Job ID = 10488212 sra ファイルのダウンロード中... Completed: 793710K bytes transferred in 79 seconds (82250K 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... Written 15259960 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3188113/SRR6039985.sra Written 15259960 spots total 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: 00:10:25 15259960 reads; of these: 15259960 (100.00%) were paired; of these: 2079771 (13.63%) aligned concordantly 0 times 11916343 (78.09%) aligned concordantly exactly 1 time 1263846 (8.28%) aligned concordantly >1 times ---- 2079771 pairs aligned concordantly 0 times; of these: 364526 (17.53%) aligned discordantly 1 time ---- 1715245 pairs aligned 0 times concordantly or discordantly; of these: 3430490 mates make up the pairs; of these: 2864158 (83.49%) aligned 0 times 350985 (10.23%) aligned exactly 1 time 215347 (6.28%) aligned >1 times 90.62% overall alignment rate Time searching: 00:10:25 Overall time: 00:10:25 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] 344401 / 13538428 = 0.0254 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, 18 Mar 2018 12:38:28: # Command line: callpeak -t SRX3188113.bam -f BAM -g 12100000 -n SRX3188113.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3188113.20 # format = BAM # ChIP-seq file = ['SRX3188113.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, 18 Mar 2018 12:38:28: #1 read tag files... INFO @ Sun, 18 Mar 2018 12:38:28: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 12:38:28: # Command line: callpeak -t SRX3188113.bam -f BAM -g 12100000 -n SRX3188113.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3188113.05 # format = BAM # ChIP-seq file = ['SRX3188113.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, 18 Mar 2018 12:38:28: #1 read tag files... INFO @ Sun, 18 Mar 2018 12:38:28: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 12:38:28: # Command line: callpeak -t SRX3188113.bam -f BAM -g 12100000 -n SRX3188113.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3188113.10 # format = BAM # ChIP-seq file = ['SRX3188113.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, 18 Mar 2018 12:38:28: #1 read tag files... INFO @ Sun, 18 Mar 2018 12:38:28: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 12:38:34: 1000000 INFO @ Sun, 18 Mar 2018 12:38:34: 1000000 INFO @ Sun, 18 Mar 2018 12:38:34: 1000000 INFO @ Sun, 18 Mar 2018 12:38:40: 2000000 INFO @ Sun, 18 Mar 2018 12:38:40: 2000000 INFO @ Sun, 18 Mar 2018 12:38:40: 2000000 INFO @ Sun, 18 Mar 2018 12:38:46: 3000000 INFO @ Sun, 18 Mar 2018 12:38:47: 3000000 INFO @ Sun, 18 Mar 2018 12:38:47: 3000000 INFO @ Sun, 18 Mar 2018 12:38:52: 4000000 INFO @ Sun, 18 Mar 2018 12:38:53: 4000000 INFO @ Sun, 18 Mar 2018 12:38:53: 4000000 INFO @ Sun, 18 Mar 2018 12:38:58: 5000000 INFO @ Sun, 18 Mar 2018 12:38:59: 5000000 INFO @ Sun, 18 Mar 2018 12:38:59: 5000000 INFO @ Sun, 18 Mar 2018 12:39:03: 6000000 INFO @ Sun, 18 Mar 2018 12:39:05: 6000000 INFO @ Sun, 18 Mar 2018 12:39:05: 6000000 INFO @ Sun, 18 Mar 2018 12:39:09: 7000000 INFO @ Sun, 18 Mar 2018 12:39:11: 7000000 INFO @ Sun, 18 Mar 2018 12:39:11: 7000000 INFO @ Sun, 18 Mar 2018 12:39:15: 8000000 INFO @ Sun, 18 Mar 2018 12:39:17: 8000000 INFO @ Sun, 18 Mar 2018 12:39:17: 8000000 INFO @ Sun, 18 Mar 2018 12:39:21: 9000000 INFO @ Sun, 18 Mar 2018 12:39:23: 9000000 INFO @ Sun, 18 Mar 2018 12:39:23: 9000000 INFO @ Sun, 18 Mar 2018 12:39:27: 10000000 INFO @ Sun, 18 Mar 2018 12:39:29: 10000000 INFO @ Sun, 18 Mar 2018 12:39:30: 10000000 INFO @ Sun, 18 Mar 2018 12:39:33: 11000000 INFO @ Sun, 18 Mar 2018 12:39:36: 11000000 INFO @ Sun, 18 Mar 2018 12:39:36: 11000000 INFO @ Sun, 18 Mar 2018 12:39:39: 12000000 INFO @ Sun, 18 Mar 2018 12:39:42: 12000000 INFO @ Sun, 18 Mar 2018 12:39:42: 12000000 INFO @ Sun, 18 Mar 2018 12:39:45: 13000000 INFO @ Sun, 18 Mar 2018 12:39:48: 13000000 INFO @ Sun, 18 Mar 2018 12:39:48: 13000000 INFO @ Sun, 18 Mar 2018 12:39:51: 14000000 INFO @ Sun, 18 Mar 2018 12:39:54: 14000000 INFO @ Sun, 18 Mar 2018 12:39:54: 14000000 INFO @ Sun, 18 Mar 2018 12:39:57: 15000000 INFO @ Sun, 18 Mar 2018 12:40:00: 15000000 INFO @ Sun, 18 Mar 2018 12:40:01: 15000000 INFO @ Sun, 18 Mar 2018 12:40:04: 16000000 INFO @ Sun, 18 Mar 2018 12:40:06: 16000000 INFO @ Sun, 18 Mar 2018 12:40:07: 16000000 INFO @ Sun, 18 Mar 2018 12:40:10: 17000000 INFO @ Sun, 18 Mar 2018 12:40:12: 17000000 INFO @ Sun, 18 Mar 2018 12:40:14: 17000000 INFO @ Sun, 18 Mar 2018 12:40:17: 18000000 INFO @ Sun, 18 Mar 2018 12:40:18: 18000000 INFO @ Sun, 18 Mar 2018 12:40:20: 18000000 INFO @ Sun, 18 Mar 2018 12:40:23: 19000000 INFO @ Sun, 18 Mar 2018 12:40:24: 19000000 INFO @ Sun, 18 Mar 2018 12:40:27: 19000000 INFO @ Sun, 18 Mar 2018 12:40:30: 20000000 INFO @ Sun, 18 Mar 2018 12:40:30: 20000000 INFO @ Sun, 18 Mar 2018 12:40:33: 20000000 INFO @ Sun, 18 Mar 2018 12:40:36: 21000000 INFO @ Sun, 18 Mar 2018 12:40:37: 21000000 INFO @ Sun, 18 Mar 2018 12:40:40: 21000000 INFO @ Sun, 18 Mar 2018 12:40:42: 22000000 INFO @ Sun, 18 Mar 2018 12:40:43: 22000000 INFO @ Sun, 18 Mar 2018 12:40:46: 22000000 INFO @ Sun, 18 Mar 2018 12:40:48: 23000000 INFO @ Sun, 18 Mar 2018 12:40:50: 23000000 INFO @ Sun, 18 Mar 2018 12:40:53: 23000000 INFO @ Sun, 18 Mar 2018 12:40:54: 24000000 INFO @ Sun, 18 Mar 2018 12:40:56: 24000000 INFO @ Sun, 18 Mar 2018 12:40:59: 24000000 INFO @ Sun, 18 Mar 2018 12:41:00: 25000000 INFO @ Sun, 18 Mar 2018 12:41:03: 25000000 INFO @ Sun, 18 Mar 2018 12:41:06: 25000000 INFO @ Sun, 18 Mar 2018 12:41:06: 26000000 INFO @ Sun, 18 Mar 2018 12:41:09: 26000000 INFO @ Sun, 18 Mar 2018 12:41:12: #1 tag size is determined as 51 bps INFO @ Sun, 18 Mar 2018 12:41:12: #1 tag size = 51 INFO @ Sun, 18 Mar 2018 12:41:12: #1 total tags in treatment: 12838394 INFO @ Sun, 18 Mar 2018 12:41:12: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 12:41:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 12:41:12: #1 tags after filtering in treatment: 8894161 INFO @ Sun, 18 Mar 2018 12:41:12: #1 Redundant rate of treatment: 0.31 INFO @ Sun, 18 Mar 2018 12:41:12: #1 finished! INFO @ Sun, 18 Mar 2018 12:41:12: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 12:41:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 12:41:12: 26000000 INFO @ Sun, 18 Mar 2018 12:41:13: #2 number of paired peaks: 0 WARNING @ Sun, 18 Mar 2018 12:41:13: 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, 18 Mar 2018 12:41:13: Process for pairing-model is terminated! cat: SRX3188113.10_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3188113.10_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 `SRX3188113.10_*.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 `SRX3188113.10_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, 18 Mar 2018 12:41:16: #1 tag size is determined as 51 bps INFO @ Sun, 18 Mar 2018 12:41:16: #1 tag size = 51 INFO @ Sun, 18 Mar 2018 12:41:16: #1 total tags in treatment: 12838394 INFO @ Sun, 18 Mar 2018 12:41:16: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 12:41:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 12:41:16: #1 tags after filtering in treatment: 8894161 INFO @ Sun, 18 Mar 2018 12:41:16: #1 Redundant rate of treatment: 0.31 INFO @ Sun, 18 Mar 2018 12:41:16: #1 finished! INFO @ Sun, 18 Mar 2018 12:41:16: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 12:41:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 12:41:17: #2 number of paired peaks: 0 WARNING @ Sun, 18 Mar 2018 12:41:17: 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, 18 Mar 2018 12:41:17: Process for pairing-model is terminated! cat: SRX3188113.20_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): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3188113.20_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 `SRX3188113.20_*.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 `SRX3188113.20_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 INFO @ Sun, 18 Mar 2018 12:41:18: #1 tag size is determined as 51 bps INFO @ Sun, 18 Mar 2018 12:41:18: #1 tag size = 51 INFO @ Sun, 18 Mar 2018 12:41:18: #1 total tags in treatment: 12838394 INFO @ Sun, 18 Mar 2018 12:41:18: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 12:41:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 12:41:18: #1 tags after filtering in treatment: 8894161 INFO @ Sun, 18 Mar 2018 12:41:18: #1 Redundant rate of treatment: 0.31 INFO @ Sun, 18 Mar 2018 12:41:18: #1 finished! INFO @ Sun, 18 Mar 2018 12:41:18: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 12:41:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 12:41:19: #2 number of paired peaks: 0 WARNING @ Sun, 18 Mar 2018 12:41:19: 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, 18 Mar 2018 12:41:19: Process for pairing-model is terminated! cat: SRX3188113.05_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): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3188113.05_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 `SRX3188113.05_*.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 `SRX3188113.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。