Job ID = 9163662 sra ファイルのダウンロード中... Completed: 610177K bytes transferred in 8 seconds (592109K 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 10147506 spots for /home/okishinya/chipatlas/results/sacCer3/SRX997486/SRR1976518.sra Written 10147506 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: 00:05:58 10147506 reads; of these: 10147506 (100.00%) were paired; of these: 3684034 (36.30%) aligned concordantly 0 times 5820359 (57.36%) aligned concordantly exactly 1 time 643113 (6.34%) aligned concordantly >1 times ---- 3684034 pairs aligned concordantly 0 times; of these: 187585 (5.09%) aligned discordantly 1 time ---- 3496449 pairs aligned 0 times concordantly or discordantly; of these: 6992898 mates make up the pairs; of these: 6704715 (95.88%) aligned 0 times 179379 (2.57%) aligned exactly 1 time 108804 (1.56%) aligned >1 times 66.96% overall alignment rate Time searching: 00:05:58 Overall time: 00:05:58 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] 2585203 / 6648501 = 0.3888 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 11:22:37: # Command line: callpeak -t SRX997486.bam -f BAM -g 12100000 -n SRX997486.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX997486.10 # format = BAM # ChIP-seq file = ['SRX997486.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 11:22:37: #1 read tag files... INFO @ Wed, 28 Jun 2017 11:22:37: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 11:22:37: # Command line: callpeak -t SRX997486.bam -f BAM -g 12100000 -n SRX997486.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX997486.20 # format = BAM # ChIP-seq file = ['SRX997486.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 11:22:37: #1 read tag files... INFO @ Wed, 28 Jun 2017 11:22:37: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 11:22:37: # Command line: callpeak -t SRX997486.bam -f BAM -g 12100000 -n SRX997486.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX997486.05 # format = BAM # ChIP-seq file = ['SRX997486.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 11:22:37: #1 read tag files... INFO @ Wed, 28 Jun 2017 11:22:37: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 11:22:43: 1000000 INFO @ Wed, 28 Jun 2017 11:22:44: 1000000 INFO @ Wed, 28 Jun 2017 11:22:44: 1000000 INFO @ Wed, 28 Jun 2017 11:22:49: 2000000 INFO @ Wed, 28 Jun 2017 11:22:50: 2000000 INFO @ Wed, 28 Jun 2017 11:22:50: 2000000 INFO @ Wed, 28 Jun 2017 11:22:55: 3000000 INFO @ Wed, 28 Jun 2017 11:22:56: 3000000 INFO @ Wed, 28 Jun 2017 11:22:56: 3000000 INFO @ Wed, 28 Jun 2017 11:23:01: 4000000 INFO @ Wed, 28 Jun 2017 11:23:02: 4000000 INFO @ Wed, 28 Jun 2017 11:23:02: 4000000 INFO @ Wed, 28 Jun 2017 11:23:07: 5000000 INFO @ Wed, 28 Jun 2017 11:23:09: 5000000 INFO @ Wed, 28 Jun 2017 11:23:09: 5000000 INFO @ Wed, 28 Jun 2017 11:23:12: 6000000 INFO @ Wed, 28 Jun 2017 11:23:15: 6000000 INFO @ Wed, 28 Jun 2017 11:23:15: 6000000 INFO @ Wed, 28 Jun 2017 11:23:18: 7000000 INFO @ Wed, 28 Jun 2017 11:23:21: 7000000 INFO @ Wed, 28 Jun 2017 11:23:21: 7000000 INFO @ Wed, 28 Jun 2017 11:23:24: 8000000 INFO @ Wed, 28 Jun 2017 11:23:26: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 11:23:26: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 11:23:26: #1 total tags in treatment: 3902988 INFO @ Wed, 28 Jun 2017 11:23:26: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 11:23:26: #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 11:23:27: #1 tags after filtering in treatment: 3342055 INFO @ Wed, 28 Jun 2017 11:23:27: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 28 Jun 2017 11:23:27: #1 finished! INFO @ Wed, 28 Jun 2017 11:23:27: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 11:23:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 11:23:27: #2 number of paired peaks: 36 WARNING @ Wed, 28 Jun 2017 11:23:27: 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 11:23:27: Process for pairing-model is terminated! cat: SRX997486.10_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 `SRX997486.10_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 `SRX997486.10_*.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 `SRX997486.10_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 11:23:27: 8000000 INFO @ Wed, 28 Jun 2017 11:23:27: 8000000 INFO @ Wed, 28 Jun 2017 11:23:30: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 11:23:30: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 11:23:30: #1 total tags in treatment: 3902988 INFO @ Wed, 28 Jun 2017 11:23:30: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 11:23:30: #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 11:23:30: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 11:23:30: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 11:23:30: #1 total tags in treatment: 3902988 INFO @ Wed, 28 Jun 2017 11:23:30: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 11:23:30: #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 11:23:30: #1 tags after filtering in treatment: 3342055 INFO @ Wed, 28 Jun 2017 11:23:30: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 28 Jun 2017 11:23:30: #1 finished! INFO @ Wed, 28 Jun 2017 11:23:30: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 11:23:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 11:23:30: #1 tags after filtering in treatment: 3342055 INFO @ Wed, 28 Jun 2017 11:23:30: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 28 Jun 2017 11:23:30: #1 finished! INFO @ Wed, 28 Jun 2017 11:23:30: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 11:23:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 11:23:30: #2 number of paired peaks: 36 WARNING @ Wed, 28 Jun 2017 11:23:30: 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 11:23:30: Process for pairing-model is terminated! cat: SRX997486.20_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) INFO @ Wed, 28 Jun 2017 11:23:30: #2 number of paired peaks: 36 WARNING @ Wed, 28 Jun 2017 11:23:30: 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 11:23:30: Process for pairing-model is terminated! rm: cannot remove `SRX997486.20_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 `SRX997486.20_*.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 `SRX997486.20_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 cat: SRX997486.05_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 `SRX997486.05_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 `SRX997486.05_*.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 `SRX997486.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。