Job ID = 10536447 sra ファイルのダウンロード中... Completed: 1351192K bytes transferred in 55 seconds (198847K 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 32815452 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671165/SRR6696917.sra Written 32815452 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: 00:17:13 32815452 reads; of these: 32815452 (100.00%) were paired; of these: 13650956 (41.60%) aligned concordantly 0 times 16730773 (50.98%) aligned concordantly exactly 1 time 2433723 (7.42%) aligned concordantly >1 times ---- 13650956 pairs aligned concordantly 0 times; of these: 47278 (0.35%) aligned discordantly 1 time ---- 13603678 pairs aligned 0 times concordantly or discordantly; of these: 27207356 mates make up the pairs; of these: 26851644 (98.69%) aligned 0 times 290222 (1.07%) aligned exactly 1 time 65490 (0.24%) aligned >1 times 59.09% overall alignment rate Time searching: 00:17:13 Overall time: 00:17:13 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] 8967758 / 19183468 = 0.4675 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 09:57:21: # Command line: callpeak -t SRX3671165.bam -f BAM -g 12100000 -n SRX3671165.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671165.05 # format = BAM # ChIP-seq file = ['SRX3671165.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 09:57:21: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:57:21: # Command line: callpeak -t SRX3671165.bam -f BAM -g 12100000 -n SRX3671165.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671165.10 # format = BAM # ChIP-seq file = ['SRX3671165.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 09:57:21: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:57:21: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:57:21: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:57:21: # Command line: callpeak -t SRX3671165.bam -f BAM -g 12100000 -n SRX3671165.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671165.20 # format = BAM # ChIP-seq file = ['SRX3671165.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 09:57:21: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:57:21: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:57:28: 1000000 INFO @ Thu, 05 Apr 2018 09:57:29: 1000000 INFO @ Thu, 05 Apr 2018 09:57:29: 1000000 INFO @ Thu, 05 Apr 2018 09:57:35: 2000000 INFO @ Thu, 05 Apr 2018 09:57:37: 2000000 INFO @ Thu, 05 Apr 2018 09:57:37: 2000000 INFO @ Thu, 05 Apr 2018 09:57:42: 3000000 INFO @ Thu, 05 Apr 2018 09:57:45: 3000000 INFO @ Thu, 05 Apr 2018 09:57:45: 3000000 INFO @ Thu, 05 Apr 2018 09:57:48: 4000000 INFO @ Thu, 05 Apr 2018 09:57:52: 4000000 INFO @ Thu, 05 Apr 2018 09:57:52: 4000000 INFO @ Thu, 05 Apr 2018 09:57:55: 5000000 INFO @ Thu, 05 Apr 2018 09:58:00: 5000000 INFO @ Thu, 05 Apr 2018 09:58:00: 5000000 INFO @ Thu, 05 Apr 2018 09:58:02: 6000000 INFO @ Thu, 05 Apr 2018 09:58:08: 6000000 INFO @ Thu, 05 Apr 2018 09:58:08: 6000000 INFO @ Thu, 05 Apr 2018 09:58:08: 7000000 INFO @ Thu, 05 Apr 2018 09:58:15: 8000000 INFO @ Thu, 05 Apr 2018 09:58:16: 7000000 INFO @ Thu, 05 Apr 2018 09:58:16: 7000000 INFO @ Thu, 05 Apr 2018 09:58:22: 9000000 INFO @ Thu, 05 Apr 2018 09:58:24: 8000000 INFO @ Thu, 05 Apr 2018 09:58:24: 8000000 INFO @ Thu, 05 Apr 2018 09:58:28: 10000000 INFO @ Thu, 05 Apr 2018 09:58:31: 9000000 INFO @ Thu, 05 Apr 2018 09:58:31: 9000000 INFO @ Thu, 05 Apr 2018 09:58:35: 11000000 INFO @ Thu, 05 Apr 2018 09:58:39: 10000000 INFO @ Thu, 05 Apr 2018 09:58:39: 10000000 INFO @ Thu, 05 Apr 2018 09:58:42: 12000000 INFO @ Thu, 05 Apr 2018 09:58:47: 11000000 INFO @ Thu, 05 Apr 2018 09:58:47: 11000000 INFO @ Thu, 05 Apr 2018 09:58:48: 13000000 INFO @ Thu, 05 Apr 2018 09:58:55: 12000000 INFO @ Thu, 05 Apr 2018 09:58:55: 12000000 INFO @ Thu, 05 Apr 2018 09:58:55: 14000000 INFO @ Thu, 05 Apr 2018 09:59:02: 15000000 INFO @ Thu, 05 Apr 2018 09:59:03: 13000000 INFO @ Thu, 05 Apr 2018 09:59:03: 13000000 INFO @ Thu, 05 Apr 2018 09:59:08: 16000000 INFO @ Thu, 05 Apr 2018 09:59:10: 14000000 INFO @ Thu, 05 Apr 2018 09:59:10: 14000000 INFO @ Thu, 05 Apr 2018 09:59:15: 17000000 INFO @ Thu, 05 Apr 2018 09:59:18: 15000000 INFO @ Thu, 05 Apr 2018 09:59:18: 15000000 INFO @ Thu, 05 Apr 2018 09:59:22: 18000000 INFO @ Thu, 05 Apr 2018 09:59:26: 16000000 INFO @ Thu, 05 Apr 2018 09:59:26: 16000000 INFO @ Thu, 05 Apr 2018 09:59:29: 19000000 INFO @ Thu, 05 Apr 2018 09:59:33: 17000000 INFO @ Thu, 05 Apr 2018 09:59:33: 17000000 INFO @ Thu, 05 Apr 2018 09:59:35: 20000000 INFO @ Thu, 05 Apr 2018 09:59:41: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:59:41: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:59:41: #1 total tags in treatment: 10209139 INFO @ Thu, 05 Apr 2018 09:59:41: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:59:41: #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 09:59:41: 18000000 INFO @ Thu, 05 Apr 2018 09:59:41: 18000000 INFO @ Thu, 05 Apr 2018 09:59:41: #1 tags after filtering in treatment: 7634639 INFO @ Thu, 05 Apr 2018 09:59:41: #1 Redundant rate of treatment: 0.25 INFO @ Thu, 05 Apr 2018 09:59:41: #1 finished! INFO @ Thu, 05 Apr 2018 09:59:41: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:59:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:59:42: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:59:42: 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 09:59:42: Process for pairing-model is terminated! cat: SRX3671165.20_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 `SRX3671165.20_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 `SRX3671165.20_*.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 `SRX3671165.20_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 09:59:49: 19000000 INFO @ Thu, 05 Apr 2018 09:59:49: 19000000 INFO @ Thu, 05 Apr 2018 09:59:56: 20000000 INFO @ Thu, 05 Apr 2018 09:59:56: 20000000 INFO @ Thu, 05 Apr 2018 10:00:02: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:00:02: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:00:02: #1 total tags in treatment: 10209139 INFO @ Thu, 05 Apr 2018 10:00:02: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:00:02: #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 10:00:02: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:00:02: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:00:02: #1 total tags in treatment: 10209139 INFO @ Thu, 05 Apr 2018 10:00:02: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:00:02: #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 10:00:03: #1 tags after filtering in treatment: 7634639 INFO @ Thu, 05 Apr 2018 10:00:03: #1 Redundant rate of treatment: 0.25 INFO @ Thu, 05 Apr 2018 10:00:03: #1 finished! INFO @ Thu, 05 Apr 2018 10:00:03: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:00:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:00:03: #1 tags after filtering in treatment: 7634639 INFO @ Thu, 05 Apr 2018 10:00:03: #1 Redundant rate of treatment: 0.25 INFO @ Thu, 05 Apr 2018 10:00:03: #1 finished! INFO @ Thu, 05 Apr 2018 10:00:03: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:00:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:00:03: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:00:03: 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 10:00:03: Process for pairing-model is terminated! cat: SRX3671165.05_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 @ Thu, 05 Apr 2018 10:00:03: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:00:03: 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 10:00:03: Process for pairing-model is terminated! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3671165.05_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 `SRX3671165.05_*.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 `SRX3671165.05_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 cat: SRX3671165.10_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 `SRX3671165.10_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 `SRX3671165.10_*.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 `SRX3671165.10_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。