Job ID = 10536524 sra ファイルのダウンロード中... Completed: 1371030K bytes transferred in 37 seconds (297710K 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 36895671 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671216/SRR6696968.sra Written 36895671 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: 00:25:05 36895671 reads; of these: 36895671 (100.00%) were paired; of these: 8947253 (24.25%) aligned concordantly 0 times 24661997 (66.84%) aligned concordantly exactly 1 time 3286421 (8.91%) aligned concordantly >1 times ---- 8947253 pairs aligned concordantly 0 times; of these: 75156 (0.84%) aligned discordantly 1 time ---- 8872097 pairs aligned 0 times concordantly or discordantly; of these: 17744194 mates make up the pairs; of these: 17476957 (98.49%) aligned 0 times 205472 (1.16%) aligned exactly 1 time 61765 (0.35%) aligned >1 times 76.32% overall alignment rate Time searching: 00:25:05 Overall time: 00:25:05 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] 11770568 / 27987197 = 0.4206 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 10:40:31: # Command line: callpeak -t SRX3671216.bam -f BAM -g 12100000 -n SRX3671216.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671216.10 # format = BAM # ChIP-seq file = ['SRX3671216.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 10:40:31: # Command line: callpeak -t SRX3671216.bam -f BAM -g 12100000 -n SRX3671216.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671216.20 # format = BAM # ChIP-seq file = ['SRX3671216.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 10:40:31: # Command line: callpeak -t SRX3671216.bam -f BAM -g 12100000 -n SRX3671216.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671216.05 # format = BAM # ChIP-seq file = ['SRX3671216.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 10:40:31: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:40:31: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:40:31: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:40:31: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:40:31: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:40:31: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:40:38: 1000000 INFO @ Thu, 05 Apr 2018 10:40:38: 1000000 INFO @ Thu, 05 Apr 2018 10:40:38: 1000000 INFO @ Thu, 05 Apr 2018 10:40:45: 2000000 INFO @ Thu, 05 Apr 2018 10:40:45: 2000000 INFO @ Thu, 05 Apr 2018 10:40:45: 2000000 INFO @ Thu, 05 Apr 2018 10:40:51: 3000000 INFO @ Thu, 05 Apr 2018 10:40:52: 3000000 INFO @ Thu, 05 Apr 2018 10:40:52: 3000000 INFO @ Thu, 05 Apr 2018 10:40:58: 4000000 INFO @ Thu, 05 Apr 2018 10:40:59: 4000000 INFO @ Thu, 05 Apr 2018 10:40:59: 4000000 INFO @ Thu, 05 Apr 2018 10:41:04: 5000000 INFO @ Thu, 05 Apr 2018 10:41:06: 5000000 INFO @ Thu, 05 Apr 2018 10:41:06: 5000000 INFO @ Thu, 05 Apr 2018 10:41:11: 6000000 INFO @ Thu, 05 Apr 2018 10:41:13: 6000000 INFO @ Thu, 05 Apr 2018 10:41:13: 6000000 INFO @ Thu, 05 Apr 2018 10:41:17: 7000000 INFO @ Thu, 05 Apr 2018 10:41:20: 7000000 INFO @ Thu, 05 Apr 2018 10:41:20: 7000000 INFO @ Thu, 05 Apr 2018 10:41:24: 8000000 INFO @ Thu, 05 Apr 2018 10:41:27: 8000000 INFO @ Thu, 05 Apr 2018 10:41:27: 8000000 INFO @ Thu, 05 Apr 2018 10:41:30: 9000000 INFO @ Thu, 05 Apr 2018 10:41:34: 9000000 INFO @ Thu, 05 Apr 2018 10:41:34: 9000000 INFO @ Thu, 05 Apr 2018 10:41:37: 10000000 INFO @ Thu, 05 Apr 2018 10:41:40: 10000000 INFO @ Thu, 05 Apr 2018 10:41:40: 10000000 INFO @ Thu, 05 Apr 2018 10:41:44: 11000000 INFO @ Thu, 05 Apr 2018 10:41:47: 11000000 INFO @ Thu, 05 Apr 2018 10:41:47: 11000000 INFO @ Thu, 05 Apr 2018 10:41:50: 12000000 INFO @ Thu, 05 Apr 2018 10:41:54: 12000000 INFO @ Thu, 05 Apr 2018 10:41:54: 12000000 INFO @ Thu, 05 Apr 2018 10:41:57: 13000000 INFO @ Thu, 05 Apr 2018 10:42:01: 13000000 INFO @ Thu, 05 Apr 2018 10:42:01: 13000000 INFO @ Thu, 05 Apr 2018 10:42:03: 14000000 INFO @ Thu, 05 Apr 2018 10:42:08: 14000000 INFO @ Thu, 05 Apr 2018 10:42:08: 14000000 INFO @ Thu, 05 Apr 2018 10:42:10: 15000000 INFO @ Thu, 05 Apr 2018 10:42:15: 15000000 INFO @ Thu, 05 Apr 2018 10:42:15: 15000000 INFO @ Thu, 05 Apr 2018 10:42:17: 16000000 INFO @ Thu, 05 Apr 2018 10:42:22: 16000000 INFO @ Thu, 05 Apr 2018 10:42:22: 16000000 INFO @ Thu, 05 Apr 2018 10:42:23: 17000000 INFO @ Thu, 05 Apr 2018 10:42:29: 17000000 INFO @ Thu, 05 Apr 2018 10:42:29: 17000000 INFO @ Thu, 05 Apr 2018 10:42:30: 18000000 INFO @ Thu, 05 Apr 2018 10:42:36: 18000000 INFO @ Thu, 05 Apr 2018 10:42:36: 18000000 INFO @ Thu, 05 Apr 2018 10:42:36: 19000000 INFO @ Thu, 05 Apr 2018 10:42:42: 19000000 INFO @ Thu, 05 Apr 2018 10:42:44: 20000000 INFO @ Thu, 05 Apr 2018 10:42:44: 19000000 INFO @ Thu, 05 Apr 2018 10:42:49: 20000000 INFO @ Thu, 05 Apr 2018 10:42:51: 21000000 INFO @ Thu, 05 Apr 2018 10:42:51: 20000000 INFO @ Thu, 05 Apr 2018 10:42:56: 21000000 INFO @ Thu, 05 Apr 2018 10:42:58: 22000000 INFO @ Thu, 05 Apr 2018 10:42:59: 21000000 INFO @ Thu, 05 Apr 2018 10:43:03: 22000000 INFO @ Thu, 05 Apr 2018 10:43:05: 23000000 INFO @ Thu, 05 Apr 2018 10:43:07: 22000000 INFO @ Thu, 05 Apr 2018 10:43:10: 23000000 INFO @ Thu, 05 Apr 2018 10:43:12: 24000000 INFO @ Thu, 05 Apr 2018 10:43:14: 23000000 INFO @ Thu, 05 Apr 2018 10:43:17: 24000000 INFO @ Thu, 05 Apr 2018 10:43:19: 25000000 INFO @ Thu, 05 Apr 2018 10:43:22: 24000000 INFO @ Thu, 05 Apr 2018 10:43:24: 25000000 INFO @ Thu, 05 Apr 2018 10:43:26: 26000000 INFO @ Thu, 05 Apr 2018 10:43:30: 25000000 INFO @ Thu, 05 Apr 2018 10:43:30: 26000000 INFO @ Thu, 05 Apr 2018 10:43:33: 27000000 INFO @ Thu, 05 Apr 2018 10:43:37: 27000000 INFO @ Thu, 05 Apr 2018 10:43:38: 26000000 INFO @ Thu, 05 Apr 2018 10:43:40: 28000000 INFO @ Thu, 05 Apr 2018 10:43:44: 28000000 INFO @ Thu, 05 Apr 2018 10:43:45: 27000000 INFO @ Thu, 05 Apr 2018 10:43:47: 29000000 INFO @ Thu, 05 Apr 2018 10:43:51: 29000000 INFO @ Thu, 05 Apr 2018 10:43:53: 28000000 INFO @ Thu, 05 Apr 2018 10:43:54: 30000000 INFO @ Thu, 05 Apr 2018 10:43:58: 30000000 INFO @ Thu, 05 Apr 2018 10:44:01: 29000000 INFO @ Thu, 05 Apr 2018 10:44:01: 31000000 INFO @ Thu, 05 Apr 2018 10:44:05: 31000000 INFO @ Thu, 05 Apr 2018 10:44:08: 32000000 INFO @ Thu, 05 Apr 2018 10:44:09: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Apr 2018 10:44:11: 32000000 INFO @ Thu, 05 Apr 2018 10:44:14: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:44:14: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:44:14: #1 total tags in treatment: 16191362 INFO @ Thu, 05 Apr 2018 10:44:14: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:44:14: #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 10:44:14: #1 tags after filtering in treatment: 6632052 INFO @ Thu, 05 Apr 2018 10:44:14: #1 Redundant rate of treatment: 0.59 INFO @ Thu, 05 Apr 2018 10:44:14: #1 finished! INFO @ Thu, 05 Apr 2018 10:44:14: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:44:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:44:15: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:44:15: 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 10:44:15: Process for pairing-model is terminated! cat: SRX3671216.20_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 `SRX3671216.20_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 `SRX3671216.20_*.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 `SRX3671216.20_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 10:44:16: 31000000 INFO @ Thu, 05 Apr 2018 10:44:17: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:44:17: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:44:17: #1 total tags in treatment: 16191362 INFO @ Thu, 05 Apr 2018 10:44:17: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:44:17: #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 10:44:17: #1 tags after filtering in treatment: 6632052 INFO @ Thu, 05 Apr 2018 10:44:17: #1 Redundant rate of treatment: 0.59 INFO @ Thu, 05 Apr 2018 10:44:17: #1 finished! INFO @ Thu, 05 Apr 2018 10:44:17: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:44:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:44:17: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:44:17: 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 10:44:17: Process for pairing-model is terminated! cat: SRX3671216.05_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3671216.05_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 `SRX3671216.05_*.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 `SRX3671216.05_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 @ Thu, 05 Apr 2018 10:44:22: 32000000 INFO @ Thu, 05 Apr 2018 10:44:27: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:44:27: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:44:27: #1 total tags in treatment: 16191362 INFO @ Thu, 05 Apr 2018 10:44:27: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:44:27: #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 10:44:28: #1 tags after filtering in treatment: 6632052 INFO @ Thu, 05 Apr 2018 10:44:28: #1 Redundant rate of treatment: 0.59 INFO @ Thu, 05 Apr 2018 10:44:28: #1 finished! INFO @ Thu, 05 Apr 2018 10:44:28: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:44:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:44:28: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:44:28: 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 10:44:28: Process for pairing-model is terminated! cat: SRX3671216.10_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 `SRX3671216.10_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 `SRX3671216.10_*.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 `SRX3671216.10_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 BigWig に変換しました。