Job ID = 9162088 sra ファイルのダウンロード中... Completed: 5789403K bytes transferred in 43 seconds (1101086K 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 184789812 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1625714/SRR3218449.sra Written 184789812 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: 00:28:59 184789812 reads; of these: 184789812 (100.00%) were paired; of these: 170125204 (92.06%) aligned concordantly 0 times 9825256 (5.32%) aligned concordantly exactly 1 time 4839352 (2.62%) aligned concordantly >1 times ---- 170125204 pairs aligned concordantly 0 times; of these: 145081 (0.09%) aligned discordantly 1 time ---- 169980123 pairs aligned 0 times concordantly or discordantly; of these: 339960246 mates make up the pairs; of these: 338284944 (99.51%) aligned 0 times 829268 (0.24%) aligned exactly 1 time 846034 (0.25%) aligned >1 times 8.47% overall alignment rate Time searching: 00:28:59 Overall time: 00:28:59 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] 4249432 / 14509012 = 0.2929 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 06:44:34: # Command line: callpeak -t SRX1625714.bam -f BAM -g 12100000 -n SRX1625714.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1625714.20 # format = BAM # ChIP-seq file = ['SRX1625714.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 06:44:34: # Command line: callpeak -t SRX1625714.bam -f BAM -g 12100000 -n SRX1625714.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1625714.10 # format = BAM # ChIP-seq file = ['SRX1625714.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 06:44:34: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:44:34: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:44:34: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:44:34: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:44:34: # Command line: callpeak -t SRX1625714.bam -f BAM -g 12100000 -n SRX1625714.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1625714.05 # format = BAM # ChIP-seq file = ['SRX1625714.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 06:44:34: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:44:34: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:44:39: 1000000 INFO @ Wed, 28 Jun 2017 06:44:39: 1000000 INFO @ Wed, 28 Jun 2017 06:44:39: 1000000 INFO @ Wed, 28 Jun 2017 06:44:44: 2000000 INFO @ Wed, 28 Jun 2017 06:44:45: 2000000 INFO @ Wed, 28 Jun 2017 06:44:45: 2000000 INFO @ Wed, 28 Jun 2017 06:44:50: 3000000 INFO @ Wed, 28 Jun 2017 06:44:50: 3000000 INFO @ Wed, 28 Jun 2017 06:44:50: 3000000 INFO @ Wed, 28 Jun 2017 06:44:55: 4000000 INFO @ Wed, 28 Jun 2017 06:44:55: 4000000 INFO @ Wed, 28 Jun 2017 06:44:55: 4000000 INFO @ Wed, 28 Jun 2017 06:45:00: 5000000 INFO @ Wed, 28 Jun 2017 06:45:00: 5000000 INFO @ Wed, 28 Jun 2017 06:45:01: 5000000 INFO @ Wed, 28 Jun 2017 06:45:05: 6000000 INFO @ Wed, 28 Jun 2017 06:45:06: 6000000 INFO @ Wed, 28 Jun 2017 06:45:06: 6000000 INFO @ Wed, 28 Jun 2017 06:45:11: 7000000 INFO @ Wed, 28 Jun 2017 06:45:11: 7000000 INFO @ Wed, 28 Jun 2017 06:45:12: 7000000 INFO @ Wed, 28 Jun 2017 06:45:16: 8000000 INFO @ Wed, 28 Jun 2017 06:45:16: 8000000 INFO @ Wed, 28 Jun 2017 06:45:18: 8000000 INFO @ Wed, 28 Jun 2017 06:45:22: 9000000 INFO @ Wed, 28 Jun 2017 06:45:22: 9000000 INFO @ Wed, 28 Jun 2017 06:45:23: 9000000 INFO @ Wed, 28 Jun 2017 06:45:27: 10000000 INFO @ Wed, 28 Jun 2017 06:45:27: 10000000 INFO @ Wed, 28 Jun 2017 06:45:29: 10000000 INFO @ Wed, 28 Jun 2017 06:45:32: 11000000 INFO @ Wed, 28 Jun 2017 06:45:33: 11000000 INFO @ Wed, 28 Jun 2017 06:45:34: 11000000 INFO @ Wed, 28 Jun 2017 06:45:37: 12000000 INFO @ Wed, 28 Jun 2017 06:45:38: 12000000 INFO @ Wed, 28 Jun 2017 06:45:40: 12000000 INFO @ Wed, 28 Jun 2017 06:45:42: 13000000 INFO @ Wed, 28 Jun 2017 06:45:43: 13000000 INFO @ Wed, 28 Jun 2017 06:45:45: 13000000 INFO @ Wed, 28 Jun 2017 06:45:47: 14000000 INFO @ Wed, 28 Jun 2017 06:45:49: 14000000 INFO @ Wed, 28 Jun 2017 06:45:51: 14000000 INFO @ Wed, 28 Jun 2017 06:45:52: 15000000 INFO @ Wed, 28 Jun 2017 06:45:53: 15000000 INFO @ Wed, 28 Jun 2017 06:45:56: 15000000 INFO @ Wed, 28 Jun 2017 06:45:56: 16000000 INFO @ Wed, 28 Jun 2017 06:45:59: 16000000 INFO @ Wed, 28 Jun 2017 06:46:01: 16000000 INFO @ Wed, 28 Jun 2017 06:46:01: 17000000 INFO @ Wed, 28 Jun 2017 06:46:04: 17000000 INFO @ Wed, 28 Jun 2017 06:46:07: 18000000 INFO @ Wed, 28 Jun 2017 06:46:07: 17000000 INFO @ Wed, 28 Jun 2017 06:46:09: 18000000 INFO @ Wed, 28 Jun 2017 06:46:12: 19000000 INFO @ Wed, 28 Jun 2017 06:46:12: 18000000 INFO @ Wed, 28 Jun 2017 06:46:15: 19000000 INFO @ Wed, 28 Jun 2017 06:46:17: 20000000 INFO @ Wed, 28 Jun 2017 06:46:18: 19000000 INFO @ Wed, 28 Jun 2017 06:46:20: 20000000 INFO @ Wed, 28 Jun 2017 06:46:22: 21000000 INFO @ Wed, 28 Jun 2017 06:46:23: 20000000 INFO @ Wed, 28 Jun 2017 06:46:25: 21000000 INFO @ Wed, 28 Jun 2017 06:46:27: 22000000 INFO @ Wed, 28 Jun 2017 06:46:29: 21000000 INFO @ Wed, 28 Jun 2017 06:46:31: 22000000 INFO @ Wed, 28 Jun 2017 06:46:31: #1 tag size is determined as 25 bps INFO @ Wed, 28 Jun 2017 06:46:31: #1 tag size = 25 INFO @ Wed, 28 Jun 2017 06:46:31: #1 total tags in treatment: 10434692 INFO @ Wed, 28 Jun 2017 06:46:31: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:46:31: #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 06:46:31: #1 tags after filtering in treatment: 5198529 INFO @ Wed, 28 Jun 2017 06:46:31: #1 Redundant rate of treatment: 0.50 INFO @ Wed, 28 Jun 2017 06:46:31: #1 finished! INFO @ Wed, 28 Jun 2017 06:46:31: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:46:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:46:31: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:46:31: 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 06:46:31: Process for pairing-model is terminated! cat: SRX1625714.05_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 `SRX1625714.05_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 `SRX1625714.05_*.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 `SRX1625714.05_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 06:46:34: 22000000 INFO @ Wed, 28 Jun 2017 06:46:35: #1 tag size is determined as 25 bps INFO @ Wed, 28 Jun 2017 06:46:35: #1 tag size = 25 INFO @ Wed, 28 Jun 2017 06:46:35: #1 total tags in treatment: 10434692 INFO @ Wed, 28 Jun 2017 06:46:35: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:46:35: #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 06:46:35: #1 tags after filtering in treatment: 5198529 INFO @ Wed, 28 Jun 2017 06:46:35: #1 Redundant rate of treatment: 0.50 INFO @ Wed, 28 Jun 2017 06:46:35: #1 finished! INFO @ Wed, 28 Jun 2017 06:46:35: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:46:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:46:36: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:46:36: 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 06:46:36: Process for pairing-model is terminated! cat: SRX1625714.10_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 `SRX1625714.10_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 `SRX1625714.10_*.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 `SRX1625714.10_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 06:46:38: #1 tag size is determined as 25 bps INFO @ Wed, 28 Jun 2017 06:46:38: #1 tag size = 25 INFO @ Wed, 28 Jun 2017 06:46:38: #1 total tags in treatment: 10434692 INFO @ Wed, 28 Jun 2017 06:46:38: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:46:38: #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 06:46:38: #1 tags after filtering in treatment: 5198529 INFO @ Wed, 28 Jun 2017 06:46:38: #1 Redundant rate of treatment: 0.50 INFO @ Wed, 28 Jun 2017 06:46:38: #1 finished! INFO @ Wed, 28 Jun 2017 06:46:38: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:46:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:46:39: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:46:39: 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 06:46:39: Process for pairing-model is terminated! cat: SRX1625714.20_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 `SRX1625714.20_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 `SRX1625714.20_*.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 `SRX1625714.20_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。