Job ID = 10536340 sra ファイルのダウンロード中... Completed: 1001752K bytes transferred in 19 seconds (417006K 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 24767794 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3433207/SRR6333848.sra Written 24767794 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: 00:18:27 24767794 reads; of these: 24767794 (100.00%) were paired; of these: 2332599 (9.42%) aligned concordantly 0 times 20612734 (83.22%) aligned concordantly exactly 1 time 1822461 (7.36%) aligned concordantly >1 times ---- 2332599 pairs aligned concordantly 0 times; of these: 192641 (8.26%) aligned discordantly 1 time ---- 2139958 pairs aligned 0 times concordantly or discordantly; of these: 4279916 mates make up the pairs; of these: 3894746 (91.00%) aligned 0 times 311969 (7.29%) aligned exactly 1 time 73201 (1.71%) aligned >1 times 92.14% overall alignment rate Time searching: 00:18:27 Overall time: 00:18:27 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 20 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] 13604316 / 22452782 = 0.6059 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 09:04:29: # Command line: callpeak -t SRX3433207.bam -f BAM -g 12100000 -n SRX3433207.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3433207.05 # format = BAM # ChIP-seq file = ['SRX3433207.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 09:04:29: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:04:29: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:04:29: # Command line: callpeak -t SRX3433207.bam -f BAM -g 12100000 -n SRX3433207.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3433207.20 # format = BAM # ChIP-seq file = ['SRX3433207.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 09:04:29: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:04:29: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:04:29: # Command line: callpeak -t SRX3433207.bam -f BAM -g 12100000 -n SRX3433207.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3433207.10 # format = BAM # ChIP-seq file = ['SRX3433207.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 09:04:29: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:04:29: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:04:35: 1000000 INFO @ Thu, 05 Apr 2018 09:04:36: 1000000 INFO @ Thu, 05 Apr 2018 09:04:36: 1000000 INFO @ Thu, 05 Apr 2018 09:04:41: 2000000 INFO @ Thu, 05 Apr 2018 09:04:42: 2000000 INFO @ Thu, 05 Apr 2018 09:04:42: 2000000 INFO @ Thu, 05 Apr 2018 09:04:47: 3000000 INFO @ Thu, 05 Apr 2018 09:04:49: 3000000 INFO @ Thu, 05 Apr 2018 09:04:49: 3000000 INFO @ Thu, 05 Apr 2018 09:04:53: 4000000 INFO @ Thu, 05 Apr 2018 09:04:55: 4000000 INFO @ Thu, 05 Apr 2018 09:04:55: 4000000 INFO @ Thu, 05 Apr 2018 09:04:58: 5000000 INFO @ Thu, 05 Apr 2018 09:05:02: 5000000 INFO @ Thu, 05 Apr 2018 09:05:02: 5000000 INFO @ Thu, 05 Apr 2018 09:05:04: 6000000 INFO @ Thu, 05 Apr 2018 09:05:08: 6000000 INFO @ Thu, 05 Apr 2018 09:05:08: 6000000 INFO @ Thu, 05 Apr 2018 09:05:10: 7000000 INFO @ Thu, 05 Apr 2018 09:05:14: 7000000 INFO @ Thu, 05 Apr 2018 09:05:14: 7000000 INFO @ Thu, 05 Apr 2018 09:05:16: 8000000 INFO @ Thu, 05 Apr 2018 09:05:20: 8000000 INFO @ Thu, 05 Apr 2018 09:05:20: 8000000 INFO @ Thu, 05 Apr 2018 09:05:22: 9000000 INFO @ Thu, 05 Apr 2018 09:05:27: 9000000 INFO @ Thu, 05 Apr 2018 09:05:27: 9000000 INFO @ Thu, 05 Apr 2018 09:05:28: 10000000 INFO @ Thu, 05 Apr 2018 09:05:33: 10000000 INFO @ Thu, 05 Apr 2018 09:05:33: 10000000 INFO @ Thu, 05 Apr 2018 09:05:33: 11000000 INFO @ Thu, 05 Apr 2018 09:05:39: 11000000 INFO @ Thu, 05 Apr 2018 09:05:39: 11000000 INFO @ Thu, 05 Apr 2018 09:05:39: 12000000 INFO @ Thu, 05 Apr 2018 09:05:45: 13000000 INFO @ Thu, 05 Apr 2018 09:05:45: 12000000 INFO @ Thu, 05 Apr 2018 09:05:45: 12000000 INFO @ Thu, 05 Apr 2018 09:05:51: 14000000 INFO @ Thu, 05 Apr 2018 09:05:51: 13000000 INFO @ Thu, 05 Apr 2018 09:05:51: 13000000 INFO @ Thu, 05 Apr 2018 09:05:57: 15000000 INFO @ Thu, 05 Apr 2018 09:05:57: 14000000 INFO @ Thu, 05 Apr 2018 09:05:57: 14000000 INFO @ Thu, 05 Apr 2018 09:06:02: 16000000 INFO @ Thu, 05 Apr 2018 09:06:03: 15000000 INFO @ Thu, 05 Apr 2018 09:06:03: 15000000 INFO @ Thu, 05 Apr 2018 09:06:08: 17000000 INFO @ Thu, 05 Apr 2018 09:06:09: 16000000 INFO @ Thu, 05 Apr 2018 09:06:09: 16000000 INFO @ Thu, 05 Apr 2018 09:06:14: 18000000 INFO @ Thu, 05 Apr 2018 09:06:16: 17000000 INFO @ Thu, 05 Apr 2018 09:06:16: 17000000 INFO @ Thu, 05 Apr 2018 09:06:16: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:06:16: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:06:16: #1 total tags in treatment: 8840282 INFO @ Thu, 05 Apr 2018 09:06:16: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:06:16: #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 09:06:17: #1 tags after filtering in treatment: 6279331 INFO @ Thu, 05 Apr 2018 09:06:17: #1 Redundant rate of treatment: 0.29 INFO @ Thu, 05 Apr 2018 09:06:17: #1 finished! INFO @ Thu, 05 Apr 2018 09:06:17: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:06:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:06:17: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:06:17: 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 09:06:17: Process for pairing-model is terminated! cat: SRX3433207.05_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 `SRX3433207.05_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 `SRX3433207.05_*.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 `SRX3433207.05_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 09:06:22: 18000000 INFO @ Thu, 05 Apr 2018 09:06:22: 18000000 INFO @ Thu, 05 Apr 2018 09:06:24: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:06:24: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:06:24: #1 total tags in treatment: 8840282 INFO @ Thu, 05 Apr 2018 09:06:24: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:06:24: #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 09:06:24: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:06:24: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:06:24: #1 total tags in treatment: 8840282 INFO @ Thu, 05 Apr 2018 09:06:24: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:06:24: #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 09:06:25: #1 tags after filtering in treatment: 6279331 INFO @ Thu, 05 Apr 2018 09:06:25: #1 tags after filtering in treatment: 6279331 INFO @ Thu, 05 Apr 2018 09:06:25: #1 Redundant rate of treatment: 0.29 INFO @ Thu, 05 Apr 2018 09:06:25: #1 Redundant rate of treatment: 0.29 INFO @ Thu, 05 Apr 2018 09:06:25: #1 finished! INFO @ Thu, 05 Apr 2018 09:06:25: #1 finished! INFO @ Thu, 05 Apr 2018 09:06:25: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:06:25: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:06:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:06:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:06:25: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:06:25: 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 09:06:25: Process for pairing-model is terminated! INFO @ Thu, 05 Apr 2018 09:06:25: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:06:25: 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 09:06:25: Process for pairing-model is terminated! cat: SRX3433207.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX3433207.10_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) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3433207.20_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 `SRX3433207.20_*.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 `SRX3433207.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません rm: cannot remove `SRX3433207.10_model.r': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling rm: cannot remove `SRX3433207.10_*.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 `SRX3433207.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。