Job ID = 9161972 sra ファイルのダウンロード中... Completed: 953009K bytes transferred in 11 seconds (681290K 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 22921217 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423704/SRR2930993.sra Written 22921217 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: 00:17:29 22921217 reads; of these: 22921217 (100.00%) were paired; of these: 2274584 (9.92%) aligned concordantly 0 times 18294288 (79.81%) aligned concordantly exactly 1 time 2352345 (10.26%) aligned concordantly >1 times ---- 2274584 pairs aligned concordantly 0 times; of these: 17870 (0.79%) aligned discordantly 1 time ---- 2256714 pairs aligned 0 times concordantly or discordantly; of these: 4513428 mates make up the pairs; of these: 4229057 (93.70%) aligned 0 times 239730 (5.31%) aligned exactly 1 time 44641 (0.99%) aligned >1 times 90.77% overall alignment rate Time searching: 00:17:29 Overall time: 00:17:29 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 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] 13711122 / 20652195 = 0.6639 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 05:33:58: # Command line: callpeak -t SRX1423704.bam -f BAM -g 12100000 -n SRX1423704.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423704.05 # format = BAM # ChIP-seq file = ['SRX1423704.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 05:33:58: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:33:58: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:33:58: # Command line: callpeak -t SRX1423704.bam -f BAM -g 12100000 -n SRX1423704.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423704.20 # format = BAM # ChIP-seq file = ['SRX1423704.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 05:33:58: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:33:58: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:33:58: # Command line: callpeak -t SRX1423704.bam -f BAM -g 12100000 -n SRX1423704.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423704.10 # format = BAM # ChIP-seq file = ['SRX1423704.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 05:33:58: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:33:58: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:34:04: 1000000 INFO @ Wed, 28 Jun 2017 05:34:04: 1000000 INFO @ Wed, 28 Jun 2017 05:34:04: 1000000 INFO @ Wed, 28 Jun 2017 05:34:10: 2000000 INFO @ Wed, 28 Jun 2017 05:34:10: 2000000 INFO @ Wed, 28 Jun 2017 05:34:10: 2000000 INFO @ Wed, 28 Jun 2017 05:34:15: 3000000 INFO @ Wed, 28 Jun 2017 05:34:15: 3000000 INFO @ Wed, 28 Jun 2017 05:34:15: 3000000 INFO @ Wed, 28 Jun 2017 05:34:21: 4000000 INFO @ Wed, 28 Jun 2017 05:34:21: 4000000 INFO @ Wed, 28 Jun 2017 05:34:21: 4000000 INFO @ Wed, 28 Jun 2017 05:34:26: 5000000 INFO @ Wed, 28 Jun 2017 05:34:26: 5000000 INFO @ Wed, 28 Jun 2017 05:34:27: 5000000 INFO @ Wed, 28 Jun 2017 05:34:32: 6000000 INFO @ Wed, 28 Jun 2017 05:34:32: 6000000 INFO @ Wed, 28 Jun 2017 05:34:33: 6000000 INFO @ Wed, 28 Jun 2017 05:34:37: 7000000 INFO @ Wed, 28 Jun 2017 05:34:38: 7000000 INFO @ Wed, 28 Jun 2017 05:34:39: 7000000 INFO @ Wed, 28 Jun 2017 05:34:43: 8000000 INFO @ Wed, 28 Jun 2017 05:34:44: 8000000 INFO @ Wed, 28 Jun 2017 05:34:45: 8000000 INFO @ Wed, 28 Jun 2017 05:34:49: 9000000 INFO @ Wed, 28 Jun 2017 05:34:50: 9000000 INFO @ Wed, 28 Jun 2017 05:34:52: 9000000 INFO @ Wed, 28 Jun 2017 05:34:55: 10000000 INFO @ Wed, 28 Jun 2017 05:34:57: 10000000 INFO @ Wed, 28 Jun 2017 05:34:59: 10000000 INFO @ Wed, 28 Jun 2017 05:35:02: 11000000 INFO @ Wed, 28 Jun 2017 05:35:04: 11000000 INFO @ Wed, 28 Jun 2017 05:35:06: 11000000 INFO @ Wed, 28 Jun 2017 05:35:08: 12000000 INFO @ Wed, 28 Jun 2017 05:35:11: 12000000 INFO @ Wed, 28 Jun 2017 05:35:12: 12000000 INFO @ Wed, 28 Jun 2017 05:35:14: 13000000 INFO @ Wed, 28 Jun 2017 05:35:16: 13000000 INFO @ Wed, 28 Jun 2017 05:35:18: 13000000 INFO @ Wed, 28 Jun 2017 05:35:19: 14000000 INFO @ Wed, 28 Jun 2017 05:35:20: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:35:20: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:35:20: #1 total tags in treatment: 6936661 INFO @ Wed, 28 Jun 2017 05:35:20: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:35:20: #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 05:35:21: #1 tags after filtering in treatment: 5585812 INFO @ Wed, 28 Jun 2017 05:35:21: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 28 Jun 2017 05:35:21: #1 finished! INFO @ Wed, 28 Jun 2017 05:35:21: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:35:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:35:21: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:35:21: 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 @ Wed, 28 Jun 2017 05:35:21: Process for pairing-model is terminated! cat: SRX1423704.20_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 `SRX1423704.20_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 `SRX1423704.20_*.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 `SRX1423704.20_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 05:35:22: 14000000 INFO @ Wed, 28 Jun 2017 05:35:23: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:35:23: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:35:23: #1 total tags in treatment: 6936661 INFO @ Wed, 28 Jun 2017 05:35:23: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:35:23: #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 05:35:24: #1 tags after filtering in treatment: 5585812 INFO @ Wed, 28 Jun 2017 05:35:24: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 28 Jun 2017 05:35:24: #1 finished! INFO @ Wed, 28 Jun 2017 05:35:24: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:35:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:35:24: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:35:24: 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 @ Wed, 28 Jun 2017 05:35:24: Process for pairing-model is terminated! cat: SRX1423704.10_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 `SRX1423704.10_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 `SRX1423704.10_*.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 `SRX1423704.10_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 05:35:24: 14000000 INFO @ Wed, 28 Jun 2017 05:35:25: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:35:25: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:35:25: #1 total tags in treatment: 6936661 INFO @ Wed, 28 Jun 2017 05:35:25: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:35:25: #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 05:35:26: #1 tags after filtering in treatment: 5585812 INFO @ Wed, 28 Jun 2017 05:35:26: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 28 Jun 2017 05:35:26: #1 finished! INFO @ Wed, 28 Jun 2017 05:35:26: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:35:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:35:26: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:35:26: 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 @ Wed, 28 Jun 2017 05:35:26: Process for pairing-model is terminated! cat: SRX1423704.05_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 `SRX1423704.05_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 `SRX1423704.05_*.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 `SRX1423704.05_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。