Job ID = 10536515 sra ファイルのダウンロード中... Completed: 1173154K bytes transferred in 32 seconds (292463K 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 32832319 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671208/SRR6696960.sra Written 32832319 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: 00:24:20 32832319 reads; of these: 32832319 (100.00%) were paired; of these: 3705852 (11.29%) aligned concordantly 0 times 24097137 (73.39%) aligned concordantly exactly 1 time 5029330 (15.32%) aligned concordantly >1 times ---- 3705852 pairs aligned concordantly 0 times; of these: 138512 (3.74%) aligned discordantly 1 time ---- 3567340 pairs aligned 0 times concordantly or discordantly; of these: 7134680 mates make up the pairs; of these: 6904248 (96.77%) aligned 0 times 114672 (1.61%) aligned exactly 1 time 115760 (1.62%) aligned >1 times 89.49% overall alignment rate Time searching: 00:24:20 Overall time: 00:24:20 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] 10486296 / 29212643 = 0.3590 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 10:37:30: # Command line: callpeak -t SRX3671208.bam -f BAM -g 12100000 -n SRX3671208.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671208.10 # format = BAM # ChIP-seq file = ['SRX3671208.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 10:37:30: # Command line: callpeak -t SRX3671208.bam -f BAM -g 12100000 -n SRX3671208.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671208.05 # format = BAM # ChIP-seq file = ['SRX3671208.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 10:37:30: # Command line: callpeak -t SRX3671208.bam -f BAM -g 12100000 -n SRX3671208.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671208.20 # format = BAM # ChIP-seq file = ['SRX3671208.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 10:37:30: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:37:30: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:37:30: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:37:30: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:37:30: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:37:30: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:37:36: 1000000 INFO @ Thu, 05 Apr 2018 10:37:36: 1000000 INFO @ Thu, 05 Apr 2018 10:37:36: 1000000 INFO @ Thu, 05 Apr 2018 10:37:41: 2000000 INFO @ Thu, 05 Apr 2018 10:37:42: 2000000 INFO @ Thu, 05 Apr 2018 10:37:42: 2000000 INFO @ Thu, 05 Apr 2018 10:37:47: 3000000 INFO @ Thu, 05 Apr 2018 10:37:48: 3000000 INFO @ Thu, 05 Apr 2018 10:37:48: 3000000 INFO @ Thu, 05 Apr 2018 10:37:52: 4000000 INFO @ Thu, 05 Apr 2018 10:37:54: 4000000 INFO @ Thu, 05 Apr 2018 10:37:54: 4000000 INFO @ Thu, 05 Apr 2018 10:37:58: 5000000 INFO @ Thu, 05 Apr 2018 10:38:00: 5000000 INFO @ Thu, 05 Apr 2018 10:38:00: 5000000 INFO @ Thu, 05 Apr 2018 10:38:03: 6000000 INFO @ Thu, 05 Apr 2018 10:38:06: 6000000 INFO @ Thu, 05 Apr 2018 10:38:07: 6000000 INFO @ Thu, 05 Apr 2018 10:38:09: 7000000 INFO @ Thu, 05 Apr 2018 10:38:12: 7000000 INFO @ Thu, 05 Apr 2018 10:38:12: 7000000 INFO @ Thu, 05 Apr 2018 10:38:14: 8000000 INFO @ Thu, 05 Apr 2018 10:38:18: 8000000 INFO @ Thu, 05 Apr 2018 10:38:19: 8000000 INFO @ Thu, 05 Apr 2018 10:38:20: 9000000 INFO @ Thu, 05 Apr 2018 10:38:25: 9000000 INFO @ Thu, 05 Apr 2018 10:38:25: 9000000 INFO @ Thu, 05 Apr 2018 10:38:25: 10000000 INFO @ Thu, 05 Apr 2018 10:38:31: 10000000 INFO @ Thu, 05 Apr 2018 10:38:31: 11000000 INFO @ Thu, 05 Apr 2018 10:38:31: 10000000 INFO @ Thu, 05 Apr 2018 10:38:36: 12000000 INFO @ Thu, 05 Apr 2018 10:38:37: 11000000 INFO @ Thu, 05 Apr 2018 10:38:37: 11000000 INFO @ Thu, 05 Apr 2018 10:38:42: 13000000 INFO @ Thu, 05 Apr 2018 10:38:43: 12000000 INFO @ Thu, 05 Apr 2018 10:38:43: 12000000 INFO @ Thu, 05 Apr 2018 10:38:47: 14000000 INFO @ Thu, 05 Apr 2018 10:38:49: 13000000 INFO @ Thu, 05 Apr 2018 10:38:50: 13000000 INFO @ Thu, 05 Apr 2018 10:38:53: 15000000 INFO @ Thu, 05 Apr 2018 10:38:55: 14000000 INFO @ Thu, 05 Apr 2018 10:38:56: 14000000 INFO @ Thu, 05 Apr 2018 10:38:58: 16000000 INFO @ Thu, 05 Apr 2018 10:39:02: 15000000 INFO @ Thu, 05 Apr 2018 10:39:02: 15000000 INFO @ Thu, 05 Apr 2018 10:39:04: 17000000 INFO @ Thu, 05 Apr 2018 10:39:08: 16000000 INFO @ Thu, 05 Apr 2018 10:39:08: 16000000 INFO @ Thu, 05 Apr 2018 10:39:09: 18000000 INFO @ Thu, 05 Apr 2018 10:39:14: 17000000 INFO @ Thu, 05 Apr 2018 10:39:14: 17000000 INFO @ Thu, 05 Apr 2018 10:39:15: 19000000 INFO @ Thu, 05 Apr 2018 10:39:20: 18000000 INFO @ Thu, 05 Apr 2018 10:39:20: 20000000 INFO @ Thu, 05 Apr 2018 10:39:21: 18000000 INFO @ Thu, 05 Apr 2018 10:39:26: 21000000 INFO @ Thu, 05 Apr 2018 10:39:26: 19000000 INFO @ Thu, 05 Apr 2018 10:39:27: 19000000 INFO @ Thu, 05 Apr 2018 10:39:31: 22000000 INFO @ Thu, 05 Apr 2018 10:39:32: 20000000 INFO @ Thu, 05 Apr 2018 10:39:33: 20000000 INFO @ Thu, 05 Apr 2018 10:39:37: 23000000 INFO @ Thu, 05 Apr 2018 10:39:39: 21000000 INFO @ Thu, 05 Apr 2018 10:39:40: 21000000 INFO @ Thu, 05 Apr 2018 10:39:42: 24000000 INFO @ Thu, 05 Apr 2018 10:39:45: 22000000 INFO @ Thu, 05 Apr 2018 10:39:46: 22000000 INFO @ Thu, 05 Apr 2018 10:39:48: 25000000 INFO @ Thu, 05 Apr 2018 10:39:51: 23000000 INFO @ Thu, 05 Apr 2018 10:39:52: 23000000 INFO @ Thu, 05 Apr 2018 10:39:53: 26000000 INFO @ Thu, 05 Apr 2018 10:39:57: 24000000 INFO @ Thu, 05 Apr 2018 10:39:58: 24000000 INFO @ Thu, 05 Apr 2018 10:39:59: 27000000 INFO @ Thu, 05 Apr 2018 10:40:03: 25000000 INFO @ Thu, 05 Apr 2018 10:40:04: 28000000 INFO @ Thu, 05 Apr 2018 10:40:05: 25000000 INFO @ Thu, 05 Apr 2018 10:40:10: 29000000 INFO @ Thu, 05 Apr 2018 10:40:10: 26000000 INFO @ Thu, 05 Apr 2018 10:40:11: 26000000 INFO @ Thu, 05 Apr 2018 10:40:15: 30000000 INFO @ Thu, 05 Apr 2018 10:40:17: 27000000 INFO @ Thu, 05 Apr 2018 10:40:18: 27000000 INFO @ Thu, 05 Apr 2018 10:40:20: 31000000 INFO @ Thu, 05 Apr 2018 10:40:23: 28000000 INFO @ Thu, 05 Apr 2018 10:40:25: 28000000 INFO @ Thu, 05 Apr 2018 10:40:26: 32000000 INFO @ Thu, 05 Apr 2018 10:40:30: 29000000 INFO @ Thu, 05 Apr 2018 10:40:31: 33000000 INFO @ Thu, 05 Apr 2018 10:40:32: 29000000 INFO @ Thu, 05 Apr 2018 10:40:37: 30000000 INFO @ Thu, 05 Apr 2018 10:40:37: 34000000 INFO @ Thu, 05 Apr 2018 10:40:38: 30000000 INFO @ Thu, 05 Apr 2018 10:40:42: 35000000 INFO @ Thu, 05 Apr 2018 10:40:43: 31000000 INFO @ Thu, 05 Apr 2018 10:40:45: 31000000 INFO @ Thu, 05 Apr 2018 10:40:48: 36000000 INFO @ Thu, 05 Apr 2018 10:40:50: 32000000 INFO @ Thu, 05 Apr 2018 10:40:52: 32000000 INFO @ Thu, 05 Apr 2018 10:40:53: 37000000 INFO @ Thu, 05 Apr 2018 10:40:57: 33000000 INFO @ Thu, 05 Apr 2018 10:40:58: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:40:58: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:40:58: #1 total tags in treatment: 18675934 INFO @ Thu, 05 Apr 2018 10:40:58: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:40:58: #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 10:40:58: #1 tags after filtering in treatment: 6919097 INFO @ Thu, 05 Apr 2018 10:40:58: #1 Redundant rate of treatment: 0.63 INFO @ Thu, 05 Apr 2018 10:40:58: #1 finished! INFO @ Thu, 05 Apr 2018 10:40:58: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:40:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:40:58: 33000000 INFO @ Thu, 05 Apr 2018 10:40:59: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:40:59: 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 @ Thu, 05 Apr 2018 10:40:59: Process for pairing-model is terminated! cat: SRX3671208.10_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 `SRX3671208.10_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 `SRX3671208.10_*.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 `SRX3671208.10_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 10:41:03: 34000000 INFO @ Thu, 05 Apr 2018 10:41:05: 34000000 INFO @ Thu, 05 Apr 2018 10:41:10: 35000000 INFO @ Thu, 05 Apr 2018 10:41:12: 35000000 INFO @ Thu, 05 Apr 2018 10:41:17: 36000000 INFO @ Thu, 05 Apr 2018 10:41:19: 36000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Apr 2018 10:41:23: 37000000 INFO @ Thu, 05 Apr 2018 10:41:25: 37000000 INFO @ Thu, 05 Apr 2018 10:41:29: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:41:29: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:41:29: #1 total tags in treatment: 18675934 INFO @ Thu, 05 Apr 2018 10:41:29: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:41:29: #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 10:41:29: #1 tags after filtering in treatment: 6919097 INFO @ Thu, 05 Apr 2018 10:41:29: #1 Redundant rate of treatment: 0.63 INFO @ Thu, 05 Apr 2018 10:41:29: #1 finished! INFO @ Thu, 05 Apr 2018 10:41:29: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:41:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:41:29: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:41:29: 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 @ Thu, 05 Apr 2018 10:41:29: Process for pairing-model is terminated! cat: SRX3671208.20_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 `SRX3671208.20_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 `SRX3671208.20_*.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 `SRX3671208.20_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 10:41:30: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:41:30: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:41:30: #1 total tags in treatment: 18675934 INFO @ Thu, 05 Apr 2018 10:41:30: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:41:30: #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 10:41:31: #1 tags after filtering in treatment: 6919097 INFO @ Thu, 05 Apr 2018 10:41:31: #1 Redundant rate of treatment: 0.63 INFO @ Thu, 05 Apr 2018 10:41:31: #1 finished! INFO @ Thu, 05 Apr 2018 10:41:31: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:41:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:41:31: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:41:31: 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 @ Thu, 05 Apr 2018 10:41:31: Process for pairing-model is terminated! cat: SRX3671208.05_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 `SRX3671208.05_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 `SRX3671208.05_*.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 `SRX3671208.05_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 BigWig に変換しました。