Job ID = 9732059 sra ファイルのダウンロード中... Completed: 277236K bytes transferred in 8 seconds (258713K 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 12430707 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675859/SRR5380636.sra Written 12430707 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: 00:05:59 12430707 reads; of these: 12430707 (100.00%) were paired; of these: 3840388 (30.89%) aligned concordantly 0 times 7561269 (60.83%) aligned concordantly exactly 1 time 1029050 (8.28%) aligned concordantly >1 times ---- 3840388 pairs aligned concordantly 0 times; of these: 583323 (15.19%) aligned discordantly 1 time ---- 3257065 pairs aligned 0 times concordantly or discordantly; of these: 6514130 mates make up the pairs; of these: 5996519 (92.05%) aligned 0 times 315891 (4.85%) aligned exactly 1 time 201720 (3.10%) aligned >1 times 75.88% overall alignment rate Time searching: 00:05:59 Overall time: 00:05:59 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] 1402963 / 9120246 = 0.1538 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 19:28:20: # Command line: callpeak -t SRX2675859.bam -f BAM -g 12100000 -n SRX2675859.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675859.10 # format = BAM # ChIP-seq file = ['SRX2675859.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 19:28:20: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:28:20: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:28:20: # Command line: callpeak -t SRX2675859.bam -f BAM -g 12100000 -n SRX2675859.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675859.05 # format = BAM # ChIP-seq file = ['SRX2675859.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 19:28:20: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:28:20: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:28:20: # Command line: callpeak -t SRX2675859.bam -f BAM -g 12100000 -n SRX2675859.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675859.20 # format = BAM # ChIP-seq file = ['SRX2675859.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 19:28:20: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:28:20: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:28:25: 1000000 INFO @ Sun, 03 Sep 2017 19:28:25: 1000000 INFO @ Sun, 03 Sep 2017 19:28:25: 1000000 INFO @ Sun, 03 Sep 2017 19:28:29: 2000000 INFO @ Sun, 03 Sep 2017 19:28:30: 2000000 INFO @ Sun, 03 Sep 2017 19:28:30: 2000000 INFO @ Sun, 03 Sep 2017 19:28:34: 3000000 INFO @ Sun, 03 Sep 2017 19:28:35: 3000000 INFO @ Sun, 03 Sep 2017 19:28:35: 3000000 INFO @ Sun, 03 Sep 2017 19:28:39: 4000000 INFO @ Sun, 03 Sep 2017 19:28:40: 4000000 INFO @ Sun, 03 Sep 2017 19:28:40: 4000000 INFO @ Sun, 03 Sep 2017 19:28:44: 5000000 INFO @ Sun, 03 Sep 2017 19:28:45: 5000000 INFO @ Sun, 03 Sep 2017 19:28:45: 5000000 INFO @ Sun, 03 Sep 2017 19:28:49: 6000000 INFO @ Sun, 03 Sep 2017 19:28:50: 6000000 INFO @ Sun, 03 Sep 2017 19:28:51: 6000000 INFO @ Sun, 03 Sep 2017 19:28:54: 7000000 INFO @ Sun, 03 Sep 2017 19:28:55: 7000000 INFO @ Sun, 03 Sep 2017 19:28:56: 7000000 INFO @ Sun, 03 Sep 2017 19:28:59: 8000000 INFO @ Sun, 03 Sep 2017 19:29:01: 8000000 INFO @ Sun, 03 Sep 2017 19:29:01: 8000000 INFO @ Sun, 03 Sep 2017 19:29:04: 9000000 INFO @ Sun, 03 Sep 2017 19:29:06: 9000000 INFO @ Sun, 03 Sep 2017 19:29:07: 9000000 INFO @ Sun, 03 Sep 2017 19:29:10: 10000000 INFO @ Sun, 03 Sep 2017 19:29:11: 10000000 INFO @ Sun, 03 Sep 2017 19:29:12: 10000000 INFO @ Sun, 03 Sep 2017 19:29:15: 11000000 INFO @ Sun, 03 Sep 2017 19:29:16: 11000000 INFO @ Sun, 03 Sep 2017 19:29:17: 11000000 INFO @ Sun, 03 Sep 2017 19:29:19: 12000000 INFO @ Sun, 03 Sep 2017 19:29:21: 12000000 INFO @ Sun, 03 Sep 2017 19:29:23: 12000000 INFO @ Sun, 03 Sep 2017 19:29:24: 13000000 INFO @ Sun, 03 Sep 2017 19:29:26: 13000000 INFO @ Sun, 03 Sep 2017 19:29:28: 13000000 INFO @ Sun, 03 Sep 2017 19:29:29: 14000000 INFO @ Sun, 03 Sep 2017 19:29:32: 14000000 INFO @ Sun, 03 Sep 2017 19:29:33: 14000000 INFO @ Sun, 03 Sep 2017 19:29:34: 15000000 INFO @ Sun, 03 Sep 2017 19:29:37: 15000000 INFO @ Sun, 03 Sep 2017 19:29:38: 15000000 INFO @ Sun, 03 Sep 2017 19:29:39: 16000000 INFO @ Sun, 03 Sep 2017 19:29:39: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:29:39: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:29:39: #1 total tags in treatment: 7204845 INFO @ Sun, 03 Sep 2017 19:29:39: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:29:39: #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 19:29:39: #1 tags after filtering in treatment: 3558969 INFO @ Sun, 03 Sep 2017 19:29:39: #1 Redundant rate of treatment: 0.51 INFO @ Sun, 03 Sep 2017 19:29:39: #1 finished! INFO @ Sun, 03 Sep 2017 19:29:39: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:29:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:29:40: #2 number of paired peaks: 21 WARNING @ Sun, 03 Sep 2017 19:29:40: Too few paired peaks (21) 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 19:29:40: Process for pairing-model is terminated! cat: SRX2675859.10_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): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675859.10_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 `SRX2675859.10_*.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 `SRX2675859.10_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 19:29:42: 16000000 INFO @ Sun, 03 Sep 2017 19:29:42: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:29:42: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:29:42: #1 total tags in treatment: 7204845 INFO @ Sun, 03 Sep 2017 19:29:42: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:29:42: #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 19:29:42: #1 tags after filtering in treatment: 3558969 INFO @ Sun, 03 Sep 2017 19:29:42: #1 Redundant rate of treatment: 0.51 INFO @ Sun, 03 Sep 2017 19:29:42: #1 finished! INFO @ Sun, 03 Sep 2017 19:29:42: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:29:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:29:43: #2 number of paired peaks: 21 WARNING @ Sun, 03 Sep 2017 19:29:43: Too few paired peaks (21) 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 19:29:43: Process for pairing-model is terminated! cat: SRX2675859.05_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): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675859.05_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 `SRX2675859.05_*.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 `SRX2675859.05_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 19:29:43: 16000000 INFO @ Sun, 03 Sep 2017 19:29:44: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:29:44: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:29:44: #1 total tags in treatment: 7204845 INFO @ Sun, 03 Sep 2017 19:29:44: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:29:44: #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 19:29:44: #1 tags after filtering in treatment: 3558969 INFO @ Sun, 03 Sep 2017 19:29:44: #1 Redundant rate of treatment: 0.51 INFO @ Sun, 03 Sep 2017 19:29:44: #1 finished! INFO @ Sun, 03 Sep 2017 19:29:44: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:29:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:29:44: #2 number of paired peaks: 21 WARNING @ Sun, 03 Sep 2017 19:29:44: Too few paired peaks (21) 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 19:29:44: Process for pairing-model is terminated! cat: SRX2675859.20_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675859.20_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 `SRX2675859.20_*.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 `SRX2675859.20_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。