Job ID = 10536377 sra ファイルのダウンロード中... Completed: 1201646K bytes transferred in 42 seconds (234136K 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 31952822 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671137/SRR6696889.sra Written 31952822 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: 00:14:01 31952822 reads; of these: 31952822 (100.00%) were paired; of these: 16005820 (50.09%) aligned concordantly 0 times 13987025 (43.77%) aligned concordantly exactly 1 time 1959977 (6.13%) aligned concordantly >1 times ---- 16005820 pairs aligned concordantly 0 times; of these: 48540 (0.30%) aligned discordantly 1 time ---- 15957280 pairs aligned 0 times concordantly or discordantly; of these: 31914560 mates make up the pairs; of these: 31624400 (99.09%) aligned 0 times 235997 (0.74%) aligned exactly 1 time 54163 (0.17%) aligned >1 times 50.51% overall alignment rate Time searching: 00:14:01 Overall time: 00:14:01 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 16 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] 6792237 / 15955887 = 0.4257 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 09:34:36: # Command line: callpeak -t SRX3671137.bam -f BAM -g 12100000 -n SRX3671137.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671137.05 # format = BAM # ChIP-seq file = ['SRX3671137.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 09:34:36: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:34:36: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:34:36: # Command line: callpeak -t SRX3671137.bam -f BAM -g 12100000 -n SRX3671137.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671137.10 # format = BAM # ChIP-seq file = ['SRX3671137.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 09:34:36: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:34:36: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:34:36: # Command line: callpeak -t SRX3671137.bam -f BAM -g 12100000 -n SRX3671137.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671137.20 # format = BAM # ChIP-seq file = ['SRX3671137.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 09:34:36: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:34:36: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:34:42: 1000000 INFO @ Thu, 05 Apr 2018 09:34:42: 1000000 INFO @ Thu, 05 Apr 2018 09:34:42: 1000000 INFO @ Thu, 05 Apr 2018 09:34:48: 2000000 INFO @ Thu, 05 Apr 2018 09:34:48: 2000000 INFO @ Thu, 05 Apr 2018 09:34:48: 2000000 INFO @ Thu, 05 Apr 2018 09:34:54: 3000000 INFO @ Thu, 05 Apr 2018 09:34:54: 3000000 INFO @ Thu, 05 Apr 2018 09:34:54: 3000000 INFO @ Thu, 05 Apr 2018 09:35:00: 4000000 INFO @ Thu, 05 Apr 2018 09:35:00: 4000000 INFO @ Thu, 05 Apr 2018 09:35:01: 4000000 INFO @ Thu, 05 Apr 2018 09:35:06: 5000000 INFO @ Thu, 05 Apr 2018 09:35:06: 5000000 INFO @ Thu, 05 Apr 2018 09:35:07: 5000000 INFO @ Thu, 05 Apr 2018 09:35:12: 6000000 INFO @ Thu, 05 Apr 2018 09:35:12: 6000000 INFO @ Thu, 05 Apr 2018 09:35:13: 6000000 INFO @ Thu, 05 Apr 2018 09:35:18: 7000000 INFO @ Thu, 05 Apr 2018 09:35:19: 7000000 INFO @ Thu, 05 Apr 2018 09:35:20: 7000000 INFO @ Thu, 05 Apr 2018 09:35:24: 8000000 INFO @ Thu, 05 Apr 2018 09:35:25: 8000000 INFO @ Thu, 05 Apr 2018 09:35:26: 8000000 INFO @ Thu, 05 Apr 2018 09:35:30: 9000000 INFO @ Thu, 05 Apr 2018 09:35:31: 9000000 INFO @ Thu, 05 Apr 2018 09:35:33: 9000000 INFO @ Thu, 05 Apr 2018 09:35:36: 10000000 INFO @ Thu, 05 Apr 2018 09:35:37: 10000000 INFO @ Thu, 05 Apr 2018 09:35:39: 10000000 INFO @ Thu, 05 Apr 2018 09:35:42: 11000000 INFO @ Thu, 05 Apr 2018 09:35:44: 11000000 INFO @ Thu, 05 Apr 2018 09:35:46: 11000000 INFO @ Thu, 05 Apr 2018 09:35:48: 12000000 INFO @ Thu, 05 Apr 2018 09:35:50: 12000000 INFO @ Thu, 05 Apr 2018 09:35:52: 12000000 INFO @ Thu, 05 Apr 2018 09:35:54: 13000000 INFO @ Thu, 05 Apr 2018 09:35:56: 13000000 INFO @ Thu, 05 Apr 2018 09:35:59: 13000000 INFO @ Thu, 05 Apr 2018 09:36:00: 14000000 INFO @ Thu, 05 Apr 2018 09:36:02: 14000000 INFO @ Thu, 05 Apr 2018 09:36:05: 14000000 INFO @ Thu, 05 Apr 2018 09:36:06: 15000000 INFO @ Thu, 05 Apr 2018 09:36:08: 15000000 INFO @ Thu, 05 Apr 2018 09:36:12: 15000000 INFO @ Thu, 05 Apr 2018 09:36:12: 16000000 INFO @ Thu, 05 Apr 2018 09:36:14: 16000000 INFO @ Thu, 05 Apr 2018 09:36:18: 16000000 INFO @ Thu, 05 Apr 2018 09:36:18: 17000000 INFO @ Thu, 05 Apr 2018 09:36:20: 17000000 INFO @ Thu, 05 Apr 2018 09:36:24: 17000000 INFO @ Thu, 05 Apr 2018 09:36:24: 18000000 INFO @ Thu, 05 Apr 2018 09:36:26: 18000000 INFO @ Thu, 05 Apr 2018 09:36:28: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:36:28: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:36:28: #1 total tags in treatment: 9158284 INFO @ Thu, 05 Apr 2018 09:36:28: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:36:28: #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 09:36:29: #1 tags after filtering in treatment: 7025137 INFO @ Thu, 05 Apr 2018 09:36:29: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 05 Apr 2018 09:36:29: #1 finished! INFO @ Thu, 05 Apr 2018 09:36:29: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:36:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:36:29: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:36:29: 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 09:36:29: Process for pairing-model is terminated! cat: SRX3671137.10_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 `SRX3671137.10_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 `SRX3671137.10_*.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 `SRX3671137.10_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 @ Thu, 05 Apr 2018 09:36:30: 18000000 INFO @ Thu, 05 Apr 2018 09:36:31: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:36:31: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:36:31: #1 total tags in treatment: 9158284 INFO @ Thu, 05 Apr 2018 09:36:31: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:36:31: #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 09:36:31: #1 tags after filtering in treatment: 7025137 INFO @ Thu, 05 Apr 2018 09:36:31: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 05 Apr 2018 09:36:31: #1 finished! INFO @ Thu, 05 Apr 2018 09:36:31: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:36:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:36:31: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:36:31: 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 09:36:31: Process for pairing-model is terminated! cat: SRX3671137.20_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3671137.20_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 `SRX3671137.20_*.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 `SRX3671137.20_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 09:36:34: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:36:34: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:36:34: #1 total tags in treatment: 9158284 INFO @ Thu, 05 Apr 2018 09:36:34: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:36:34: #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 09:36:34: #1 tags after filtering in treatment: 7025137 INFO @ Thu, 05 Apr 2018 09:36:34: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 05 Apr 2018 09:36:34: #1 finished! INFO @ Thu, 05 Apr 2018 09:36:34: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:36:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:36:35: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:36:35: 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 09:36:35: Process for pairing-model is terminated! cat: SRX3671137.05_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 `SRX3671137.05_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 `SRX3671137.05_*.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 `SRX3671137.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。