Job ID = 9732103 sra ファイルのダウンロード中... Completed: 335941K bytes transferred in 7 seconds (360514K 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 14564296 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675893/SRR5380669.sra Written 14564296 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: 00:06:18 14564296 reads; of these: 14564296 (100.00%) were paired; of these: 4279862 (29.39%) aligned concordantly 0 times 9102168 (62.50%) aligned concordantly exactly 1 time 1182266 (8.12%) aligned concordantly >1 times ---- 4279862 pairs aligned concordantly 0 times; of these: 681081 (15.91%) aligned discordantly 1 time ---- 3598781 pairs aligned 0 times concordantly or discordantly; of these: 7197562 mates make up the pairs; of these: 6331249 (87.96%) aligned 0 times 594597 (8.26%) aligned exactly 1 time 271716 (3.78%) aligned >1 times 78.26% overall alignment rate Time searching: 00:06:18 Overall time: 00:06:18 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] 1391186 / 10601636 = 0.1312 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 @ Sun, 03 Sep 2017 19:45:52: # Command line: callpeak -t SRX2675893.bam -f BAM -g 12100000 -n SRX2675893.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675893.20 # format = BAM # ChIP-seq file = ['SRX2675893.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 @ Sun, 03 Sep 2017 19:45:52: # Command line: callpeak -t SRX2675893.bam -f BAM -g 12100000 -n SRX2675893.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675893.10 # format = BAM # ChIP-seq file = ['SRX2675893.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 @ Sun, 03 Sep 2017 19:45:52: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:45:52: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:45:52: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:45:52: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:45:52: # Command line: callpeak -t SRX2675893.bam -f BAM -g 12100000 -n SRX2675893.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675893.05 # format = BAM # ChIP-seq file = ['SRX2675893.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 @ Sun, 03 Sep 2017 19:45:52: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:45:52: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:45:57: 1000000 INFO @ Sun, 03 Sep 2017 19:45:57: 1000000 INFO @ Sun, 03 Sep 2017 19:45:57: 1000000 INFO @ Sun, 03 Sep 2017 19:46:02: 2000000 INFO @ Sun, 03 Sep 2017 19:46:02: 2000000 INFO @ Sun, 03 Sep 2017 19:46:02: 2000000 INFO @ Sun, 03 Sep 2017 19:46:07: 3000000 INFO @ Sun, 03 Sep 2017 19:46:07: 3000000 INFO @ Sun, 03 Sep 2017 19:46:07: 3000000 INFO @ Sun, 03 Sep 2017 19:46:11: 4000000 INFO @ Sun, 03 Sep 2017 19:46:12: 4000000 INFO @ Sun, 03 Sep 2017 19:46:12: 4000000 INFO @ Sun, 03 Sep 2017 19:46:16: 5000000 INFO @ Sun, 03 Sep 2017 19:46:17: 5000000 INFO @ Sun, 03 Sep 2017 19:46:17: 5000000 INFO @ Sun, 03 Sep 2017 19:46:21: 6000000 INFO @ Sun, 03 Sep 2017 19:46:21: 6000000 INFO @ Sun, 03 Sep 2017 19:46:22: 6000000 INFO @ Sun, 03 Sep 2017 19:46:25: 7000000 INFO @ Sun, 03 Sep 2017 19:46:26: 7000000 INFO @ Sun, 03 Sep 2017 19:46:27: 7000000 INFO @ Sun, 03 Sep 2017 19:46:30: 8000000 INFO @ Sun, 03 Sep 2017 19:46:31: 8000000 INFO @ Sun, 03 Sep 2017 19:46:32: 8000000 INFO @ Sun, 03 Sep 2017 19:46:35: 9000000 INFO @ Sun, 03 Sep 2017 19:46:36: 9000000 INFO @ Sun, 03 Sep 2017 19:46:36: 9000000 INFO @ Sun, 03 Sep 2017 19:46:39: 10000000 INFO @ Sun, 03 Sep 2017 19:46:41: 10000000 INFO @ Sun, 03 Sep 2017 19:46:41: 10000000 INFO @ Sun, 03 Sep 2017 19:46:44: 11000000 INFO @ Sun, 03 Sep 2017 19:46:46: 11000000 INFO @ Sun, 03 Sep 2017 19:46:46: 11000000 INFO @ Sun, 03 Sep 2017 19:46:49: 12000000 INFO @ Sun, 03 Sep 2017 19:46:51: 12000000 INFO @ Sun, 03 Sep 2017 19:46:51: 12000000 INFO @ Sun, 03 Sep 2017 19:46:54: 13000000 INFO @ Sun, 03 Sep 2017 19:46:55: 13000000 INFO @ Sun, 03 Sep 2017 19:46:56: 13000000 INFO @ Sun, 03 Sep 2017 19:46:59: 14000000 INFO @ Sun, 03 Sep 2017 19:47:00: 14000000 INFO @ Sun, 03 Sep 2017 19:47:00: 14000000 INFO @ Sun, 03 Sep 2017 19:47:04: 15000000 INFO @ Sun, 03 Sep 2017 19:47:05: 15000000 INFO @ Sun, 03 Sep 2017 19:47:05: 15000000 INFO @ Sun, 03 Sep 2017 19:47:08: 16000000 INFO @ Sun, 03 Sep 2017 19:47:10: 16000000 INFO @ Sun, 03 Sep 2017 19:47:10: 16000000 INFO @ Sun, 03 Sep 2017 19:47:13: 17000000 INFO @ Sun, 03 Sep 2017 19:47:15: 17000000 INFO @ Sun, 03 Sep 2017 19:47:15: 17000000 INFO @ Sun, 03 Sep 2017 19:47:18: 18000000 INFO @ Sun, 03 Sep 2017 19:47:20: 18000000 INFO @ Sun, 03 Sep 2017 19:47:20: 18000000 INFO @ Sun, 03 Sep 2017 19:47:22: 19000000 INFO @ Sun, 03 Sep 2017 19:47:25: 19000000 INFO @ Sun, 03 Sep 2017 19:47:25: 19000000 INFO @ Sun, 03 Sep 2017 19:47:27: 20000000 INFO @ Sun, 03 Sep 2017 19:47:27: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:47:27: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:47:27: #1 total tags in treatment: 8898856 INFO @ Sun, 03 Sep 2017 19:47:27: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:47:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:47:27: #1 tags after filtering in treatment: 4403058 INFO @ Sun, 03 Sep 2017 19:47:27: #1 Redundant rate of treatment: 0.51 INFO @ Sun, 03 Sep 2017 19:47:27: #1 finished! INFO @ Sun, 03 Sep 2017 19:47:27: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:47:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:47:27: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:47:27: 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 @ Sun, 03 Sep 2017 19:47:27: Process for pairing-model is terminated! cat: SRX2675893.10_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675893.10_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 `SRX2675893.10_*.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 `SRX2675893.10_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 @ Sun, 03 Sep 2017 19:47:29: 20000000 INFO @ Sun, 03 Sep 2017 19:47:29: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:47:29: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:47:29: #1 total tags in treatment: 8898856 INFO @ Sun, 03 Sep 2017 19:47:29: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:47:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:47:30: #1 tags after filtering in treatment: 4403058 INFO @ Sun, 03 Sep 2017 19:47:30: #1 Redundant rate of treatment: 0.51 INFO @ Sun, 03 Sep 2017 19:47:30: #1 finished! INFO @ Sun, 03 Sep 2017 19:47:30: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:47:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:47:30: 20000000 INFO @ Sun, 03 Sep 2017 19:47:30: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:47:30: 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 @ Sun, 03 Sep 2017 19:47:30: Process for pairing-model is terminated! cat: SRX2675893.05_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 `SRX2675893.05_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 `SRX2675893.05_*.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 `SRX2675893.05_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 @ Sun, 03 Sep 2017 19:47:30: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:47:30: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:47:30: #1 total tags in treatment: 8898856 INFO @ Sun, 03 Sep 2017 19:47:30: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:47:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:47:30: #1 tags after filtering in treatment: 4403058 INFO @ Sun, 03 Sep 2017 19:47:30: #1 Redundant rate of treatment: 0.51 INFO @ Sun, 03 Sep 2017 19:47:30: #1 finished! INFO @ Sun, 03 Sep 2017 19:47:30: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:47:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:47:31: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:47:31: 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 @ Sun, 03 Sep 2017 19:47:31: Process for pairing-model is terminated! cat: SRX2675893.20_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 `SRX2675893.20_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 `SRX2675893.20_*.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 `SRX2675893.20_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。