Job ID = 9161998 sra ファイルのダウンロード中... Completed: 1579161K bytes transferred in 18 seconds (710435K 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 24995164 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423730/SRR2931019.sra Written 24995164 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: 00:17:47 24995164 reads; of these: 24995164 (100.00%) were paired; of these: 4124707 (16.50%) aligned concordantly 0 times 18643377 (74.59%) aligned concordantly exactly 1 time 2227080 (8.91%) aligned concordantly >1 times ---- 4124707 pairs aligned concordantly 0 times; of these: 58620 (1.42%) aligned discordantly 1 time ---- 4066087 pairs aligned 0 times concordantly or discordantly; of these: 8132174 mates make up the pairs; of these: 7798676 (95.90%) aligned 0 times 273418 (3.36%) aligned exactly 1 time 60080 (0.74%) aligned >1 times 84.40% overall alignment rate Time searching: 00:17:47 Overall time: 00:17:47 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] 15074497 / 20887677 = 0.7217 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 05:40:01: # Command line: callpeak -t SRX1423730.bam -f BAM -g 12100000 -n SRX1423730.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423730.10 # format = BAM # ChIP-seq file = ['SRX1423730.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 05:40:01: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:40:01: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:40:01: # Command line: callpeak -t SRX1423730.bam -f BAM -g 12100000 -n SRX1423730.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423730.20 # format = BAM # ChIP-seq file = ['SRX1423730.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 05:40:01: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:40:01: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:40:01: # Command line: callpeak -t SRX1423730.bam -f BAM -g 12100000 -n SRX1423730.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423730.05 # format = BAM # ChIP-seq file = ['SRX1423730.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 05:40:01: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:40:01: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:40:07: 1000000 INFO @ Wed, 28 Jun 2017 05:40:07: 1000000 INFO @ Wed, 28 Jun 2017 05:40:07: 1000000 INFO @ Wed, 28 Jun 2017 05:40:12: 2000000 INFO @ Wed, 28 Jun 2017 05:40:12: 2000000 INFO @ Wed, 28 Jun 2017 05:40:13: 2000000 INFO @ Wed, 28 Jun 2017 05:40:18: 3000000 INFO @ Wed, 28 Jun 2017 05:40:18: 3000000 INFO @ Wed, 28 Jun 2017 05:40:18: 3000000 INFO @ Wed, 28 Jun 2017 05:40:23: 4000000 INFO @ Wed, 28 Jun 2017 05:40:23: 4000000 INFO @ Wed, 28 Jun 2017 05:40:24: 4000000 INFO @ Wed, 28 Jun 2017 05:40:29: 5000000 INFO @ Wed, 28 Jun 2017 05:40:29: 5000000 INFO @ Wed, 28 Jun 2017 05:40:30: 5000000 INFO @ Wed, 28 Jun 2017 05:40:34: 6000000 INFO @ Wed, 28 Jun 2017 05:40:34: 6000000 INFO @ Wed, 28 Jun 2017 05:40:36: 6000000 INFO @ Wed, 28 Jun 2017 05:40:40: 7000000 INFO @ Wed, 28 Jun 2017 05:40:40: 7000000 INFO @ Wed, 28 Jun 2017 05:40:41: 7000000 INFO @ Wed, 28 Jun 2017 05:40:45: 8000000 INFO @ Wed, 28 Jun 2017 05:40:46: 8000000 INFO @ Wed, 28 Jun 2017 05:40:47: 8000000 INFO @ Wed, 28 Jun 2017 05:40:51: 9000000 INFO @ Wed, 28 Jun 2017 05:40:51: 9000000 INFO @ Wed, 28 Jun 2017 05:40:53: 9000000 INFO @ Wed, 28 Jun 2017 05:40:57: 10000000 INFO @ Wed, 28 Jun 2017 05:40:57: 10000000 INFO @ Wed, 28 Jun 2017 05:40:59: 10000000 INFO @ Wed, 28 Jun 2017 05:41:03: 11000000 INFO @ Wed, 28 Jun 2017 05:41:03: 11000000 INFO @ Wed, 28 Jun 2017 05:41:04: 11000000 INFO @ Wed, 28 Jun 2017 05:41:08: 12000000 INFO @ Wed, 28 Jun 2017 05:41:09: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:41:09: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:41:09: #1 total tags in treatment: 5812838 INFO @ Wed, 28 Jun 2017 05:41:09: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:41:09: #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 05:41:09: 12000000 INFO @ Wed, 28 Jun 2017 05:41:09: #1 tags after filtering in treatment: 4576985 INFO @ Wed, 28 Jun 2017 05:41:09: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 28 Jun 2017 05:41:09: #1 finished! INFO @ Wed, 28 Jun 2017 05:41:09: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:41:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:41:09: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:41:09: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:41:09: #1 total tags in treatment: 5812838 INFO @ Wed, 28 Jun 2017 05:41:09: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:41:09: #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 05:41:09: #2 number of paired peaks: 36 WARNING @ Wed, 28 Jun 2017 05:41:09: Too few paired peaks (36) 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 05:41:09: Process for pairing-model is terminated! cat: SRX1423730.05_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 `SRX1423730.05_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 `SRX1423730.05_*.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 `SRX1423730.05_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 05:41:09: #1 tags after filtering in treatment: 4576985 INFO @ Wed, 28 Jun 2017 05:41:09: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 28 Jun 2017 05:41:09: #1 finished! INFO @ Wed, 28 Jun 2017 05:41:09: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:41:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:41:09: #2 number of paired peaks: 36 WARNING @ Wed, 28 Jun 2017 05:41:09: Too few paired peaks (36) 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 05:41:09: Process for pairing-model is terminated! cat: SRX1423730.20_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 `SRX1423730.20_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 `SRX1423730.20_*.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 `SRX1423730.20_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 05:41:10: 12000000 INFO @ Wed, 28 Jun 2017 05:41:10: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:41:10: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:41:10: #1 total tags in treatment: 5812838 INFO @ Wed, 28 Jun 2017 05:41:10: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:41:10: #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 05:41:10: #1 tags after filtering in treatment: 4576985 INFO @ Wed, 28 Jun 2017 05:41:10: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 28 Jun 2017 05:41:10: #1 finished! INFO @ Wed, 28 Jun 2017 05:41:10: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:41:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:41:11: #2 number of paired peaks: 36 WARNING @ Wed, 28 Jun 2017 05:41:11: Too few paired peaks (36) 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 05:41:11: Process for pairing-model is terminated! cat: SRX1423730.10_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 `SRX1423730.10_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 `SRX1423730.10_*.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 `SRX1423730.10_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。