Job ID = 10536496 sra ファイルのダウンロード中... Completed: 1430632K bytes transferred in 41 seconds (283313K 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 31196418 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671192/SRR6696944.sra Written 31196418 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: 00:12:29 31196418 reads; of these: 31196418 (100.00%) were paired; of these: 16997920 (54.49%) aligned concordantly 0 times 12486336 (40.02%) aligned concordantly exactly 1 time 1712162 (5.49%) aligned concordantly >1 times ---- 16997920 pairs aligned concordantly 0 times; of these: 15890 (0.09%) aligned discordantly 1 time ---- 16982030 pairs aligned 0 times concordantly or discordantly; of these: 33964060 mates make up the pairs; of these: 33673626 (99.14%) aligned 0 times 241210 (0.71%) aligned exactly 1 time 49224 (0.14%) aligned >1 times 46.03% overall alignment rate Time searching: 00:12:29 Overall time: 00:12:29 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] 11783826 / 14206899 = 0.8294 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 10:14:08: # Command line: callpeak -t SRX3671192.bam -f BAM -g 12100000 -n SRX3671192.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671192.10 # format = BAM # ChIP-seq file = ['SRX3671192.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 10:14:08: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:14:08: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:14:08: # Command line: callpeak -t SRX3671192.bam -f BAM -g 12100000 -n SRX3671192.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671192.05 # format = BAM # ChIP-seq file = ['SRX3671192.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 10:14:08: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:14:08: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:14:08: # Command line: callpeak -t SRX3671192.bam -f BAM -g 12100000 -n SRX3671192.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671192.20 # format = BAM # ChIP-seq file = ['SRX3671192.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 10:14:08: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:14:08: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:14:13: 1000000 INFO @ Thu, 05 Apr 2018 10:14:13: 1000000 INFO @ Thu, 05 Apr 2018 10:14:13: 1000000 INFO @ Thu, 05 Apr 2018 10:14:19: 2000000 INFO @ Thu, 05 Apr 2018 10:14:19: 2000000 INFO @ Thu, 05 Apr 2018 10:14:19: 2000000 INFO @ Thu, 05 Apr 2018 10:14:24: 3000000 INFO @ Thu, 05 Apr 2018 10:14:24: 3000000 INFO @ Thu, 05 Apr 2018 10:14:24: 3000000 INFO @ Thu, 05 Apr 2018 10:14:29: 4000000 INFO @ Thu, 05 Apr 2018 10:14:30: 4000000 INFO @ Thu, 05 Apr 2018 10:14:30: 4000000 INFO @ Thu, 05 Apr 2018 10:14:34: 5000000 INFO @ Thu, 05 Apr 2018 10:14:35: 5000000 INFO @ Thu, 05 Apr 2018 10:14:35: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:14:35: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:14:35: #1 total tags in treatment: 2424707 INFO @ Thu, 05 Apr 2018 10:14:35: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:14:35: #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 10:14:35: #1 tags after filtering in treatment: 2096097 INFO @ Thu, 05 Apr 2018 10:14:35: #1 Redundant rate of treatment: 0.14 INFO @ Thu, 05 Apr 2018 10:14:35: #1 finished! INFO @ Thu, 05 Apr 2018 10:14:35: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:14:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:14:35: 5000000 INFO @ Thu, 05 Apr 2018 10:14:35: #2 number of paired peaks: 74 WARNING @ Thu, 05 Apr 2018 10:14:35: Too few paired peaks (74) 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 10:14:35: Process for pairing-model is terminated! cat: SRX3671192.10_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 `SRX3671192.10_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 `SRX3671192.10_*.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 `SRX3671192.10_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 @ Thu, 05 Apr 2018 10:14:36: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:14:36: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:14:36: #1 total tags in treatment: 2424707 INFO @ Thu, 05 Apr 2018 10:14:36: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:14:36: #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 10:14:36: #1 tags after filtering in treatment: 2096097 INFO @ Thu, 05 Apr 2018 10:14:36: #1 Redundant rate of treatment: 0.14 INFO @ Thu, 05 Apr 2018 10:14:36: #1 finished! INFO @ Thu, 05 Apr 2018 10:14:36: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:14:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:14:36: #2 number of paired peaks: 74 WARNING @ Thu, 05 Apr 2018 10:14:36: Too few paired peaks (74) 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 10:14:36: Process for pairing-model is terminated! cat: SRX3671192.20_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 `SRX3671192.20_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 `SRX3671192.20_*.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 `SRX3671192.20_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 10:14:36: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:14:36: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:14:36: #1 total tags in treatment: 2424707 INFO @ Thu, 05 Apr 2018 10:14:36: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:14:36: #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 10:14:36: #1 tags after filtering in treatment: 2096097 INFO @ Thu, 05 Apr 2018 10:14:36: #1 Redundant rate of treatment: 0.14 INFO @ Thu, 05 Apr 2018 10:14:36: #1 finished! INFO @ Thu, 05 Apr 2018 10:14:36: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:14:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:14:36: #2 number of paired peaks: 74 WARNING @ Thu, 05 Apr 2018 10:14:36: Too few paired peaks (74) 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 10:14:36: Process for pairing-model is terminated! cat: SRX3671192.05_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3671192.05_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 `SRX3671192.05_*.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 `SRX3671192.05_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。