Job ID = 9163499 sra ファイルのダウンロード中... Completed: 1119262K bytes transferred in 11 seconds (776272K 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 26043234 spots for /home/okishinya/chipatlas/results/sacCer3/SRX739220/SRR1619675.sra Written 26043234 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: 00:13:06 26043234 reads; of these: 26043234 (100.00%) were paired; of these: 11998349 (46.07%) aligned concordantly 0 times 10143814 (38.95%) aligned concordantly exactly 1 time 3901071 (14.98%) aligned concordantly >1 times ---- 11998349 pairs aligned concordantly 0 times; of these: 377703 (3.15%) aligned discordantly 1 time ---- 11620646 pairs aligned 0 times concordantly or discordantly; of these: 23241292 mates make up the pairs; of these: 21944297 (94.42%) aligned 0 times 673693 (2.90%) aligned exactly 1 time 623302 (2.68%) aligned >1 times 57.87% overall alignment rate Time searching: 00:13:06 Overall time: 00:13:06 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 12 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] 8533469 / 14312606 = 0.5962 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 11:09:23: # Command line: callpeak -t SRX739220.bam -f BAM -g 12100000 -n SRX739220.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX739220.05 # format = BAM # ChIP-seq file = ['SRX739220.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 11:09:23: #1 read tag files... INFO @ Wed, 28 Jun 2017 11:09:23: # Command line: callpeak -t SRX739220.bam -f BAM -g 12100000 -n SRX739220.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX739220.20 # format = BAM # ChIP-seq file = ['SRX739220.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 11:09:23: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 11:09:23: #1 read tag files... INFO @ Wed, 28 Jun 2017 11:09:23: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 11:09:23: # Command line: callpeak -t SRX739220.bam -f BAM -g 12100000 -n SRX739220.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX739220.10 # format = BAM # ChIP-seq file = ['SRX739220.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 11:09:23: #1 read tag files... INFO @ Wed, 28 Jun 2017 11:09:23: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 11:09:30: 1000000 INFO @ Wed, 28 Jun 2017 11:09:30: 1000000 INFO @ Wed, 28 Jun 2017 11:09:30: 1000000 INFO @ Wed, 28 Jun 2017 11:09:36: 2000000 INFO @ Wed, 28 Jun 2017 11:09:36: 2000000 INFO @ Wed, 28 Jun 2017 11:09:37: 2000000 INFO @ Wed, 28 Jun 2017 11:09:43: 3000000 INFO @ Wed, 28 Jun 2017 11:09:43: 3000000 INFO @ Wed, 28 Jun 2017 11:09:43: 3000000 INFO @ Wed, 28 Jun 2017 11:09:49: 4000000 INFO @ Wed, 28 Jun 2017 11:09:49: 4000000 INFO @ Wed, 28 Jun 2017 11:09:50: 4000000 INFO @ Wed, 28 Jun 2017 11:09:56: 5000000 INFO @ Wed, 28 Jun 2017 11:09:56: 5000000 INFO @ Wed, 28 Jun 2017 11:09:56: 5000000 INFO @ Wed, 28 Jun 2017 11:10:02: 6000000 INFO @ Wed, 28 Jun 2017 11:10:02: 6000000 INFO @ Wed, 28 Jun 2017 11:10:03: 6000000 INFO @ Wed, 28 Jun 2017 11:10:08: 7000000 INFO @ Wed, 28 Jun 2017 11:10:08: 7000000 INFO @ Wed, 28 Jun 2017 11:10:09: 7000000 INFO @ Wed, 28 Jun 2017 11:10:14: 8000000 INFO @ Wed, 28 Jun 2017 11:10:14: 8000000 INFO @ Wed, 28 Jun 2017 11:10:15: 8000000 INFO @ Wed, 28 Jun 2017 11:10:19: 9000000 INFO @ Wed, 28 Jun 2017 11:10:20: 9000000 INFO @ Wed, 28 Jun 2017 11:10:21: 9000000 INFO @ Wed, 28 Jun 2017 11:10:25: 10000000 INFO @ Wed, 28 Jun 2017 11:10:25: 10000000 INFO @ Wed, 28 Jun 2017 11:10:26: 10000000 INFO @ Wed, 28 Jun 2017 11:10:31: 11000000 INFO @ Wed, 28 Jun 2017 11:10:32: 11000000 INFO @ Wed, 28 Jun 2017 11:10:32: 11000000 INFO @ Wed, 28 Jun 2017 11:10:36: 12000000 INFO @ Wed, 28 Jun 2017 11:10:38: 12000000 INFO @ Wed, 28 Jun 2017 11:10:38: 12000000 INFO @ Wed, 28 Jun 2017 11:10:42: 13000000 INFO @ Wed, 28 Jun 2017 11:10:42: #1 tag size is determined as 40 bps INFO @ Wed, 28 Jun 2017 11:10:42: #1 tag size = 40 INFO @ Wed, 28 Jun 2017 11:10:42: #1 total tags in treatment: 5699652 INFO @ Wed, 28 Jun 2017 11:10:42: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 11:10:42: #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 11:10:42: #1 tags after filtering in treatment: 3784559 INFO @ Wed, 28 Jun 2017 11:10:42: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 28 Jun 2017 11:10:42: #1 finished! INFO @ Wed, 28 Jun 2017 11:10:42: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 11:10:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 11:10:43: #2 number of paired peaks: 32 WARNING @ Wed, 28 Jun 2017 11:10:43: Too few paired peaks (32) 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 11:10:43: Process for pairing-model is terminated! cat: SRX739220.05_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 `SRX739220.05_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 `SRX739220.05_*.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 `SRX739220.05_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 11:10:43: 13000000 INFO @ Wed, 28 Jun 2017 11:10:43: 13000000 INFO @ Wed, 28 Jun 2017 11:10:44: #1 tag size is determined as 40 bps INFO @ Wed, 28 Jun 2017 11:10:44: #1 tag size = 40 INFO @ Wed, 28 Jun 2017 11:10:44: #1 total tags in treatment: 5699652 INFO @ Wed, 28 Jun 2017 11:10:44: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 11:10:44: #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 11:10:44: #1 tag size is determined as 40 bps INFO @ Wed, 28 Jun 2017 11:10:44: #1 tag size = 40 INFO @ Wed, 28 Jun 2017 11:10:44: #1 total tags in treatment: 5699652 INFO @ Wed, 28 Jun 2017 11:10:44: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 11:10:44: #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 11:10:44: #1 tags after filtering in treatment: 3784559 INFO @ Wed, 28 Jun 2017 11:10:44: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 28 Jun 2017 11:10:44: #1 finished! INFO @ Wed, 28 Jun 2017 11:10:44: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 11:10:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 11:10:44: #1 tags after filtering in treatment: 3784559 INFO @ Wed, 28 Jun 2017 11:10:44: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 28 Jun 2017 11:10:44: #1 finished! INFO @ Wed, 28 Jun 2017 11:10:44: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 11:10:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 11:10:44: #2 number of paired peaks: 32 WARNING @ Wed, 28 Jun 2017 11:10:44: Too few paired peaks (32) 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 11:10:44: Process for pairing-model is terminated! cat: SRX739220.20_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 `SRX739220.20_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 `SRX739220.20_*.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 `SRX739220.20_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 11:10:44: #2 number of paired peaks: 32 WARNING @ Wed, 28 Jun 2017 11:10:44: Too few paired peaks (32) 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 11:10:44: Process for pairing-model is terminated! cat: SRX739220.10_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 `SRX739220.10_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 `SRX739220.10_*.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 `SRX739220.10_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。