Job ID = 9732044 sra ファイルのダウンロード中... Completed: 260635K bytes transferred in 10 seconds (201184K 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 11863838 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675848/SRR5380624.sra Written 11863838 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: 00:05:27 11863838 reads; of these: 11863838 (100.00%) were paired; of these: 2393480 (20.17%) aligned concordantly 0 times 8607277 (72.55%) aligned concordantly exactly 1 time 863081 (7.27%) aligned concordantly >1 times ---- 2393480 pairs aligned concordantly 0 times; of these: 626265 (26.17%) aligned discordantly 1 time ---- 1767215 pairs aligned 0 times concordantly or discordantly; of these: 3534430 mates make up the pairs; of these: 3027991 (85.67%) aligned 0 times 337755 (9.56%) aligned exactly 1 time 168684 (4.77%) aligned >1 times 87.24% overall alignment rate Time searching: 00:05:27 Overall time: 00:05:27 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] 1207951 / 9968170 = 0.1212 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 19:20:27: # Command line: callpeak -t SRX2675848.bam -f BAM -g 12100000 -n SRX2675848.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675848.10 # format = BAM # ChIP-seq file = ['SRX2675848.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 19:20:27: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:20:27: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:20:27: # Command line: callpeak -t SRX2675848.bam -f BAM -g 12100000 -n SRX2675848.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675848.20 # format = BAM # ChIP-seq file = ['SRX2675848.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 19:20:27: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:20:27: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:20:27: # Command line: callpeak -t SRX2675848.bam -f BAM -g 12100000 -n SRX2675848.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675848.05 # format = BAM # ChIP-seq file = ['SRX2675848.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 19:20:27: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:20:27: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:20:33: 1000000 INFO @ Sun, 03 Sep 2017 19:20:33: 1000000 INFO @ Sun, 03 Sep 2017 19:20:33: 1000000 INFO @ Sun, 03 Sep 2017 19:20:38: 2000000 INFO @ Sun, 03 Sep 2017 19:20:39: 2000000 INFO @ Sun, 03 Sep 2017 19:20:39: 2000000 INFO @ Sun, 03 Sep 2017 19:20:43: 3000000 INFO @ Sun, 03 Sep 2017 19:20:44: 3000000 INFO @ Sun, 03 Sep 2017 19:20:44: 3000000 INFO @ Sun, 03 Sep 2017 19:20:48: 4000000 INFO @ Sun, 03 Sep 2017 19:20:50: 4000000 INFO @ Sun, 03 Sep 2017 19:20:50: 4000000 INFO @ Sun, 03 Sep 2017 19:20:53: 5000000 INFO @ Sun, 03 Sep 2017 19:20:56: 5000000 INFO @ Sun, 03 Sep 2017 19:20:56: 5000000 INFO @ Sun, 03 Sep 2017 19:20:58: 6000000 INFO @ Sun, 03 Sep 2017 19:21:01: 6000000 INFO @ Sun, 03 Sep 2017 19:21:01: 6000000 INFO @ Sun, 03 Sep 2017 19:21:03: 7000000 INFO @ Sun, 03 Sep 2017 19:21:07: 7000000 INFO @ Sun, 03 Sep 2017 19:21:07: 7000000 INFO @ Sun, 03 Sep 2017 19:21:09: 8000000 INFO @ Sun, 03 Sep 2017 19:21:13: 8000000 INFO @ Sun, 03 Sep 2017 19:21:13: 8000000 INFO @ Sun, 03 Sep 2017 19:21:14: 9000000 INFO @ Sun, 03 Sep 2017 19:21:18: 9000000 INFO @ Sun, 03 Sep 2017 19:21:18: 9000000 INFO @ Sun, 03 Sep 2017 19:21:19: 10000000 INFO @ Sun, 03 Sep 2017 19:21:24: 10000000 INFO @ Sun, 03 Sep 2017 19:21:24: 10000000 INFO @ Sun, 03 Sep 2017 19:21:24: 11000000 INFO @ Sun, 03 Sep 2017 19:21:29: 12000000 INFO @ Sun, 03 Sep 2017 19:21:30: 11000000 INFO @ Sun, 03 Sep 2017 19:21:30: 11000000 INFO @ Sun, 03 Sep 2017 19:21:34: 13000000 INFO @ Sun, 03 Sep 2017 19:21:35: 12000000 INFO @ Sun, 03 Sep 2017 19:21:35: 12000000 INFO @ Sun, 03 Sep 2017 19:21:40: 14000000 INFO @ Sun, 03 Sep 2017 19:21:41: 13000000 INFO @ Sun, 03 Sep 2017 19:21:41: 13000000 INFO @ Sun, 03 Sep 2017 19:21:45: 15000000 INFO @ Sun, 03 Sep 2017 19:21:46: 14000000 INFO @ Sun, 03 Sep 2017 19:21:46: 14000000 INFO @ Sun, 03 Sep 2017 19:21:50: 16000000 INFO @ Sun, 03 Sep 2017 19:21:52: 15000000 INFO @ Sun, 03 Sep 2017 19:21:52: 15000000 INFO @ Sun, 03 Sep 2017 19:21:55: 17000000 INFO @ Sun, 03 Sep 2017 19:21:58: 16000000 INFO @ Sun, 03 Sep 2017 19:21:58: 16000000 INFO @ Sun, 03 Sep 2017 19:22:00: 18000000 INFO @ Sun, 03 Sep 2017 19:22:02: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:22:02: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:22:02: #1 total tags in treatment: 8268611 INFO @ Sun, 03 Sep 2017 19:22:02: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:22:02: #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 19:22:02: #1 tags after filtering in treatment: 3997436 INFO @ Sun, 03 Sep 2017 19:22:02: #1 Redundant rate of treatment: 0.52 INFO @ Sun, 03 Sep 2017 19:22:02: #1 finished! INFO @ Sun, 03 Sep 2017 19:22:02: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:22:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:22:02: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:22:02: 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, 03 Sep 2017 19:22:02: Process for pairing-model is terminated! cat: SRX2675848.10_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 `SRX2675848.10_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 `SRX2675848.10_*.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 `SRX2675848.10_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 19:22:03: 17000000 INFO @ Sun, 03 Sep 2017 19:22:03: 17000000 INFO @ Sun, 03 Sep 2017 19:22:09: 18000000 INFO @ Sun, 03 Sep 2017 19:22:09: 18000000 INFO @ Sun, 03 Sep 2017 19:22:10: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:22:10: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:22:10: #1 total tags in treatment: 8268611 INFO @ Sun, 03 Sep 2017 19:22:10: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:22:10: #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 19:22:10: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:22:10: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:22:10: #1 total tags in treatment: 8268611 INFO @ Sun, 03 Sep 2017 19:22:10: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:22:10: #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 19:22:11: #1 tags after filtering in treatment: 3997436 INFO @ Sun, 03 Sep 2017 19:22:11: #1 Redundant rate of treatment: 0.52 INFO @ Sun, 03 Sep 2017 19:22:11: #1 finished! INFO @ Sun, 03 Sep 2017 19:22:11: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:22:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:22:11: #1 tags after filtering in treatment: 3997436 INFO @ Sun, 03 Sep 2017 19:22:11: #1 Redundant rate of treatment: 0.52 INFO @ Sun, 03 Sep 2017 19:22:11: #1 finished! INFO @ Sun, 03 Sep 2017 19:22:11: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:22:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:22:11: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:22:11: 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 19:22:11: Process for pairing-model is terminated! cat: SRX2675848.05_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 `SRX2675848.05_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 `SRX2675848.05_*.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 `SRX2675848.05_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 19:22:11: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:22:11: 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 19:22:11: Process for pairing-model is terminated! cat: SRX2675848.20_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 `SRX2675848.20_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 `SRX2675848.20_*.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 `SRX2675848.20_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。