Job ID = 9161795 sra ファイルのダウンロード中... Completed: 1244877K bytes transferred in 16 seconds (634951K 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 20561687 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1044181/SRR2045662.sra Written 20561687 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: 00:16:34 20561687 reads; of these: 20561687 (100.00%) were paired; of these: 2438921 (11.86%) aligned concordantly 0 times 14775192 (71.86%) aligned concordantly exactly 1 time 3347574 (16.28%) aligned concordantly >1 times ---- 2438921 pairs aligned concordantly 0 times; of these: 454353 (18.63%) aligned discordantly 1 time ---- 1984568 pairs aligned 0 times concordantly or discordantly; of these: 3969136 mates make up the pairs; of these: 3387417 (85.34%) aligned 0 times 247572 (6.24%) aligned exactly 1 time 334147 (8.42%) aligned >1 times 91.76% overall alignment rate Time searching: 00:16:34 Overall time: 00:16:34 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 16 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] 1167412 / 18405594 = 0.0634 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 05:04:47: # Command line: callpeak -t SRX1044181.bam -f BAM -g 12100000 -n SRX1044181.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1044181.10 # format = BAM # ChIP-seq file = ['SRX1044181.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 05:04:47: # Command line: callpeak -t SRX1044181.bam -f BAM -g 12100000 -n SRX1044181.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1044181.20 # format = BAM # ChIP-seq file = ['SRX1044181.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 05:04:47: # Command line: callpeak -t SRX1044181.bam -f BAM -g 12100000 -n SRX1044181.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1044181.05 # format = BAM # ChIP-seq file = ['SRX1044181.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 05:04:47: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:04:47: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:04:47: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:04:47: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:04:47: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:04:47: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:04:54: 1000000 INFO @ Wed, 28 Jun 2017 05:04:54: 1000000 INFO @ Wed, 28 Jun 2017 05:04:54: 1000000 INFO @ Wed, 28 Jun 2017 05:05:00: 2000000 INFO @ Wed, 28 Jun 2017 05:05:00: 2000000 INFO @ Wed, 28 Jun 2017 05:05:00: 2000000 INFO @ Wed, 28 Jun 2017 05:05:07: 3000000 INFO @ Wed, 28 Jun 2017 05:05:07: 3000000 INFO @ Wed, 28 Jun 2017 05:05:07: 3000000 INFO @ Wed, 28 Jun 2017 05:05:14: 4000000 INFO @ Wed, 28 Jun 2017 05:05:14: 4000000 INFO @ Wed, 28 Jun 2017 05:05:14: 4000000 INFO @ Wed, 28 Jun 2017 05:05:20: 5000000 INFO @ Wed, 28 Jun 2017 05:05:20: 5000000 INFO @ Wed, 28 Jun 2017 05:05:20: 5000000 INFO @ Wed, 28 Jun 2017 05:05:27: 6000000 INFO @ Wed, 28 Jun 2017 05:05:28: 6000000 INFO @ Wed, 28 Jun 2017 05:05:28: 6000000 INFO @ Wed, 28 Jun 2017 05:05:33: 7000000 INFO @ Wed, 28 Jun 2017 05:05:35: 7000000 INFO @ Wed, 28 Jun 2017 05:05:35: 7000000 INFO @ Wed, 28 Jun 2017 05:05:40: 8000000 INFO @ Wed, 28 Jun 2017 05:05:42: 8000000 INFO @ Wed, 28 Jun 2017 05:05:42: 8000000 INFO @ Wed, 28 Jun 2017 05:05:46: 9000000 INFO @ Wed, 28 Jun 2017 05:05:48: 9000000 INFO @ Wed, 28 Jun 2017 05:05:48: 9000000 INFO @ Wed, 28 Jun 2017 05:05:53: 10000000 INFO @ Wed, 28 Jun 2017 05:05:54: 10000000 INFO @ Wed, 28 Jun 2017 05:05:54: 10000000 INFO @ Wed, 28 Jun 2017 05:05:59: 11000000 INFO @ Wed, 28 Jun 2017 05:06:01: 11000000 INFO @ Wed, 28 Jun 2017 05:06:01: 11000000 INFO @ Wed, 28 Jun 2017 05:06:06: 12000000 INFO @ Wed, 28 Jun 2017 05:06:07: 12000000 INFO @ Wed, 28 Jun 2017 05:06:07: 12000000 INFO @ Wed, 28 Jun 2017 05:06:12: 13000000 INFO @ Wed, 28 Jun 2017 05:06:14: 13000000 INFO @ Wed, 28 Jun 2017 05:06:14: 13000000 INFO @ Wed, 28 Jun 2017 05:06:19: 14000000 INFO @ Wed, 28 Jun 2017 05:06:21: 14000000 INFO @ Wed, 28 Jun 2017 05:06:21: 14000000 INFO @ Wed, 28 Jun 2017 05:06:28: 15000000 INFO @ Wed, 28 Jun 2017 05:06:29: 15000000 INFO @ Wed, 28 Jun 2017 05:06:29: 15000000 INFO @ Wed, 28 Jun 2017 05:06:37: 16000000 INFO @ Wed, 28 Jun 2017 05:06:37: 16000000 INFO @ Wed, 28 Jun 2017 05:06:37: 16000000 INFO @ Wed, 28 Jun 2017 05:06:45: 17000000 INFO @ Wed, 28 Jun 2017 05:06:45: 17000000 INFO @ Wed, 28 Jun 2017 05:06:46: 17000000 INFO @ Wed, 28 Jun 2017 05:06:52: 18000000 INFO @ Wed, 28 Jun 2017 05:06:53: 18000000 INFO @ Wed, 28 Jun 2017 05:06:54: 18000000 INFO @ Wed, 28 Jun 2017 05:07:01: 19000000 INFO @ Wed, 28 Jun 2017 05:07:01: 19000000 INFO @ Wed, 28 Jun 2017 05:07:04: 19000000 INFO @ Wed, 28 Jun 2017 05:07:10: 20000000 INFO @ Wed, 28 Jun 2017 05:07:10: 20000000 INFO @ Wed, 28 Jun 2017 05:07:14: 20000000 INFO @ Wed, 28 Jun 2017 05:07:19: 21000000 INFO @ Wed, 28 Jun 2017 05:07:19: 21000000 INFO @ Wed, 28 Jun 2017 05:07:23: 21000000 INFO @ Wed, 28 Jun 2017 05:07:27: 22000000 INFO @ Wed, 28 Jun 2017 05:07:28: 22000000 INFO @ Wed, 28 Jun 2017 05:07:33: 22000000 INFO @ Wed, 28 Jun 2017 05:07:36: 23000000 INFO @ Wed, 28 Jun 2017 05:07:36: 23000000 INFO @ Wed, 28 Jun 2017 05:07:42: 23000000 INFO @ Wed, 28 Jun 2017 05:07:45: 24000000 INFO @ Wed, 28 Jun 2017 05:07:45: 24000000 INFO @ Wed, 28 Jun 2017 05:07:51: 24000000 INFO @ Wed, 28 Jun 2017 05:07:53: 25000000 INFO @ Wed, 28 Jun 2017 05:07:54: 25000000 INFO @ Wed, 28 Jun 2017 05:08:00: 25000000 INFO @ Wed, 28 Jun 2017 05:08:02: 26000000 INFO @ Wed, 28 Jun 2017 05:08:02: 26000000 INFO @ Wed, 28 Jun 2017 05:08:08: 26000000 INFO @ Wed, 28 Jun 2017 05:08:09: 27000000 INFO @ Wed, 28 Jun 2017 05:08:09: 27000000 INFO @ Wed, 28 Jun 2017 05:08:15: 27000000 INFO @ Wed, 28 Jun 2017 05:08:16: 28000000 INFO @ Wed, 28 Jun 2017 05:08:17: 28000000 INFO @ Wed, 28 Jun 2017 05:08:22: 28000000 INFO @ Wed, 28 Jun 2017 05:08:24: 29000000 INFO @ Wed, 28 Jun 2017 05:08:24: 29000000 INFO @ Wed, 28 Jun 2017 05:08:29: 29000000 INFO @ Wed, 28 Jun 2017 05:08:31: 30000000 INFO @ Wed, 28 Jun 2017 05:08:31: 30000000 INFO @ Wed, 28 Jun 2017 05:08:36: 30000000 INFO @ Wed, 28 Jun 2017 05:08:38: 31000000 INFO @ Wed, 28 Jun 2017 05:08:39: 31000000 INFO @ Wed, 28 Jun 2017 05:08:43: 31000000 INFO @ Wed, 28 Jun 2017 05:08:46: 32000000 INFO @ Wed, 28 Jun 2017 05:08:46: 32000000 INFO @ Wed, 28 Jun 2017 05:08:51: 32000000 INFO @ Wed, 28 Jun 2017 05:08:53: 33000000 INFO @ Wed, 28 Jun 2017 05:08:53: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 28 Jun 2017 05:08:58: 33000000 INFO @ Wed, 28 Jun 2017 05:09:00: 34000000 INFO @ Wed, 28 Jun 2017 05:09:00: 34000000 INFO @ Wed, 28 Jun 2017 05:09:05: 34000000 INFO @ Wed, 28 Jun 2017 05:09:07: 35000000 INFO @ Wed, 28 Jun 2017 05:09:07: 35000000 INFO @ Wed, 28 Jun 2017 05:09:10: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:09:10: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:09:10: #1 total tags in treatment: 16963049 INFO @ Wed, 28 Jun 2017 05:09:10: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:09:10: #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 05:09:10: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:09:10: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:09:10: #1 total tags in treatment: 16963049 INFO @ Wed, 28 Jun 2017 05:09:10: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:09:10: #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 05:09:10: #1 tags after filtering in treatment: 10719576 INFO @ Wed, 28 Jun 2017 05:09:10: #1 Redundant rate of treatment: 0.37 INFO @ Wed, 28 Jun 2017 05:09:10: #1 finished! INFO @ Wed, 28 Jun 2017 05:09:10: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:09:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:09:11: #1 tags after filtering in treatment: 10719576 INFO @ Wed, 28 Jun 2017 05:09:11: #1 Redundant rate of treatment: 0.37 INFO @ Wed, 28 Jun 2017 05:09:11: #1 finished! INFO @ Wed, 28 Jun 2017 05:09:11: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:09:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:09:11: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:09:11: 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 05:09:11: Process for pairing-model is terminated! cat: SRX1044181.10_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 `SRX1044181.10_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 `SRX1044181.10_*.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 `SRX1044181.10_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 @ Wed, 28 Jun 2017 05:09:11: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:09:11: 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 05:09:11: Process for pairing-model is terminated! cat: SRX1044181.05_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 `SRX1044181.05_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 `SRX1044181.05_*.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 `SRX1044181.05_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 05:09:13: 35000000 INFO @ Wed, 28 Jun 2017 05:09:16: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:09:16: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:09:16: #1 total tags in treatment: 16963049 INFO @ Wed, 28 Jun 2017 05:09:16: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:09:16: #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 05:09:16: #1 tags after filtering in treatment: 10719576 INFO @ Wed, 28 Jun 2017 05:09:16: #1 Redundant rate of treatment: 0.37 INFO @ Wed, 28 Jun 2017 05:09:16: #1 finished! INFO @ Wed, 28 Jun 2017 05:09:16: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:09:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:09:17: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:09:17: 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 @ Wed, 28 Jun 2017 05:09:17: Process for pairing-model is terminated! cat: SRX1044181.20_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 `SRX1044181.20_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 `SRX1044181.20_*.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 `SRX1044181.20_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 BigWig に変換しました。