Job ID = 10536343 sra ファイルのダウンロード中... Completed: 1047727K bytes transferred in 28 seconds (299618K 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 26860312 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3433210/SRR6333851.sra Written 26860312 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: 00:18:46 26860312 reads; of these: 26860312 (100.00%) were paired; of these: 4677180 (17.41%) aligned concordantly 0 times 20113640 (74.88%) aligned concordantly exactly 1 time 2069492 (7.70%) aligned concordantly >1 times ---- 4677180 pairs aligned concordantly 0 times; of these: 89742 (1.92%) aligned discordantly 1 time ---- 4587438 pairs aligned 0 times concordantly or discordantly; of these: 9174876 mates make up the pairs; of these: 8841221 (96.36%) aligned 0 times 279117 (3.04%) aligned exactly 1 time 54538 (0.59%) aligned >1 times 83.54% overall alignment rate Time searching: 00:18:46 Overall time: 00:18:46 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] 15424771 / 22193589 = 0.6950 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 09:14:02: # Command line: callpeak -t SRX3433210.bam -f BAM -g 12100000 -n SRX3433210.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3433210.20 # format = BAM # ChIP-seq file = ['SRX3433210.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 09:14:02: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:14:02: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:14:02: # Command line: callpeak -t SRX3433210.bam -f BAM -g 12100000 -n SRX3433210.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3433210.05 # format = BAM # ChIP-seq file = ['SRX3433210.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 09:14:02: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:14:02: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:14:02: # Command line: callpeak -t SRX3433210.bam -f BAM -g 12100000 -n SRX3433210.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3433210.10 # format = BAM # ChIP-seq file = ['SRX3433210.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 09:14:02: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:14:02: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:14:08: 1000000 INFO @ Thu, 05 Apr 2018 09:14:09: 1000000 INFO @ Thu, 05 Apr 2018 09:14:09: 1000000 INFO @ Thu, 05 Apr 2018 09:14:15: 2000000 INFO @ Thu, 05 Apr 2018 09:14:16: 2000000 INFO @ Thu, 05 Apr 2018 09:14:16: 2000000 INFO @ Thu, 05 Apr 2018 09:14:22: 3000000 INFO @ Thu, 05 Apr 2018 09:14:23: 3000000 INFO @ Thu, 05 Apr 2018 09:14:23: 3000000 INFO @ Thu, 05 Apr 2018 09:14:29: 4000000 INFO @ Thu, 05 Apr 2018 09:14:30: 4000000 INFO @ Thu, 05 Apr 2018 09:14:30: 4000000 INFO @ Thu, 05 Apr 2018 09:14:35: 5000000 INFO @ Thu, 05 Apr 2018 09:14:38: 5000000 INFO @ Thu, 05 Apr 2018 09:14:38: 5000000 INFO @ Thu, 05 Apr 2018 09:14:42: 6000000 INFO @ Thu, 05 Apr 2018 09:14:45: 6000000 INFO @ Thu, 05 Apr 2018 09:14:45: 6000000 INFO @ Thu, 05 Apr 2018 09:14:49: 7000000 INFO @ Thu, 05 Apr 2018 09:14:53: 7000000 INFO @ Thu, 05 Apr 2018 09:14:53: 7000000 INFO @ Thu, 05 Apr 2018 09:14:55: 8000000 INFO @ Thu, 05 Apr 2018 09:15:00: 8000000 INFO @ Thu, 05 Apr 2018 09:15:00: 8000000 INFO @ Thu, 05 Apr 2018 09:15:02: 9000000 INFO @ Thu, 05 Apr 2018 09:15:07: 9000000 INFO @ Thu, 05 Apr 2018 09:15:07: 9000000 INFO @ Thu, 05 Apr 2018 09:15:09: 10000000 INFO @ Thu, 05 Apr 2018 09:15:15: 10000000 INFO @ Thu, 05 Apr 2018 09:15:15: 10000000 INFO @ Thu, 05 Apr 2018 09:15:15: 11000000 INFO @ Thu, 05 Apr 2018 09:15:22: 12000000 INFO @ Thu, 05 Apr 2018 09:15:22: 11000000 INFO @ Thu, 05 Apr 2018 09:15:22: 11000000 INFO @ Thu, 05 Apr 2018 09:15:29: 13000000 INFO @ Thu, 05 Apr 2018 09:15:30: 12000000 INFO @ Thu, 05 Apr 2018 09:15:30: 12000000 INFO @ Thu, 05 Apr 2018 09:15:35: 14000000 INFO @ Thu, 05 Apr 2018 09:15:35: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:15:35: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:15:35: #1 total tags in treatment: 6763667 INFO @ Thu, 05 Apr 2018 09:15:35: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:15:35: #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 09:15:36: #1 tags after filtering in treatment: 5032658 INFO @ Thu, 05 Apr 2018 09:15:36: #1 Redundant rate of treatment: 0.26 INFO @ Thu, 05 Apr 2018 09:15:36: #1 finished! INFO @ Thu, 05 Apr 2018 09:15:36: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:15:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:15:36: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:15:36: 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 09:15:36: Process for pairing-model is terminated! cat: SRX3433210.05_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3433210.05_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 `SRX3433210.05_*.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 `SRX3433210.05_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 09:15:37: 13000000 INFO @ Thu, 05 Apr 2018 09:15:37: 13000000 INFO @ Thu, 05 Apr 2018 09:15:44: 14000000 INFO @ Thu, 05 Apr 2018 09:15:44: 14000000 INFO @ Thu, 05 Apr 2018 09:15:45: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:15:45: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:15:45: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:15:45: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:15:45: #1 total tags in treatment: 6763667 INFO @ Thu, 05 Apr 2018 09:15:45: #1 total tags in treatment: 6763667 INFO @ Thu, 05 Apr 2018 09:15:45: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:15:45: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:15:45: #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 09:15:45: #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 09:15:45: #1 tags after filtering in treatment: 5032658 INFO @ Thu, 05 Apr 2018 09:15:45: #1 tags after filtering in treatment: 5032658 INFO @ Thu, 05 Apr 2018 09:15:45: #1 Redundant rate of treatment: 0.26 INFO @ Thu, 05 Apr 2018 09:15:45: #1 Redundant rate of treatment: 0.26 INFO @ Thu, 05 Apr 2018 09:15:45: #1 finished! INFO @ Thu, 05 Apr 2018 09:15:45: #1 finished! INFO @ Thu, 05 Apr 2018 09:15:45: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:15:45: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:15:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:15:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:15:45: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:15:45: 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 09:15:45: Process for pairing-model is terminated! INFO @ Thu, 05 Apr 2018 09:15:45: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:15:45: 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 09:15:45: Process for pairing-model is terminated! cat: SRX3433210.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX3433210.20_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) pass1 - making usageList (0 chroms): 1 millis rm: cannot remove `SRX3433210.10_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 `SRX3433210.10_*.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 `SRX3433210.10_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 needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3433210.20_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 `SRX3433210.20_*.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 `SRX3433210.20_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。