun, 03 Sep 2017 19:28:27: 2000000 INFO @ Sun, 03 Sep 2017 19:28:32: 3000000 INFO @ Sun, 03 Sep 2017 19:28:32: 3000000 INFO @ Sun, 03 Sep 2017 19:28:32: 3000000 INFO @ Sun, 03 Sep 2017 19:28:37: 4000000 INFO @ Sun, 03 Sep 2017 19:28:37: 4000000 INFO @ Sun, 03 Sep 2017 19:28:37: 4000000 INFO @ Sun, 03 Sep 2017 19:28:42: 5000000 INFO @ Sun, 03 Sep 2017 19:28:42: 5000000 INFO @ Sun, 03 Sep 2017 19:28:42: 5000000 INFO @ Sun, 03 Sep 2017 19:28:47: 6000000 INFO @ Sun, 03 Sep 2017 19:28:47: 6000000 INFO @ Sun, 03 Sep 2017 19:28:48: 6000000 INFO @ Sun, 03 Sep 2017 19:28:52: 7000000 INFO @ Sun, 03 Sep 2017 19:28:53: 7000000 INFO @ Sun, 03 Sep 2017 19:28:53: 7000000 INFO @ Sun, 03 Sep 2017 19:28:57: 8000000 INFO @ Sun, 03 Sep 2017 19:28:58: 8000000 INFO @ Sun, 03 Sep 2017 19:28:58: 8000000 INFO @ Sun, 03 Sep 2017 19:29:02: 9000000 INFO @ Sun, 03 Sep 2017 19:29:03: 9000000 INFO @ Sun, 03 Sep 2017 19:29:03: 9000000 INFO @ Sun, 03 Sep 2017 19:29:07: 10000000 INFO @ Sun, 03 Sep 2017 19:29:08: 10000000 INFO @ Sun, 03 Sep 2017 19:29:09: 10000000 INFO @ Sun, 03 Sep 2017 19:29:12: 11000000 INFO @ Sun, 03 Sep 2017 19:29:13: 11000000 INFO @ Sun, 03 Sep 2017 19:29:14: 11000000 INFO @ Sun, 03 Sep 2017 19:29:17: 12000000 INFO @ Sun, 03 Sep 2017 19:29:19: 12000000 INFO @ Sun, 03 Sep 2017 19:29:19: 12000000 INFO @ Sun, 03 Sep 2017 19:29:23: 13000000 INFO @ Sun, 03 Sep 2017 19:29:24: 13000000 INFO @ Sun, 03 Sep 2017 19:29:25: 13000000 INFO @ Sun, 03 Sep 2017 19:29:28: 14000000 INFO @ Sun, 03 Sep 2017 19:29:29: 14000000 INFO @ Sun, 03 Sep 2017 19:29:30: 14000000 INFO @ Sun, 03 Sep 2017 19:29:33: 15000000 INFO @ Sun, 03 Sep 2017 19:29:34: 15000000 INFO @ Sun, 03 Sep 2017 19:29:35: 15000000 INFO @ Sun, 03 Sep 2017 19:29:38: 16000000 INFO @ Sun, 03 Sep 2017 19:29:39: 16000000 INFO @ Sun, 03 Sep 2017 19:29:41: 16000000 INFO @ Sun, 03 Sep 2017 19:29:42: 17000000 INFO @ Sun, 03 Sep 2017 19:29:44: 17000000 INFO @ Sun, 03 Sep 2017 19:29:46: 17000000 INFO @ Sun, 03 Sep 2017 19:29:47: 18000000 INFO @ Sun, 03 Sep 2017 19:29:49: 18000000 INFO @ Sun, 03 Sep 2017 19:29:51: 18000000 INFO @ Sun, 03 Sep 2017 19:29:52: 19000000 INFO @ Sun, 03 Sep 2017 19:29:54: 19000000 INFO @ Sun, 03 Sep 2017 19:29:56: 19000000 INFO @ Sun, 03 Sep 2017 19:29:57: 20000000 INFO @ Sun, 03 Sep 2017 19:30:00: 20000000 INFO @ Sun, 03 Sep 2017 19:30:01: 20000000 INFO @ Sun, 03 Sep 2017 19:30:02: 21000000 INFO @ Sun, 03 Sep 2017 19:30:05: 21000000 INFO @ Sun, 03 Sep 2017 19:30:07: 21000000 INFO @ Sun, 03 Sep 2017 19:30:07: 22000000 INFO @ Sun, 03 Sep 2017 19:30:10: 22000000 INFO @ Sun, 03 Sep 2017 19:30:12: 22000000 INFO @ Sun, 03 Sep 2017 19:30:12: 23000000 INFO @ Sun, 03 Sep 2017 19:30:15: 23000000 INFO @ Sun, 03 Sep 2017 19:30:17: 23000000 INFO @ Sun, 03 Sep 2017 19:30:17: 24000000 INFO @ Sun, 03 Sep 2017 19:30:20: 24000000 INFO @ Sun, 03 Sep 2017 19:30:22: 25000000 INFO @ Sun, 03 Sep 2017 19:30:22: 24000000 INFO @ Sun, 03 Sep 2017 19:30:25: 25000000 INFO @ Sun, 03 Sep 2017 19:30:27: 26000000 INFO @ Sun, 03 Sep 2017 19:30:27: 25000000 INFO @ Sun, 03 Sep 2017 19:30:30: 26000000 INFO @ Sun, 03 Sep 2017 19:30:32: 27000000 INFO @ Sun, 03 Sep 2017 19:30:32: 26000000 INFO @ Sun, 03 Sep 2017 19:30:35: 27000000 INFO @ Sun, 03 Sep 2017 19:30:37: 28000000 INFO @ Sun, 03 Sep 2017 19:30:38: 27000000 INFO @ Sun, 03 Sep 2017 19:30:40: 28000000 INFO @ Sun, 03 Sep 2017 19:30:42: 29000000 INFO @ Sun, 03 Sep 2017 19:30:43: 28000000 INFO @ Sun, 03 Sep 2017 19:30:45: 29000000 INFO @ Sun, 03 Sep 2017 19:30:47: 30000000 INFO @ Sun, 03 Sep 2017 19:30:48: 29000000 INFO @ Sun, 03 Sep 2017 19:30:51: 30000000 INFO @ Sun, 03 Sep 2017 19:30:51: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:30:51: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:30:51: #1 total tags in treatment: 13814017 INFO @ Sun, 03 Sep 2017 19:30:51: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:30:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:30:52: #1 tags after filtering in treatment: 5478990 INFO @ Sun, 03 Sep 2017 19:30:52: #1 Redundant rate of treatment: 0.60 INFO @ Sun, 03 Sep 2017 19:30:52: #1 finished! INFO @ Sun, 03 Sep 2017 19:30:52: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:30:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:30:52: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:30:52: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sun, 03 Sep 2017 19:30:52: Process for pairing-model is terminated! cat: SRX2675847.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675847.05_model.r': 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 `SRX2675847.05_*.xls': 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 `SRX2675847.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 19:30:54: 30000000 INFO @ Sun, 03 Sep 2017 19:30:55: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:30:55: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:30:55: #1 total tags in treatment: 13814017 INFO @ Sun, 03 Sep 2017 19:30:55: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:30:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:30:55: #1 tags after filtering in treatment: 5478990 INFO @ Sun, 03 Sep 2017 19:30:55: #1 Redundant rate of treatment: 0.60 INFO @ Sun, 03 Sep 2017 19:30:55: #1 finished! INFO @ Sun, 03 Sep 2017 19:30:55: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:30:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:30:56: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:30:56: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sun, 03 Sep 2017 19:30:56: Process for pairing-model is terminated! cat: SRX2675847.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675847.10_model.r': 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 `SRX2675847.10_*.xls': 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 `SRX2675847.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 19:30:58: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:30:58: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:30:58: #1 total tags in treatment: 13814017 INFO @ Sun, 03 Sep 2017 19:30:58: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:30:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:30:58: #1 tags after filtering in treatment: 5478990 INFO @ Sun, 03 Sep 2017 19:30:58: #1 Redundant rate of treatment: 0.60 INFO @ Sun, 03 Sep 2017 19:30:58: #1 finished! INFO @ Sun, 03 Sep 2017 19:30:58: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:30:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:30:59: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:30:59: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sun, 03 Sep 2017 19:30:59: Process for pairing-model is terminated! cat: SRX2675847.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675847.20_model.r': 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 `SRX2675847.20_*.xls': 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 `SRX2675847.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。