Job ID = 10536375 sra ファイルのダウンロード中... Completed: 1630251K bytes transferred in 45 seconds (291230K 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 40307324 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671136/SRR6696888.sra Written 40307324 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: 00:26:41 40307324 reads; of these: 40307324 (100.00%) were paired; of these: 8978066 (22.27%) aligned concordantly 0 times 27781760 (68.92%) aligned concordantly exactly 1 time 3547498 (8.80%) aligned concordantly >1 times ---- 8978066 pairs aligned concordantly 0 times; of these: 129825 (1.45%) aligned discordantly 1 time ---- 8848241 pairs aligned 0 times concordantly or discordantly; of these: 17696482 mates make up the pairs; of these: 17050924 (96.35%) aligned 0 times 530872 (3.00%) aligned exactly 1 time 114686 (0.65%) aligned >1 times 78.85% overall alignment rate Time searching: 00:26:41 Overall time: 00:26:41 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 28 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] 22848471 / 31366338 = 0.7284 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 09:45:45: # Command line: callpeak -t SRX3671136.bam -f BAM -g 12100000 -n SRX3671136.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671136.05 # format = BAM # ChIP-seq file = ['SRX3671136.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 09:45:45: # Command line: callpeak -t SRX3671136.bam -f BAM -g 12100000 -n SRX3671136.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671136.20 # format = BAM # ChIP-seq file = ['SRX3671136.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 09:45:45: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:45:45: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:45:45: # Command line: callpeak -t SRX3671136.bam -f BAM -g 12100000 -n SRX3671136.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671136.10 # format = BAM # ChIP-seq file = ['SRX3671136.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 09:45:45: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:45:45: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:45:45: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:45:45: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:45:50: 1000000 INFO @ Thu, 05 Apr 2018 09:45:51: 1000000 INFO @ Thu, 05 Apr 2018 09:45:51: 1000000 INFO @ Thu, 05 Apr 2018 09:45:56: 2000000 INFO @ Thu, 05 Apr 2018 09:45:56: 2000000 INFO @ Thu, 05 Apr 2018 09:45:56: 2000000 INFO @ Thu, 05 Apr 2018 09:46:01: 3000000 INFO @ Thu, 05 Apr 2018 09:46:02: 3000000 INFO @ Thu, 05 Apr 2018 09:46:02: 3000000 INFO @ Thu, 05 Apr 2018 09:46:07: 4000000 INFO @ Thu, 05 Apr 2018 09:46:07: 4000000 INFO @ Thu, 05 Apr 2018 09:46:07: 4000000 INFO @ Thu, 05 Apr 2018 09:46:12: 5000000 INFO @ Thu, 05 Apr 2018 09:46:13: 5000000 INFO @ Thu, 05 Apr 2018 09:46:13: 5000000 INFO @ Thu, 05 Apr 2018 09:46:18: 6000000 INFO @ Thu, 05 Apr 2018 09:46:18: 6000000 INFO @ Thu, 05 Apr 2018 09:46:19: 6000000 INFO @ Thu, 05 Apr 2018 09:46:24: 7000000 INFO @ Thu, 05 Apr 2018 09:46:24: 7000000 INFO @ Thu, 05 Apr 2018 09:46:25: 7000000 INFO @ Thu, 05 Apr 2018 09:46:29: 8000000 INFO @ Thu, 05 Apr 2018 09:46:29: 8000000 INFO @ Thu, 05 Apr 2018 09:46:31: 8000000 INFO @ Thu, 05 Apr 2018 09:46:35: 9000000 INFO @ Thu, 05 Apr 2018 09:46:35: 9000000 INFO @ Thu, 05 Apr 2018 09:46:36: 9000000 INFO @ Thu, 05 Apr 2018 09:46:40: 10000000 INFO @ Thu, 05 Apr 2018 09:46:40: 10000000 INFO @ Thu, 05 Apr 2018 09:46:42: 10000000 INFO @ Thu, 05 Apr 2018 09:46:46: 11000000 INFO @ Thu, 05 Apr 2018 09:46:46: 11000000 INFO @ Thu, 05 Apr 2018 09:46:49: 11000000 INFO @ Thu, 05 Apr 2018 09:46:51: 12000000 INFO @ Thu, 05 Apr 2018 09:46:53: 12000000 INFO @ Thu, 05 Apr 2018 09:46:55: 12000000 INFO @ Thu, 05 Apr 2018 09:46:57: 13000000 INFO @ Thu, 05 Apr 2018 09:47:00: 13000000 INFO @ Thu, 05 Apr 2018 09:47:02: 13000000 INFO @ Thu, 05 Apr 2018 09:47:04: 14000000 INFO @ Thu, 05 Apr 2018 09:47:06: 14000000 INFO @ Thu, 05 Apr 2018 09:47:08: 14000000 INFO @ Thu, 05 Apr 2018 09:47:10: 15000000 INFO @ Thu, 05 Apr 2018 09:47:13: 15000000 INFO @ Thu, 05 Apr 2018 09:47:14: 15000000 INFO @ Thu, 05 Apr 2018 09:47:16: 16000000 INFO @ Thu, 05 Apr 2018 09:47:18: 16000000 INFO @ Thu, 05 Apr 2018 09:47:20: 16000000 INFO @ Thu, 05 Apr 2018 09:47:21: 17000000 INFO @ Thu, 05 Apr 2018 09:47:23: 17000000 INFO @ Thu, 05 Apr 2018 09:47:26: 17000000 INFO @ Thu, 05 Apr 2018 09:47:26: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:47:26: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:47:26: #1 total tags in treatment: 8491679 INFO @ Thu, 05 Apr 2018 09:47:26: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:47:26: #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 09:47:27: #1 tags after filtering in treatment: 6576326 INFO @ Thu, 05 Apr 2018 09:47:27: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 05 Apr 2018 09:47:27: #1 finished! INFO @ Thu, 05 Apr 2018 09:47:27: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:47:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:47:27: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:47:27: 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 09:47:27: Process for pairing-model is terminated! cat: SRX3671136.05_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 `SRX3671136.05_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 `SRX3671136.05_*.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 `SRX3671136.05_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 09:47:28: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:47:28: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:47:28: #1 total tags in treatment: 8491679 INFO @ Thu, 05 Apr 2018 09:47:28: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:47:28: #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 09:47:28: #1 tags after filtering in treatment: 6576326 INFO @ Thu, 05 Apr 2018 09:47:28: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 05 Apr 2018 09:47:28: #1 finished! INFO @ Thu, 05 Apr 2018 09:47:28: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:47:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:47:29: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:47:29: 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 09:47:29: Process for pairing-model is terminated! cat: SRX3671136.10_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 `SRX3671136.10_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 `SRX3671136.10_*.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 `SRX3671136.10_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 09:47:31: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:47:31: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:47:31: #1 total tags in treatment: 8491679 INFO @ Thu, 05 Apr 2018 09:47:31: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:47:31: #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 09:47:31: #1 tags after filtering in treatment: 6576326 INFO @ Thu, 05 Apr 2018 09:47:31: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 05 Apr 2018 09:47:31: #1 finished! INFO @ Thu, 05 Apr 2018 09:47:31: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:47:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:47:31: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:47:31: 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 09:47:31: Process for pairing-model is terminated! cat: SRX3671136.20_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 `SRX3671136.20_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 `SRX3671136.20_*.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 `SRX3671136.20_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。