Job ID = 10536409 sra ファイルのダウンロード中... Completed: 1433942K bytes transferred in 50 seconds (233104K 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 27699398 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671154/SRR6696906.sra Written 27699398 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: 00:21:02 27699398 reads; of these: 27699398 (100.00%) were paired; of these: 1114820 (4.02%) aligned concordantly 0 times 22345178 (80.67%) aligned concordantly exactly 1 time 4239400 (15.31%) aligned concordantly >1 times ---- 1114820 pairs aligned concordantly 0 times; of these: 47166 (4.23%) aligned discordantly 1 time ---- 1067654 pairs aligned 0 times concordantly or discordantly; of these: 2135308 mates make up the pairs; of these: 1786152 (83.65%) aligned 0 times 259797 (12.17%) aligned exactly 1 time 89359 (4.18%) aligned >1 times 96.78% overall alignment rate Time searching: 00:21:02 Overall time: 00:21:02 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 24 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] 12269080 / 26605214 = 0.4612 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 @ Thu, 05 Apr 2018 09:54:59: # Command line: callpeak -t SRX3671154.bam -f BAM -g 12100000 -n SRX3671154.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671154.10 # format = BAM # ChIP-seq file = ['SRX3671154.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 @ Thu, 05 Apr 2018 09:54:59: # Command line: callpeak -t SRX3671154.bam -f BAM -g 12100000 -n SRX3671154.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671154.20 # format = BAM # ChIP-seq file = ['SRX3671154.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 @ Thu, 05 Apr 2018 09:54:59: # Command line: callpeak -t SRX3671154.bam -f BAM -g 12100000 -n SRX3671154.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671154.05 # format = BAM # ChIP-seq file = ['SRX3671154.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 @ Thu, 05 Apr 2018 09:54:59: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:54:59: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:54:59: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:54:59: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:54:59: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:54:59: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:55:05: 1000000 INFO @ Thu, 05 Apr 2018 09:55:05: 1000000 INFO @ Thu, 05 Apr 2018 09:55:05: 1000000 INFO @ Thu, 05 Apr 2018 09:55:11: 2000000 INFO @ Thu, 05 Apr 2018 09:55:12: 2000000 INFO @ Thu, 05 Apr 2018 09:55:12: 2000000 INFO @ Thu, 05 Apr 2018 09:55:17: 3000000 INFO @ Thu, 05 Apr 2018 09:55:18: 3000000 INFO @ Thu, 05 Apr 2018 09:55:18: 3000000 INFO @ Thu, 05 Apr 2018 09:55:23: 4000000 INFO @ Thu, 05 Apr 2018 09:55:25: 4000000 INFO @ Thu, 05 Apr 2018 09:55:25: 4000000 INFO @ Thu, 05 Apr 2018 09:55:28: 5000000 INFO @ Thu, 05 Apr 2018 09:55:31: 5000000 INFO @ Thu, 05 Apr 2018 09:55:31: 5000000 INFO @ Thu, 05 Apr 2018 09:55:34: 6000000 INFO @ Thu, 05 Apr 2018 09:55:38: 6000000 INFO @ Thu, 05 Apr 2018 09:55:38: 6000000 INFO @ Thu, 05 Apr 2018 09:55:40: 7000000 INFO @ Thu, 05 Apr 2018 09:55:44: 7000000 INFO @ Thu, 05 Apr 2018 09:55:44: 7000000 INFO @ Thu, 05 Apr 2018 09:55:46: 8000000 INFO @ Thu, 05 Apr 2018 09:55:51: 8000000 INFO @ Thu, 05 Apr 2018 09:55:51: 8000000 INFO @ Thu, 05 Apr 2018 09:55:52: 9000000 INFO @ Thu, 05 Apr 2018 09:55:57: 9000000 INFO @ Thu, 05 Apr 2018 09:55:57: 9000000 INFO @ Thu, 05 Apr 2018 09:55:57: 10000000 INFO @ Thu, 05 Apr 2018 09:56:03: 11000000 INFO @ Thu, 05 Apr 2018 09:56:04: 10000000 INFO @ Thu, 05 Apr 2018 09:56:04: 10000000 INFO @ Thu, 05 Apr 2018 09:56:09: 12000000 INFO @ Thu, 05 Apr 2018 09:56:10: 11000000 INFO @ Thu, 05 Apr 2018 09:56:10: 11000000 INFO @ Thu, 05 Apr 2018 09:56:15: 13000000 INFO @ Thu, 05 Apr 2018 09:56:16: 12000000 INFO @ Thu, 05 Apr 2018 09:56:16: 12000000 INFO @ Thu, 05 Apr 2018 09:56:20: 14000000 INFO @ Thu, 05 Apr 2018 09:56:23: 13000000 INFO @ Thu, 05 Apr 2018 09:56:23: 13000000 INFO @ Thu, 05 Apr 2018 09:56:26: 15000000 INFO @ Thu, 05 Apr 2018 09:56:29: 14000000 INFO @ Thu, 05 Apr 2018 09:56:29: 14000000 INFO @ Thu, 05 Apr 2018 09:56:32: 16000000 INFO @ Thu, 05 Apr 2018 09:56:35: 15000000 INFO @ Thu, 05 Apr 2018 09:56:35: 15000000 INFO @ Thu, 05 Apr 2018 09:56:38: 17000000 INFO @ Thu, 05 Apr 2018 09:56:42: 16000000 INFO @ Thu, 05 Apr 2018 09:56:42: 16000000 INFO @ Thu, 05 Apr 2018 09:56:43: 18000000 INFO @ Thu, 05 Apr 2018 09:56:48: 17000000 INFO @ Thu, 05 Apr 2018 09:56:48: 17000000 INFO @ Thu, 05 Apr 2018 09:56:49: 19000000 INFO @ Thu, 05 Apr 2018 09:56:54: 18000000 INFO @ Thu, 05 Apr 2018 09:56:54: 18000000 INFO @ Thu, 05 Apr 2018 09:56:55: 20000000 INFO @ Thu, 05 Apr 2018 09:57:00: 19000000 INFO @ Thu, 05 Apr 2018 09:57:00: 19000000 INFO @ Thu, 05 Apr 2018 09:57:00: 21000000 INFO @ Thu, 05 Apr 2018 09:57:06: 22000000 INFO @ Thu, 05 Apr 2018 09:57:06: 20000000 INFO @ Thu, 05 Apr 2018 09:57:06: 20000000 INFO @ Thu, 05 Apr 2018 09:57:12: 23000000 INFO @ Thu, 05 Apr 2018 09:57:13: 21000000 INFO @ Thu, 05 Apr 2018 09:57:13: 21000000 INFO @ Thu, 05 Apr 2018 09:57:18: 24000000 INFO @ Thu, 05 Apr 2018 09:57:19: 22000000 INFO @ Thu, 05 Apr 2018 09:57:19: 22000000 INFO @ Thu, 05 Apr 2018 09:57:23: 25000000 INFO @ Thu, 05 Apr 2018 09:57:25: 23000000 INFO @ Thu, 05 Apr 2018 09:57:25: 23000000 INFO @ Thu, 05 Apr 2018 09:57:29: 26000000 INFO @ Thu, 05 Apr 2018 09:57:31: 24000000 INFO @ Thu, 05 Apr 2018 09:57:31: 24000000 INFO @ Thu, 05 Apr 2018 09:57:35: 27000000 INFO @ Thu, 05 Apr 2018 09:57:38: 25000000 INFO @ Thu, 05 Apr 2018 09:57:38: 25000000 INFO @ Thu, 05 Apr 2018 09:57:41: 28000000 INFO @ Thu, 05 Apr 2018 09:57:44: 26000000 INFO @ Thu, 05 Apr 2018 09:57:44: 26000000 INFO @ Thu, 05 Apr 2018 09:57:47: 29000000 INFO @ Thu, 05 Apr 2018 09:57:47: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:57:47: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:57:47: #1 total tags in treatment: 14318996 INFO @ Thu, 05 Apr 2018 09:57:47: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:57:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:57:47: #1 tags after filtering in treatment: 9428674 INFO @ Thu, 05 Apr 2018 09:57:47: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 05 Apr 2018 09:57:47: #1 finished! INFO @ Thu, 05 Apr 2018 09:57:47: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:57:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:57:48: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:57:48: 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 @ Thu, 05 Apr 2018 09:57:48: Process for pairing-model is terminated! cat: SRX3671154.20_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 `SRX3671154.20_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 `SRX3671154.20_*.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 `SRX3671154.20_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 @ Thu, 05 Apr 2018 09:57:50: 27000000 INFO @ Thu, 05 Apr 2018 09:57:50: 27000000 INFO @ Thu, 05 Apr 2018 09:57:56: 28000000 INFO @ Thu, 05 Apr 2018 09:57:56: 28000000 INFO @ Thu, 05 Apr 2018 09:58:02: 29000000 INFO @ Thu, 05 Apr 2018 09:58:02: 29000000 INFO @ Thu, 05 Apr 2018 09:58:03: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:58:03: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:58:03: #1 total tags in treatment: 14318996 INFO @ Thu, 05 Apr 2018 09:58:03: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:58:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:58:03: #1 tags after filtering in treatment: 9428674 INFO @ Thu, 05 Apr 2018 09:58:03: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 05 Apr 2018 09:58:03: #1 finished! INFO @ Thu, 05 Apr 2018 09:58:03: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:58:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:58:03: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:58:03: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:58:03: #1 total tags in treatment: 14318996 INFO @ Thu, 05 Apr 2018 09:58:03: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:58:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:58:03: #1 tags after filtering in treatment: 9428674 INFO @ Thu, 05 Apr 2018 09:58:03: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 05 Apr 2018 09:58:03: #1 finished! INFO @ Thu, 05 Apr 2018 09:58:03: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:58:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:58:03: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:58:03: 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 @ Thu, 05 Apr 2018 09:58:03: Process for pairing-model is terminated! cat: SRX3671154.10_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): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3671154.10_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 `SRX3671154.10_*.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 `SRX3671154.10_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 @ Thu, 05 Apr 2018 09:58:04: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:58:04: 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 @ Thu, 05 Apr 2018 09:58:04: Process for pairing-model is terminated! cat: SRX3671154.05_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3671154.05_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 `SRX3671154.05_*.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 `SRX3671154.05_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。