Job ID = 9732099 sra ファイルのダウンロード中... Completed: 404427K bytes transferred in 11 seconds (279982K 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 17365751 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675890/SRR5380666.sra Written 17365751 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: 00:06:51 17365751 reads; of these: 17365751 (100.00%) were paired; of these: 5739850 (33.05%) aligned concordantly 0 times 10528031 (60.63%) aligned concordantly exactly 1 time 1097870 (6.32%) aligned concordantly >1 times ---- 5739850 pairs aligned concordantly 0 times; of these: 759181 (13.23%) aligned discordantly 1 time ---- 4980669 pairs aligned 0 times concordantly or discordantly; of these: 9961338 mates make up the pairs; of these: 9077034 (91.12%) aligned 0 times 648319 (6.51%) aligned exactly 1 time 235985 (2.37%) aligned >1 times 73.87% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 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 8 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] 1647371 / 12172021 = 0.1353 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 19:46:56: # Command line: callpeak -t SRX2675890.bam -f BAM -g 12100000 -n SRX2675890.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675890.10 # format = BAM # ChIP-seq file = ['SRX2675890.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 19:46:56: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:46:56: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:46:56: # Command line: callpeak -t SRX2675890.bam -f BAM -g 12100000 -n SRX2675890.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675890.20 # format = BAM # ChIP-seq file = ['SRX2675890.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 19:46:56: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:46:56: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:46:56: # Command line: callpeak -t SRX2675890.bam -f BAM -g 12100000 -n SRX2675890.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675890.05 # format = BAM # ChIP-seq file = ['SRX2675890.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 19:46:56: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:46:56: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:47:02: 1000000 INFO @ Sun, 03 Sep 2017 19:47:02: 1000000 INFO @ Sun, 03 Sep 2017 19:47:02: 1000000 INFO @ Sun, 03 Sep 2017 19:47:08: 2000000 INFO @ Sun, 03 Sep 2017 19:47:08: 2000000 INFO @ Sun, 03 Sep 2017 19:47:09: 2000000 INFO @ Sun, 03 Sep 2017 19:47:14: 3000000 INFO @ Sun, 03 Sep 2017 19:47:14: 3000000 INFO @ Sun, 03 Sep 2017 19:47:15: 3000000 INFO @ Sun, 03 Sep 2017 19:47:20: 4000000 INFO @ Sun, 03 Sep 2017 19:47:20: 4000000 INFO @ Sun, 03 Sep 2017 19:47:20: 4000000 INFO @ Sun, 03 Sep 2017 19:47:25: 5000000 INFO @ Sun, 03 Sep 2017 19:47:25: 5000000 INFO @ Sun, 03 Sep 2017 19:47:25: 5000000 INFO @ Sun, 03 Sep 2017 19:47:31: 6000000 INFO @ Sun, 03 Sep 2017 19:47:31: 6000000 INFO @ Sun, 03 Sep 2017 19:47:31: 6000000 INFO @ Sun, 03 Sep 2017 19:47:36: 7000000 INFO @ Sun, 03 Sep 2017 19:47:37: 7000000 INFO @ Sun, 03 Sep 2017 19:47:37: 7000000 INFO @ Sun, 03 Sep 2017 19:47:41: 8000000 INFO @ Sun, 03 Sep 2017 19:47:42: 8000000 INFO @ Sun, 03 Sep 2017 19:47:42: 8000000 INFO @ Sun, 03 Sep 2017 19:47:46: 9000000 INFO @ Sun, 03 Sep 2017 19:47:48: 9000000 INFO @ Sun, 03 Sep 2017 19:47:48: 9000000 INFO @ Sun, 03 Sep 2017 19:47:51: 10000000 INFO @ Sun, 03 Sep 2017 19:47:53: 10000000 INFO @ Sun, 03 Sep 2017 19:47:53: 10000000 INFO @ Sun, 03 Sep 2017 19:47:57: 11000000 INFO @ Sun, 03 Sep 2017 19:47:58: 11000000 INFO @ Sun, 03 Sep 2017 19:47:58: 11000000 INFO @ Sun, 03 Sep 2017 19:48:02: 12000000 INFO @ Sun, 03 Sep 2017 19:48:03: 12000000 INFO @ Sun, 03 Sep 2017 19:48:04: 12000000 INFO @ Sun, 03 Sep 2017 19:48:07: 13000000 INFO @ Sun, 03 Sep 2017 19:48:09: 13000000 INFO @ Sun, 03 Sep 2017 19:48:09: 13000000 INFO @ Sun, 03 Sep 2017 19:48:12: 14000000 INFO @ Sun, 03 Sep 2017 19:48:14: 14000000 INFO @ Sun, 03 Sep 2017 19:48:14: 14000000 INFO @ Sun, 03 Sep 2017 19:48:17: 15000000 INFO @ Sun, 03 Sep 2017 19:48:20: 15000000 INFO @ Sun, 03 Sep 2017 19:48:20: 15000000 INFO @ Sun, 03 Sep 2017 19:48:22: 16000000 INFO @ Sun, 03 Sep 2017 19:48:25: 16000000 INFO @ Sun, 03 Sep 2017 19:48:25: 16000000 INFO @ Sun, 03 Sep 2017 19:48:28: 17000000 INFO @ Sun, 03 Sep 2017 19:48:30: 17000000 INFO @ Sun, 03 Sep 2017 19:48:31: 17000000 INFO @ Sun, 03 Sep 2017 19:48:33: 18000000 INFO @ Sun, 03 Sep 2017 19:48:36: 18000000 INFO @ Sun, 03 Sep 2017 19:48:36: 18000000 INFO @ Sun, 03 Sep 2017 19:48:38: 19000000 INFO @ Sun, 03 Sep 2017 19:48:41: 19000000 INFO @ Sun, 03 Sep 2017 19:48:41: 19000000 INFO @ Sun, 03 Sep 2017 19:48:43: 20000000 INFO @ Sun, 03 Sep 2017 19:48:46: 20000000 INFO @ Sun, 03 Sep 2017 19:48:47: 20000000 INFO @ Sun, 03 Sep 2017 19:48:48: 21000000 INFO @ Sun, 03 Sep 2017 19:48:52: 21000000 INFO @ Sun, 03 Sep 2017 19:48:52: 21000000 INFO @ Sun, 03 Sep 2017 19:48:53: 22000000 INFO @ Sun, 03 Sep 2017 19:48:55: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:48:55: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:48:55: #1 total tags in treatment: 9989423 INFO @ Sun, 03 Sep 2017 19:48:55: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:48:55: #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 19:48:56: #1 tags after filtering in treatment: 4617693 INFO @ Sun, 03 Sep 2017 19:48:56: #1 Redundant rate of treatment: 0.54 INFO @ Sun, 03 Sep 2017 19:48:56: #1 finished! INFO @ Sun, 03 Sep 2017 19:48:56: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:48:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:48:56: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:48:56: 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 19:48:56: Process for pairing-model is terminated! cat: SRX2675890.20_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): 11 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675890.20_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 `SRX2675890.20_*.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 `SRX2675890.20_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, 03 Sep 2017 19:48:57: 22000000 INFO @ Sun, 03 Sep 2017 19:48:58: 22000000 INFO @ Sun, 03 Sep 2017 19:48:59: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:48:59: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:48:59: #1 total tags in treatment: 9989423 INFO @ Sun, 03 Sep 2017 19:48:59: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:48:59: #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 19:48:59: #1 tags after filtering in treatment: 4617693 INFO @ Sun, 03 Sep 2017 19:48:59: #1 Redundant rate of treatment: 0.54 INFO @ Sun, 03 Sep 2017 19:48:59: #1 finished! INFO @ Sun, 03 Sep 2017 19:48:59: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:48:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:48:59: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:48:59: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:48:59: #1 total tags in treatment: 9989423 INFO @ Sun, 03 Sep 2017 19:48:59: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:48:59: #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 19:49:00: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:49:00: 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 19:49:00: Process for pairing-model is terminated! cat: SRX2675890.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Sun, 03 Sep 2017 19:49:00: #1 tags after filtering in treatment: 4617693 INFO @ Sun, 03 Sep 2017 19:49:00: #1 Redundant rate of treatment: 0.54 INFO @ Sun, 03 Sep 2017 19:49:00: #1 finished! INFO @ Sun, 03 Sep 2017 19:49:00: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:49:00: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (0 chroms): 13 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675890.05_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 `SRX2675890.05_*.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 `SRX2675890.05_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 19:49:00: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:49:00: 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 19:49:00: Process for pairing-model is terminated! cat: SRX2675890.10_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): 10 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675890.10_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 `SRX2675890.10_*.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 `SRX2675890.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。