Job ID = 9160174 sra ファイルのダウンロード中... Completed: 946254K bytes transferred in 65 seconds (117486K 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 22168024 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2831021/SRR5572336.sra Written 22168024 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: 00:18:00 22168024 reads; of these: 22168024 (100.00%) were paired; of these: 636363 (2.87%) aligned concordantly 0 times 17823232 (80.40%) aligned concordantly exactly 1 time 3708429 (16.73%) aligned concordantly >1 times ---- 636363 pairs aligned concordantly 0 times; of these: 8408 (1.32%) aligned discordantly 1 time ---- 627955 pairs aligned 0 times concordantly or discordantly; of these: 1255910 mates make up the pairs; of these: 1169970 (93.16%) aligned 0 times 58219 (4.64%) aligned exactly 1 time 27721 (2.21%) aligned >1 times 97.36% overall alignment rate Time searching: 00:18:00 Overall time: 00:18:00 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 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 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] 2554882 / 21534780 = 0.1186 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 @ Wed, 28 Jun 2017 02:30:13: # Command line: callpeak -t SRX2831021.bam -f BAM -g 12100000 -n SRX2831021.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2831021.10 # format = BAM # ChIP-seq file = ['SRX2831021.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 @ Wed, 28 Jun 2017 02:30:13: #1 read tag files... INFO @ Wed, 28 Jun 2017 02:30:13: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 02:30:13: # Command line: callpeak -t SRX2831021.bam -f BAM -g 12100000 -n SRX2831021.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2831021.05 # format = BAM # ChIP-seq file = ['SRX2831021.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 @ Wed, 28 Jun 2017 02:30:13: #1 read tag files... INFO @ Wed, 28 Jun 2017 02:30:13: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 02:30:13: # Command line: callpeak -t SRX2831021.bam -f BAM -g 12100000 -n SRX2831021.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2831021.20 # format = BAM # ChIP-seq file = ['SRX2831021.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 @ Wed, 28 Jun 2017 02:30:13: #1 read tag files... INFO @ Wed, 28 Jun 2017 02:30:13: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 02:30:19: 1000000 INFO @ Wed, 28 Jun 2017 02:30:20: 1000000 INFO @ Wed, 28 Jun 2017 02:30:20: 1000000 INFO @ Wed, 28 Jun 2017 02:30:26: 2000000 INFO @ Wed, 28 Jun 2017 02:30:27: 2000000 INFO @ Wed, 28 Jun 2017 02:30:27: 2000000 INFO @ Wed, 28 Jun 2017 02:30:32: 3000000 INFO @ Wed, 28 Jun 2017 02:30:34: 3000000 INFO @ Wed, 28 Jun 2017 02:30:34: 3000000 INFO @ Wed, 28 Jun 2017 02:30:39: 4000000 INFO @ Wed, 28 Jun 2017 02:30:42: 4000000 INFO @ Wed, 28 Jun 2017 02:30:42: 4000000 INFO @ Wed, 28 Jun 2017 02:30:45: 5000000 INFO @ Wed, 28 Jun 2017 02:30:49: 5000000 INFO @ Wed, 28 Jun 2017 02:30:49: 5000000 INFO @ Wed, 28 Jun 2017 02:30:52: 6000000 INFO @ Wed, 28 Jun 2017 02:30:56: 6000000 INFO @ Wed, 28 Jun 2017 02:30:56: 6000000 INFO @ Wed, 28 Jun 2017 02:30:58: 7000000 INFO @ Wed, 28 Jun 2017 02:31:03: 7000000 INFO @ Wed, 28 Jun 2017 02:31:03: 7000000 INFO @ Wed, 28 Jun 2017 02:31:06: 8000000 INFO @ Wed, 28 Jun 2017 02:31:10: 8000000 INFO @ Wed, 28 Jun 2017 02:31:10: 8000000 INFO @ Wed, 28 Jun 2017 02:31:15: 9000000 INFO @ Wed, 28 Jun 2017 02:31:17: 9000000 INFO @ Wed, 28 Jun 2017 02:31:17: 9000000 INFO @ Wed, 28 Jun 2017 02:31:23: 10000000 INFO @ Wed, 28 Jun 2017 02:31:25: 10000000 INFO @ Wed, 28 Jun 2017 02:31:25: 10000000 INFO @ Wed, 28 Jun 2017 02:31:32: 11000000 INFO @ Wed, 28 Jun 2017 02:31:33: 11000000 INFO @ Wed, 28 Jun 2017 02:31:33: 11000000 INFO @ Wed, 28 Jun 2017 02:31:40: 12000000 INFO @ Wed, 28 Jun 2017 02:31:40: 12000000 INFO @ Wed, 28 Jun 2017 02:31:40: 12000000 INFO @ Wed, 28 Jun 2017 02:31:47: 13000000 INFO @ Wed, 28 Jun 2017 02:31:47: 13000000 INFO @ Wed, 28 Jun 2017 02:31:48: 13000000 INFO @ Wed, 28 Jun 2017 02:31:55: 14000000 INFO @ Wed, 28 Jun 2017 02:31:55: 14000000 INFO @ Wed, 28 Jun 2017 02:31:56: 14000000 INFO @ Wed, 28 Jun 2017 02:32:02: 15000000 INFO @ Wed, 28 Jun 2017 02:32:02: 15000000 INFO @ Wed, 28 Jun 2017 02:32:05: 15000000 INFO @ Wed, 28 Jun 2017 02:32:10: 16000000 INFO @ Wed, 28 Jun 2017 02:32:10: 16000000 INFO @ Wed, 28 Jun 2017 02:32:13: 16000000 INFO @ Wed, 28 Jun 2017 02:32:17: 17000000 INFO @ Wed, 28 Jun 2017 02:32:17: 17000000 INFO @ Wed, 28 Jun 2017 02:32:22: 17000000 INFO @ Wed, 28 Jun 2017 02:32:24: 18000000 INFO @ Wed, 28 Jun 2017 02:32:24: 18000000 INFO @ Wed, 28 Jun 2017 02:32:31: 18000000 INFO @ Wed, 28 Jun 2017 02:32:33: 19000000 INFO @ Wed, 28 Jun 2017 02:32:33: 19000000 INFO @ Wed, 28 Jun 2017 02:32:39: 19000000 INFO @ Wed, 28 Jun 2017 02:32:40: 20000000 INFO @ Wed, 28 Jun 2017 02:32:40: 20000000 INFO @ Wed, 28 Jun 2017 02:32:48: 21000000 INFO @ Wed, 28 Jun 2017 02:32:48: 21000000 INFO @ Wed, 28 Jun 2017 02:32:48: 20000000 INFO @ Wed, 28 Jun 2017 02:32:55: 22000000 INFO @ Wed, 28 Jun 2017 02:32:55: 22000000 INFO @ Wed, 28 Jun 2017 02:32:56: 21000000 INFO @ Wed, 28 Jun 2017 02:33:03: 23000000 INFO @ Wed, 28 Jun 2017 02:33:03: 23000000 INFO @ Wed, 28 Jun 2017 02:33:05: 22000000 INFO @ Wed, 28 Jun 2017 02:33:11: 24000000 INFO @ Wed, 28 Jun 2017 02:33:11: 24000000 INFO @ Wed, 28 Jun 2017 02:33:13: 23000000 INFO @ Wed, 28 Jun 2017 02:33:18: 25000000 INFO @ Wed, 28 Jun 2017 02:33:18: 25000000 INFO @ Wed, 28 Jun 2017 02:33:22: 24000000 INFO @ Wed, 28 Jun 2017 02:33:26: 26000000 INFO @ Wed, 28 Jun 2017 02:33:26: 26000000 INFO @ Wed, 28 Jun 2017 02:33:31: 25000000 INFO @ Wed, 28 Jun 2017 02:33:33: 27000000 INFO @ Wed, 28 Jun 2017 02:33:33: 27000000 INFO @ Wed, 28 Jun 2017 02:33:39: 26000000 INFO @ Wed, 28 Jun 2017 02:33:41: 28000000 INFO @ Wed, 28 Jun 2017 02:33:41: 28000000 INFO @ Wed, 28 Jun 2017 02:33:48: 27000000 INFO @ Wed, 28 Jun 2017 02:33:49: 29000000 INFO @ Wed, 28 Jun 2017 02:33:49: 29000000 INFO @ Wed, 28 Jun 2017 02:33:56: 30000000 INFO @ Wed, 28 Jun 2017 02:33:56: 30000000 INFO @ Wed, 28 Jun 2017 02:33:56: 28000000 INFO @ Wed, 28 Jun 2017 02:34:04: 31000000 INFO @ Wed, 28 Jun 2017 02:34:04: 31000000 INFO @ Wed, 28 Jun 2017 02:34:05: 29000000 INFO @ Wed, 28 Jun 2017 02:34:12: 32000000 INFO @ Wed, 28 Jun 2017 02:34:12: 32000000 INFO @ Wed, 28 Jun 2017 02:34:14: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 28 Jun 2017 02:34:20: 33000000 INFO @ Wed, 28 Jun 2017 02:34:20: 33000000 INFO @ Wed, 28 Jun 2017 02:34:24: 31000000 INFO @ Wed, 28 Jun 2017 02:34:29: 34000000 INFO @ Wed, 28 Jun 2017 02:34:29: 34000000 INFO @ Wed, 28 Jun 2017 02:34:34: 32000000 BigWig に変換しました。 INFO @ Wed, 28 Jun 2017 02:34:38: 35000000 INFO @ Wed, 28 Jun 2017 02:34:38: 35000000 INFO @ Wed, 28 Jun 2017 02:34:45: 33000000 INFO @ Wed, 28 Jun 2017 02:34:47: 36000000 INFO @ Wed, 28 Jun 2017 02:34:48: 36000000 INFO @ Wed, 28 Jun 2017 02:34:55: 34000000 INFO @ Wed, 28 Jun 2017 02:34:56: 37000000 INFO @ Wed, 28 Jun 2017 02:34:58: 37000000 INFO @ Wed, 28 Jun 2017 02:35:04: 38000000 INFO @ Wed, 28 Jun 2017 02:35:05: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 02:35:05: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 02:35:05: #1 total tags in treatment: 18977022 INFO @ Wed, 28 Jun 2017 02:35:05: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 02:35:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 02:35:05: #1 tags after filtering in treatment: 12213305 INFO @ Wed, 28 Jun 2017 02:35:05: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 28 Jun 2017 02:35:05: #1 finished! INFO @ Wed, 28 Jun 2017 02:35:05: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 02:35:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 02:35:05: 35000000 INFO @ Wed, 28 Jun 2017 02:35:06: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 02:35:06: 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 @ Wed, 28 Jun 2017 02:35:06: Process for pairing-model is terminated! cat: SRX2831021.05_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 `SRX2831021.05_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 `SRX2831021.05_*.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 `SRX2831021.05_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 @ Wed, 28 Jun 2017 02:35:09: 38000000 INFO @ Wed, 28 Jun 2017 02:35:09: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 02:35:09: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 02:35:09: #1 total tags in treatment: 18977022 INFO @ Wed, 28 Jun 2017 02:35:09: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 02:35:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 02:35:10: #1 tags after filtering in treatment: 12213305 INFO @ Wed, 28 Jun 2017 02:35:10: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 28 Jun 2017 02:35:10: #1 finished! INFO @ Wed, 28 Jun 2017 02:35:10: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 02:35:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 02:35:11: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 02:35:11: 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 @ Wed, 28 Jun 2017 02:35:11: Process for pairing-model is terminated! cat: SRX2831021.20_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 `SRX2831021.20_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 `SRX2831021.20_*.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 `SRX2831021.20_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 @ Wed, 28 Jun 2017 02:35:15: 36000000 INFO @ Wed, 28 Jun 2017 02:35:23: 37000000 INFO @ Wed, 28 Jun 2017 02:35:30: 38000000 INFO @ Wed, 28 Jun 2017 02:35:30: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 02:35:30: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 02:35:30: #1 total tags in treatment: 18977022 INFO @ Wed, 28 Jun 2017 02:35:30: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 02:35:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 02:35:31: #1 tags after filtering in treatment: 12213305 INFO @ Wed, 28 Jun 2017 02:35:31: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 28 Jun 2017 02:35:31: #1 finished! INFO @ Wed, 28 Jun 2017 02:35:31: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 02:35:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 02:35:31: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 02:35:31: 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 @ Wed, 28 Jun 2017 02:35:31: Process for pairing-model is terminated! cat: SRX2831021.10_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 `SRX2831021.10_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 `SRX2831021.10_*.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 `SRX2831021.10_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