Job ID = 10488213 sra ファイルのダウンロード中... Completed: 697843K bytes transferred in 72 seconds (78486K 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 13435138 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3188114/SRR6039986.sra Written 13435138 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: 00:09:41 13435138 reads; of these: 13435138 (100.00%) were paired; of these: 2313934 (17.22%) aligned concordantly 0 times 9648895 (71.82%) aligned concordantly exactly 1 time 1472309 (10.96%) aligned concordantly >1 times ---- 2313934 pairs aligned concordantly 0 times; of these: 413630 (17.88%) aligned discordantly 1 time ---- 1900304 pairs aligned 0 times concordantly or discordantly; of these: 3800608 mates make up the pairs; of these: 3149949 (82.88%) aligned 0 times 359489 (9.46%) aligned exactly 1 time 291170 (7.66%) aligned >1 times 88.28% overall alignment rate Time searching: 00:09:41 Overall time: 00:09:41 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 12 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] 364787 / 11528340 = 0.0316 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, 18 Mar 2018 12:36:23: # Command line: callpeak -t SRX3188114.bam -f BAM -g 12100000 -n SRX3188114.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3188114.20 # format = BAM # ChIP-seq file = ['SRX3188114.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, 18 Mar 2018 12:36:23: #1 read tag files... INFO @ Sun, 18 Mar 2018 12:36:23: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 12:36:23: # Command line: callpeak -t SRX3188114.bam -f BAM -g 12100000 -n SRX3188114.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3188114.10 # format = BAM # ChIP-seq file = ['SRX3188114.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, 18 Mar 2018 12:36:23: #1 read tag files... INFO @ Sun, 18 Mar 2018 12:36:23: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 12:36:23: # Command line: callpeak -t SRX3188114.bam -f BAM -g 12100000 -n SRX3188114.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3188114.05 # format = BAM # ChIP-seq file = ['SRX3188114.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, 18 Mar 2018 12:36:23: #1 read tag files... INFO @ Sun, 18 Mar 2018 12:36:23: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 12:36:29: 1000000 INFO @ Sun, 18 Mar 2018 12:36:30: 1000000 INFO @ Sun, 18 Mar 2018 12:36:30: 1000000 INFO @ Sun, 18 Mar 2018 12:36:36: 2000000 INFO @ Sun, 18 Mar 2018 12:36:36: 2000000 INFO @ Sun, 18 Mar 2018 12:36:36: 2000000 INFO @ Sun, 18 Mar 2018 12:36:42: 3000000 INFO @ Sun, 18 Mar 2018 12:36:44: 3000000 INFO @ Sun, 18 Mar 2018 12:36:44: 3000000 INFO @ Sun, 18 Mar 2018 12:36:49: 4000000 INFO @ Sun, 18 Mar 2018 12:36:52: 4000000 INFO @ Sun, 18 Mar 2018 12:36:52: 4000000 INFO @ Sun, 18 Mar 2018 12:36:55: 5000000 INFO @ Sun, 18 Mar 2018 12:36:59: 5000000 INFO @ Sun, 18 Mar 2018 12:36:59: 5000000 INFO @ Sun, 18 Mar 2018 12:37:02: 6000000 INFO @ Sun, 18 Mar 2018 12:37:06: 6000000 INFO @ Sun, 18 Mar 2018 12:37:06: 6000000 INFO @ Sun, 18 Mar 2018 12:37:08: 7000000 INFO @ Sun, 18 Mar 2018 12:37:12: 7000000 INFO @ Sun, 18 Mar 2018 12:37:12: 7000000 INFO @ Sun, 18 Mar 2018 12:37:15: 8000000 INFO @ Sun, 18 Mar 2018 12:37:19: 8000000 INFO @ Sun, 18 Mar 2018 12:37:19: 8000000 INFO @ Sun, 18 Mar 2018 12:37:21: 9000000 INFO @ Sun, 18 Mar 2018 12:37:26: 9000000 INFO @ Sun, 18 Mar 2018 12:37:26: 9000000 INFO @ Sun, 18 Mar 2018 12:37:28: 10000000 INFO @ Sun, 18 Mar 2018 12:37:33: 10000000 INFO @ Sun, 18 Mar 2018 12:37:33: 10000000 INFO @ Sun, 18 Mar 2018 12:37:35: 11000000 INFO @ Sun, 18 Mar 2018 12:37:40: 11000000 INFO @ Sun, 18 Mar 2018 12:37:40: 11000000 INFO @ Sun, 18 Mar 2018 12:37:41: 12000000 INFO @ Sun, 18 Mar 2018 12:37:47: 12000000 INFO @ Sun, 18 Mar 2018 12:37:47: 12000000 INFO @ Sun, 18 Mar 2018 12:37:48: 13000000 INFO @ Sun, 18 Mar 2018 12:37:53: 13000000 INFO @ Sun, 18 Mar 2018 12:37:53: 13000000 INFO @ Sun, 18 Mar 2018 12:37:54: 14000000 INFO @ Sun, 18 Mar 2018 12:38:00: 14000000 INFO @ Sun, 18 Mar 2018 12:38:00: 14000000 INFO @ Sun, 18 Mar 2018 12:38:01: 15000000 INFO @ Sun, 18 Mar 2018 12:38:07: 16000000 INFO @ Sun, 18 Mar 2018 12:38:08: 15000000 INFO @ Sun, 18 Mar 2018 12:38:08: 15000000 INFO @ Sun, 18 Mar 2018 12:38:14: 17000000 INFO @ Sun, 18 Mar 2018 12:38:14: 16000000 INFO @ Sun, 18 Mar 2018 12:38:14: 16000000 INFO @ Sun, 18 Mar 2018 12:38:21: 18000000 INFO @ Sun, 18 Mar 2018 12:38:21: 17000000 INFO @ Sun, 18 Mar 2018 12:38:21: 17000000 INFO @ Sun, 18 Mar 2018 12:38:27: 19000000 INFO @ Sun, 18 Mar 2018 12:38:28: 18000000 INFO @ Sun, 18 Mar 2018 12:38:28: 18000000 INFO @ Sun, 18 Mar 2018 12:38:34: 20000000 INFO @ Sun, 18 Mar 2018 12:38:34: 19000000 INFO @ Sun, 18 Mar 2018 12:38:34: 19000000 INFO @ Sun, 18 Mar 2018 12:38:40: 21000000 INFO @ Sun, 18 Mar 2018 12:38:41: 20000000 INFO @ Sun, 18 Mar 2018 12:38:41: 20000000 INFO @ Sun, 18 Mar 2018 12:38:47: 22000000 INFO @ Sun, 18 Mar 2018 12:38:49: 21000000 INFO @ Sun, 18 Mar 2018 12:38:49: 21000000 INFO @ Sun, 18 Mar 2018 12:38:53: #1 tag size is determined as 51 bps INFO @ Sun, 18 Mar 2018 12:38:53: #1 tag size = 51 INFO @ Sun, 18 Mar 2018 12:38:53: #1 total tags in treatment: 10763439 INFO @ Sun, 18 Mar 2018 12:38:53: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 12:38:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 12:38:54: #1 tags after filtering in treatment: 7832185 INFO @ Sun, 18 Mar 2018 12:38:54: #1 Redundant rate of treatment: 0.27 INFO @ Sun, 18 Mar 2018 12:38:54: #1 finished! INFO @ Sun, 18 Mar 2018 12:38:54: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 12:38:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 12:38:54: #2 number of paired peaks: 0 WARNING @ Sun, 18 Mar 2018 12:38:54: 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, 18 Mar 2018 12:38:54: Process for pairing-model is terminated! cat: SRX3188114.05_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 `SRX3188114.05_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 `SRX3188114.05_*.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 `SRX3188114.05_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, 18 Mar 2018 12:38:55: 22000000 INFO @ Sun, 18 Mar 2018 12:38:55: 22000000 INFO @ Sun, 18 Mar 2018 12:39:02: #1 tag size is determined as 51 bps INFO @ Sun, 18 Mar 2018 12:39:02: #1 tag size = 51 INFO @ Sun, 18 Mar 2018 12:39:02: #1 total tags in treatment: 10763439 INFO @ Sun, 18 Mar 2018 12:39:02: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 12:39:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 12:39:02: #1 tag size is determined as 51 bps INFO @ Sun, 18 Mar 2018 12:39:02: #1 tag size = 51 INFO @ Sun, 18 Mar 2018 12:39:02: #1 total tags in treatment: 10763439 INFO @ Sun, 18 Mar 2018 12:39:02: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 12:39:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 12:39:02: #1 tags after filtering in treatment: 7832185 INFO @ Sun, 18 Mar 2018 12:39:02: #1 Redundant rate of treatment: 0.27 INFO @ Sun, 18 Mar 2018 12:39:02: #1 finished! INFO @ Sun, 18 Mar 2018 12:39:02: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 12:39:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 12:39:02: #1 tags after filtering in treatment: 7832185 INFO @ Sun, 18 Mar 2018 12:39:02: #1 Redundant rate of treatment: 0.27 INFO @ Sun, 18 Mar 2018 12:39:02: #1 finished! INFO @ Sun, 18 Mar 2018 12:39:02: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 12:39:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 12:39:02: #2 number of paired peaks: 0 WARNING @ Sun, 18 Mar 2018 12:39:02: 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, 18 Mar 2018 12:39:02: Process for pairing-model is terminated! INFO @ Sun, 18 Mar 2018 12:39:02: #2 number of paired peaks: 0 WARNING @ Sun, 18 Mar 2018 12:39:02: 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, 18 Mar 2018 12:39:02: Process for pairing-model is terminated! cat: SRX3188114.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX3188114.20_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 `SRX3188114.10_model.r': そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms)rm: : 1 millis cannot remove `SRX3188114.10_*.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 `SRX3188114.10_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 needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3188114.20_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 `SRX3188114.20_*.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 `SRX3188114.20_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。