Job ID = 10536341 sra ファイルのダウンロード中... Completed: 1107610K bytes transferred in 75 seconds (120858K 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 28026164 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3433208/SRR6333849.sra Written 28026164 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: 00:20:17 28026164 reads; of these: 28026164 (100.00%) were paired; of these: 3919535 (13.99%) aligned concordantly 0 times 21970886 (78.39%) aligned concordantly exactly 1 time 2135743 (7.62%) aligned concordantly >1 times ---- 3919535 pairs aligned concordantly 0 times; of these: 110740 (2.83%) aligned discordantly 1 time ---- 3808795 pairs aligned 0 times concordantly or discordantly; of these: 7617590 mates make up the pairs; of these: 7193644 (94.43%) aligned 0 times 355894 (4.67%) aligned exactly 1 time 68052 (0.89%) aligned >1 times 87.17% overall alignment rate Time searching: 00:20:17 Overall time: 00:20:17 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] 18152056 / 24118800 = 0.7526 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 09:09:09: # Command line: callpeak -t SRX3433208.bam -f BAM -g 12100000 -n SRX3433208.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3433208.05 # format = BAM # ChIP-seq file = ['SRX3433208.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 09:09:09: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:09:09: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:09:09: # Command line: callpeak -t SRX3433208.bam -f BAM -g 12100000 -n SRX3433208.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3433208.20 # format = BAM # ChIP-seq file = ['SRX3433208.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 09:09:09: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:09:09: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:09:09: # Command line: callpeak -t SRX3433208.bam -f BAM -g 12100000 -n SRX3433208.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3433208.10 # format = BAM # ChIP-seq file = ['SRX3433208.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 09:09:09: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:09:09: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:09:17: 1000000 INFO @ Thu, 05 Apr 2018 09:09:17: 1000000 INFO @ Thu, 05 Apr 2018 09:09:18: 1000000 INFO @ Thu, 05 Apr 2018 09:09:25: 2000000 INFO @ Thu, 05 Apr 2018 09:09:25: 2000000 INFO @ Thu, 05 Apr 2018 09:09:26: 2000000 INFO @ Thu, 05 Apr 2018 09:09:33: 3000000 INFO @ Thu, 05 Apr 2018 09:09:33: 3000000 INFO @ Thu, 05 Apr 2018 09:09:35: 3000000 INFO @ Thu, 05 Apr 2018 09:09:40: 4000000 INFO @ Thu, 05 Apr 2018 09:09:40: 4000000 INFO @ Thu, 05 Apr 2018 09:09:43: 4000000 INFO @ Thu, 05 Apr 2018 09:09:48: 5000000 INFO @ Thu, 05 Apr 2018 09:09:48: 5000000 INFO @ Thu, 05 Apr 2018 09:09:52: 5000000 INFO @ Thu, 05 Apr 2018 09:09:56: 6000000 INFO @ Thu, 05 Apr 2018 09:09:56: 6000000 INFO @ Thu, 05 Apr 2018 09:10:00: 6000000 INFO @ Thu, 05 Apr 2018 09:10:04: 7000000 INFO @ Thu, 05 Apr 2018 09:10:04: 7000000 INFO @ Thu, 05 Apr 2018 09:10:08: 7000000 INFO @ Thu, 05 Apr 2018 09:10:11: 8000000 INFO @ Thu, 05 Apr 2018 09:10:11: 8000000 INFO @ Thu, 05 Apr 2018 09:10:17: 8000000 INFO @ Thu, 05 Apr 2018 09:10:19: 9000000 INFO @ Thu, 05 Apr 2018 09:10:19: 9000000 INFO @ Thu, 05 Apr 2018 09:10:25: 9000000 INFO @ Thu, 05 Apr 2018 09:10:27: 10000000 INFO @ Thu, 05 Apr 2018 09:10:27: 10000000 INFO @ Thu, 05 Apr 2018 09:10:34: 10000000 INFO @ Thu, 05 Apr 2018 09:10:35: 11000000 INFO @ Thu, 05 Apr 2018 09:10:35: 11000000 INFO @ Thu, 05 Apr 2018 09:10:42: 11000000 INFO @ Thu, 05 Apr 2018 09:10:42: 12000000 INFO @ Thu, 05 Apr 2018 09:10:42: 12000000 INFO @ Thu, 05 Apr 2018 09:10:47: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:10:47: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:10:47: #1 total tags in treatment: 5960741 INFO @ Thu, 05 Apr 2018 09:10:47: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:10:47: #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 09:10:47: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:10:47: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:10:47: #1 total tags in treatment: 5960741 INFO @ Thu, 05 Apr 2018 09:10:47: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:10:47: #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 09:10:47: #1 tags after filtering in treatment: 4591864 INFO @ Thu, 05 Apr 2018 09:10:47: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 05 Apr 2018 09:10:47: #1 finished! INFO @ Thu, 05 Apr 2018 09:10:47: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:10:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:10:47: #1 tags after filtering in treatment: 4591864 INFO @ Thu, 05 Apr 2018 09:10:47: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 05 Apr 2018 09:10:47: #1 finished! INFO @ Thu, 05 Apr 2018 09:10:47: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:10:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:10:47: #2 number of paired peaks: 18 WARNING @ Thu, 05 Apr 2018 09:10:47: Too few paired peaks (18) 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 09:10:47: Process for pairing-model is terminated! INFO @ Thu, 05 Apr 2018 09:10:47: #2 number of paired peaks: 18 WARNING @ Thu, 05 Apr 2018 09:10:47: Too few paired peaks (18) 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 09:10:47: Process for pairing-model is terminated! cat: SRX3433208.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX3433208.20_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3433208.05_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 `SRX3433208.05_*.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 `SRX3433208.05_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3433208.20_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 `SRX3433208.20_*.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 `SRX3433208.20_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 09:10:50: 12000000 INFO @ Thu, 05 Apr 2018 09:10:55: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:10:55: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:10:55: #1 total tags in treatment: 5960741 INFO @ Thu, 05 Apr 2018 09:10:55: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:10:55: #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 09:10:55: #1 tags after filtering in treatment: 4591864 INFO @ Thu, 05 Apr 2018 09:10:55: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 05 Apr 2018 09:10:55: #1 finished! INFO @ Thu, 05 Apr 2018 09:10:55: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:10:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:10:55: #2 number of paired peaks: 18 WARNING @ Thu, 05 Apr 2018 09:10:55: Too few paired peaks (18) 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 09:10:55: Process for pairing-model is terminated! cat: SRX3433208.10_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 `SRX3433208.10_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 `SRX3433208.10_*.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 `SRX3433208.10_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。