Job ID = 10937535 sra ファイルのダウンロード中... Completed: 467618K bytes transferred in 59 seconds (64746K 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... Read 4856055 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010329/SRR5833328.sra Written 4856055 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010329/SRR5833328.sra 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: 00:06:36 4856055 reads; of these: 4856055 (100.00%) were paired; of these: 429504 (8.84%) aligned concordantly 0 times 3841465 (79.11%) aligned concordantly exactly 1 time 585086 (12.05%) aligned concordantly >1 times ---- 429504 pairs aligned concordantly 0 times; of these: 28067 (6.53%) aligned discordantly 1 time ---- 401437 pairs aligned 0 times concordantly or discordantly; of these: 802874 mates make up the pairs; of these: 745772 (92.89%) aligned 0 times 38497 (4.79%) aligned exactly 1 time 18605 (2.32%) aligned >1 times 92.32% overall alignment rate Time searching: 00:06:36 Overall time: 00:06:36 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_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] 75204 / 4446719 = 0.0169 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 @ Fri, 10 Aug 2018 02:43:23: # Command line: callpeak -t SRX3010329.bam -f BAM -g 12100000 -n SRX3010329.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3010329.05 # format = BAM # ChIP-seq file = ['SRX3010329.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 @ Fri, 10 Aug 2018 02:43:23: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:43:23: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:43:23: # Command line: callpeak -t SRX3010329.bam -f BAM -g 12100000 -n SRX3010329.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3010329.10 # format = BAM # ChIP-seq file = ['SRX3010329.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 @ Fri, 10 Aug 2018 02:43:23: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:43:23: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:43:23: # Command line: callpeak -t SRX3010329.bam -f BAM -g 12100000 -n SRX3010329.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3010329.20 # format = BAM # ChIP-seq file = ['SRX3010329.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 @ Fri, 10 Aug 2018 02:43:23: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:43:23: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:43:34: 1000000 INFO @ Fri, 10 Aug 2018 02:43:34: 1000000 INFO @ Fri, 10 Aug 2018 02:43:35: 1000000 INFO @ Fri, 10 Aug 2018 02:43:46: 2000000 INFO @ Fri, 10 Aug 2018 02:43:46: 2000000 INFO @ Fri, 10 Aug 2018 02:43:49: 2000000 INFO @ Fri, 10 Aug 2018 02:43:57: 3000000 INFO @ Fri, 10 Aug 2018 02:43:57: 3000000 INFO @ Fri, 10 Aug 2018 02:44:03: 3000000 INFO @ Fri, 10 Aug 2018 02:44:09: 4000000 INFO @ Fri, 10 Aug 2018 02:44:09: 4000000 INFO @ Fri, 10 Aug 2018 02:44:15: 4000000 INFO @ Fri, 10 Aug 2018 02:44:20: 5000000 INFO @ Fri, 10 Aug 2018 02:44:20: 5000000 INFO @ Fri, 10 Aug 2018 02:44:26: 5000000 INFO @ Fri, 10 Aug 2018 02:44:31: 6000000 INFO @ Fri, 10 Aug 2018 02:44:31: 6000000 INFO @ Fri, 10 Aug 2018 02:44:37: 6000000 INFO @ Fri, 10 Aug 2018 02:44:43: 7000000 INFO @ Fri, 10 Aug 2018 02:44:43: 7000000 INFO @ Fri, 10 Aug 2018 02:44:49: 7000000 INFO @ Fri, 10 Aug 2018 02:44:54: 8000000 INFO @ Fri, 10 Aug 2018 02:44:54: 8000000 INFO @ Fri, 10 Aug 2018 02:45:00: 8000000 INFO @ Fri, 10 Aug 2018 02:45:03: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:45:03: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:45:03: #1 total tags in treatment: 4351461 INFO @ Fri, 10 Aug 2018 02:45:03: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:45:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:45:03: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:45:03: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:45:03: #1 total tags in treatment: 4351461 INFO @ Fri, 10 Aug 2018 02:45:03: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:45:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:45:03: #1 tags after filtering in treatment: 3522635 INFO @ Fri, 10 Aug 2018 02:45:03: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Aug 2018 02:45:03: #1 finished! INFO @ Fri, 10 Aug 2018 02:45:03: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:45:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:45:03: #1 tags after filtering in treatment: 3522635 INFO @ Fri, 10 Aug 2018 02:45:03: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Aug 2018 02:45:03: #1 finished! INFO @ Fri, 10 Aug 2018 02:45:03: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:45:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:45:03: #2 number of paired peaks: 93 WARNING @ Fri, 10 Aug 2018 02:45:03: Too few paired peaks (93) 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 @ Fri, 10 Aug 2018 02:45:03: Process for pairing-model is terminated! cat: SRX3010329.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Fri, 10 Aug 2018 02:45:03: #2 number of paired peaks: 93 WARNING @ Fri, 10 Aug 2018 02:45:03: Too few paired peaks (93) 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 @ Fri, 10 Aug 2018 02:45:03: Process for pairing-model is terminated! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3010329.20_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 `SRX3010329.20_*.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 `SRX3010329.20_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 cat: SRX3010329.10_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 `SRX3010329.10_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 `SRX3010329.10_*.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 `SRX3010329.10_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 @ Fri, 10 Aug 2018 02:45:09: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:45:09: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:45:09: #1 total tags in treatment: 4351461 INFO @ Fri, 10 Aug 2018 02:45:09: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:45:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:45:09: #1 tags after filtering in treatment: 3522635 INFO @ Fri, 10 Aug 2018 02:45:09: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Aug 2018 02:45:09: #1 finished! INFO @ Fri, 10 Aug 2018 02:45:09: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:45:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:45:09: #2 number of paired peaks: 93 WARNING @ Fri, 10 Aug 2018 02:45:09: Too few paired peaks (93) 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 @ Fri, 10 Aug 2018 02:45:09: Process for pairing-model is terminated! cat: SRX3010329.05_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 `SRX3010329.05_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 `SRX3010329.05_*.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 `SRX3010329.05_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。