Job ID = 9161960 sra ファイルのダウンロード中... Completed: 1608216K bytes transferred in 16 seconds (800307K 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 26707317 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423694/SRR2930983.sra Written 26707317 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: 00:21:32 26707317 reads; of these: 26707317 (100.00%) were paired; of these: 1572118 (5.89%) aligned concordantly 0 times 22350510 (83.69%) aligned concordantly exactly 1 time 2784689 (10.43%) aligned concordantly >1 times ---- 1572118 pairs aligned concordantly 0 times; of these: 41296 (2.63%) aligned discordantly 1 time ---- 1530822 pairs aligned 0 times concordantly or discordantly; of these: 3061644 mates make up the pairs; of these: 2781302 (90.84%) aligned 0 times 228935 (7.48%) aligned exactly 1 time 51407 (1.68%) aligned >1 times 94.79% overall alignment rate Time searching: 00:21:32 Overall time: 00:21:32 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 24 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] 11302629 / 25145812 = 0.4495 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 05:41:24: # Command line: callpeak -t SRX1423694.bam -f BAM -g 12100000 -n SRX1423694.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423694.05 # format = BAM # ChIP-seq file = ['SRX1423694.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 05:41:24: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:41:24: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:41:24: # Command line: callpeak -t SRX1423694.bam -f BAM -g 12100000 -n SRX1423694.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423694.20 # format = BAM # ChIP-seq file = ['SRX1423694.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 05:41:24: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:41:24: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:41:24: # Command line: callpeak -t SRX1423694.bam -f BAM -g 12100000 -n SRX1423694.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423694.10 # format = BAM # ChIP-seq file = ['SRX1423694.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 05:41:24: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:41:24: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:41:31: 1000000 INFO @ Wed, 28 Jun 2017 05:41:31: 1000000 INFO @ Wed, 28 Jun 2017 05:41:31: 1000000 INFO @ Wed, 28 Jun 2017 05:41:38: 2000000 INFO @ Wed, 28 Jun 2017 05:41:38: 2000000 INFO @ Wed, 28 Jun 2017 05:41:39: 2000000 INFO @ Wed, 28 Jun 2017 05:41:44: 3000000 INFO @ Wed, 28 Jun 2017 05:41:45: 3000000 INFO @ Wed, 28 Jun 2017 05:41:47: 3000000 INFO @ Wed, 28 Jun 2017 05:41:51: 4000000 INFO @ Wed, 28 Jun 2017 05:41:51: 4000000 INFO @ Wed, 28 Jun 2017 05:41:54: 4000000 INFO @ Wed, 28 Jun 2017 05:41:57: 5000000 INFO @ Wed, 28 Jun 2017 05:41:57: 5000000 INFO @ Wed, 28 Jun 2017 05:42:00: 5000000 INFO @ Wed, 28 Jun 2017 05:42:03: 6000000 INFO @ Wed, 28 Jun 2017 05:42:03: 6000000 INFO @ Wed, 28 Jun 2017 05:42:06: 6000000 INFO @ Wed, 28 Jun 2017 05:42:09: 7000000 INFO @ Wed, 28 Jun 2017 05:42:09: 7000000 INFO @ Wed, 28 Jun 2017 05:42:13: 7000000 INFO @ Wed, 28 Jun 2017 05:42:15: 8000000 INFO @ Wed, 28 Jun 2017 05:42:16: 8000000 INFO @ Wed, 28 Jun 2017 05:42:20: 8000000 INFO @ Wed, 28 Jun 2017 05:42:21: 9000000 INFO @ Wed, 28 Jun 2017 05:42:22: 9000000 INFO @ Wed, 28 Jun 2017 05:42:27: 9000000 INFO @ Wed, 28 Jun 2017 05:42:27: 10000000 INFO @ Wed, 28 Jun 2017 05:42:28: 10000000 INFO @ Wed, 28 Jun 2017 05:42:33: 10000000 INFO @ Wed, 28 Jun 2017 05:42:33: 11000000 INFO @ Wed, 28 Jun 2017 05:42:34: 11000000 INFO @ Wed, 28 Jun 2017 05:42:39: 12000000 INFO @ Wed, 28 Jun 2017 05:42:39: 11000000 INFO @ Wed, 28 Jun 2017 05:42:40: 12000000 INFO @ Wed, 28 Jun 2017 05:42:45: 13000000 INFO @ Wed, 28 Jun 2017 05:42:46: 12000000 INFO @ Wed, 28 Jun 2017 05:42:47: 13000000 INFO @ Wed, 28 Jun 2017 05:42:50: 14000000 INFO @ Wed, 28 Jun 2017 05:42:53: 13000000 INFO @ Wed, 28 Jun 2017 05:42:53: 14000000 INFO @ Wed, 28 Jun 2017 05:42:56: 15000000 INFO @ Wed, 28 Jun 2017 05:42:59: 14000000 INFO @ Wed, 28 Jun 2017 05:42:59: 15000000 INFO @ Wed, 28 Jun 2017 05:43:02: 16000000 INFO @ Wed, 28 Jun 2017 05:43:05: 16000000 INFO @ Wed, 28 Jun 2017 05:43:05: 15000000 INFO @ Wed, 28 Jun 2017 05:43:08: 17000000 INFO @ Wed, 28 Jun 2017 05:43:12: 17000000 INFO @ Wed, 28 Jun 2017 05:43:13: 16000000 INFO @ Wed, 28 Jun 2017 05:43:15: 18000000 INFO @ Wed, 28 Jun 2017 05:43:19: 18000000 INFO @ Wed, 28 Jun 2017 05:43:21: 17000000 INFO @ Wed, 28 Jun 2017 05:43:22: 19000000 INFO @ Wed, 28 Jun 2017 05:43:26: 19000000 INFO @ Wed, 28 Jun 2017 05:43:28: 20000000 INFO @ Wed, 28 Jun 2017 05:43:29: 18000000 INFO @ Wed, 28 Jun 2017 05:43:33: 20000000 INFO @ Wed, 28 Jun 2017 05:43:35: 21000000 INFO @ Wed, 28 Jun 2017 05:43:37: 19000000 INFO @ Wed, 28 Jun 2017 05:43:40: 21000000 INFO @ Wed, 28 Jun 2017 05:43:43: 22000000 INFO @ Wed, 28 Jun 2017 05:43:45: 20000000 INFO @ Wed, 28 Jun 2017 05:43:48: 22000000 INFO @ Wed, 28 Jun 2017 05:43:50: 23000000 INFO @ Wed, 28 Jun 2017 05:43:54: 21000000 INFO @ Wed, 28 Jun 2017 05:43:55: 23000000 INFO @ Wed, 28 Jun 2017 05:43:57: 24000000 INFO @ Wed, 28 Jun 2017 05:44:02: 22000000 INFO @ Wed, 28 Jun 2017 05:44:02: 24000000 INFO @ Wed, 28 Jun 2017 05:44:05: 25000000 INFO @ Wed, 28 Jun 2017 05:44:10: 25000000 INFO @ Wed, 28 Jun 2017 05:44:10: 23000000 INFO @ Wed, 28 Jun 2017 05:44:12: 26000000 INFO @ Wed, 28 Jun 2017 05:44:17: 26000000 INFO @ Wed, 28 Jun 2017 05:44:19: 24000000 INFO @ Wed, 28 Jun 2017 05:44:19: 27000000 INFO @ Wed, 28 Jun 2017 05:44:24: 27000000 INFO @ Wed, 28 Jun 2017 05:44:26: 28000000 INFO @ Wed, 28 Jun 2017 05:44:26: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:44:26: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:44:26: #1 total tags in treatment: 13838743 INFO @ Wed, 28 Jun 2017 05:44:26: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:44:26: #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 05:44:27: #1 tags after filtering in treatment: 9687152 INFO @ Wed, 28 Jun 2017 05:44:27: #1 Redundant rate of treatment: 0.30 INFO @ Wed, 28 Jun 2017 05:44:27: #1 finished! INFO @ Wed, 28 Jun 2017 05:44:27: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:44:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:44:27: 25000000 INFO @ Wed, 28 Jun 2017 05:44:27: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:44:27: 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 05:44:27: Process for pairing-model is terminated! cat: SRX1423694.10_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 `SRX1423694.10_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 `SRX1423694.10_*.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 `SRX1423694.10_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 05:44:31: 28000000 INFO @ Wed, 28 Jun 2017 05:44:32: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:44:32: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:44:32: #1 total tags in treatment: 13838743 INFO @ Wed, 28 Jun 2017 05:44:32: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:44:32: #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 05:44:32: #1 tags after filtering in treatment: 9687152 INFO @ Wed, 28 Jun 2017 05:44:32: #1 Redundant rate of treatment: 0.30 INFO @ Wed, 28 Jun 2017 05:44:32: #1 finished! INFO @ Wed, 28 Jun 2017 05:44:32: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:44:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:44:33: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:44:33: 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 05:44:33: Process for pairing-model is terminated! cat: SRX1423694.05_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 `SRX1423694.05_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 `SRX1423694.05_*.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 `SRX1423694.05_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 05:44:34: 26000000 INFO @ Wed, 28 Jun 2017 05:44:40: 27000000 INFO @ Wed, 28 Jun 2017 05:44:46: 28000000 INFO @ Wed, 28 Jun 2017 05:44:46: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:44:46: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:44:46: #1 total tags in treatment: 13838743 INFO @ Wed, 28 Jun 2017 05:44:46: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:44:46: #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 05:44:47: #1 tags after filtering in treatment: 9687152 INFO @ Wed, 28 Jun 2017 05:44:47: #1 Redundant rate of treatment: 0.30 INFO @ Wed, 28 Jun 2017 05:44:47: #1 finished! INFO @ Wed, 28 Jun 2017 05:44:47: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:44:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:44:47: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:44:47: 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 05:44:47: Process for pairing-model is terminated! cat: SRX1423694.20_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 `SRX1423694.20_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 `SRX1423694.20_*.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 `SRX1423694.20_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。