Job ID = 11162636 sra ファイルのダウンロード中... Completed: 511564K bytes transferred in 16 seconds (254227K 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 15180995 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3709388/SRR6736440.sra Written 15180995 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3709388/SRR6736440.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: 00:10:33 15180995 reads; of these: 15180995 (100.00%) were paired; of these: 1028213 (6.77%) aligned concordantly 0 times 12031960 (79.26%) aligned concordantly exactly 1 time 2120822 (13.97%) aligned concordantly >1 times ---- 1028213 pairs aligned concordantly 0 times; of these: 39060 (3.80%) aligned discordantly 1 time ---- 989153 pairs aligned 0 times concordantly or discordantly; of these: 1978306 mates make up the pairs; of these: 1450627 (73.33%) aligned 0 times 413761 (20.91%) aligned exactly 1 time 113918 (5.76%) aligned >1 times 95.22% overall alignment rate Time searching: 00:10:33 Overall time: 00:10:33 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 8 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] 11034154 / 14175095 = 0.7784 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 @ Wed, 05 Sep 2018 10:54:52: # Command line: callpeak -t SRX3709388.bam -f BAM -g 12100000 -n SRX3709388.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3709388.20 # format = BAM # ChIP-seq file = ['SRX3709388.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 @ Wed, 05 Sep 2018 10:54:52: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:54:52: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:54:52: # Command line: callpeak -t SRX3709388.bam -f BAM -g 12100000 -n SRX3709388.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3709388.05 # format = BAM # ChIP-seq file = ['SRX3709388.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 @ Wed, 05 Sep 2018 10:54:52: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:54:52: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:54:52: # Command line: callpeak -t SRX3709388.bam -f BAM -g 12100000 -n SRX3709388.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3709388.10 # format = BAM # ChIP-seq file = ['SRX3709388.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 @ Wed, 05 Sep 2018 10:54:52: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:54:52: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:54:57: 1000000 INFO @ Wed, 05 Sep 2018 10:54:57: 1000000 INFO @ Wed, 05 Sep 2018 10:54:57: 1000000 INFO @ Wed, 05 Sep 2018 10:55:03: 2000000 INFO @ Wed, 05 Sep 2018 10:55:03: 2000000 INFO @ Wed, 05 Sep 2018 10:55:04: 2000000 INFO @ Wed, 05 Sep 2018 10:55:09: 3000000 INFO @ Wed, 05 Sep 2018 10:55:09: 3000000 INFO @ Wed, 05 Sep 2018 10:55:10: 3000000 INFO @ Wed, 05 Sep 2018 10:55:15: 4000000 INFO @ Wed, 05 Sep 2018 10:55:15: 4000000 INFO @ Wed, 05 Sep 2018 10:55:16: 4000000 INFO @ Wed, 05 Sep 2018 10:55:22: 5000000 INFO @ Wed, 05 Sep 2018 10:55:22: 5000000 INFO @ Wed, 05 Sep 2018 10:55:23: 5000000 INFO @ Wed, 05 Sep 2018 10:55:29: 6000000 INFO @ Wed, 05 Sep 2018 10:55:29: 6000000 INFO @ Wed, 05 Sep 2018 10:55:29: 6000000 INFO @ Wed, 05 Sep 2018 10:55:35: #1 tag size is determined as 40 bps INFO @ Wed, 05 Sep 2018 10:55:35: #1 tag size = 40 INFO @ Wed, 05 Sep 2018 10:55:35: #1 total tags in treatment: 3139437 INFO @ Wed, 05 Sep 2018 10:55:35: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:55:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:55:35: #1 tag size is determined as 40 bps INFO @ Wed, 05 Sep 2018 10:55:35: #1 tag size = 40 INFO @ Wed, 05 Sep 2018 10:55:35: #1 total tags in treatment: 3139437 INFO @ Wed, 05 Sep 2018 10:55:35: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:55:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:55:35: #1 tags after filtering in treatment: 2554262 INFO @ Wed, 05 Sep 2018 10:55:35: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 05 Sep 2018 10:55:35: #1 finished! INFO @ Wed, 05 Sep 2018 10:55:35: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:55:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:55:35: #1 tags after filtering in treatment: 2554262 INFO @ Wed, 05 Sep 2018 10:55:35: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 05 Sep 2018 10:55:35: #1 finished! INFO @ Wed, 05 Sep 2018 10:55:35: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:55:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:55:35: #2 number of paired peaks: 42 WARNING @ Wed, 05 Sep 2018 10:55:35: Too few paired peaks (42) 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 @ Wed, 05 Sep 2018 10:55:35: Process for pairing-model is terminated! cat: SRX3709388.20_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 @ Wed, 05 Sep 2018 10:55:35: #2 number of paired peaks: 42 WARNING @ Wed, 05 Sep 2018 10:55:35: Too few paired peaks (42) 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 @ Wed, 05 Sep 2018 10:55:35: Process for pairing-model is terminated! pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) cat: SRX3709388.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません rm: cannot remove `SRX3709388.20_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 `SRX3709388.20_*.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 `SRX3709388.20_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 pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3709388.10_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 `SRX3709388.10_*.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 `SRX3709388.10_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 @ Wed, 05 Sep 2018 10:55:36: #1 tag size is determined as 40 bps INFO @ Wed, 05 Sep 2018 10:55:36: #1 tag size = 40 INFO @ Wed, 05 Sep 2018 10:55:36: #1 total tags in treatment: 3139437 INFO @ Wed, 05 Sep 2018 10:55:36: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:55:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:55:36: #1 tags after filtering in treatment: 2554262 INFO @ Wed, 05 Sep 2018 10:55:36: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 05 Sep 2018 10:55:36: #1 finished! INFO @ Wed, 05 Sep 2018 10:55:36: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:55:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:55:36: #2 number of paired peaks: 42 WARNING @ Wed, 05 Sep 2018 10:55:36: Too few paired peaks (42) 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 @ Wed, 05 Sep 2018 10:55:36: Process for pairing-model is terminated! cat: SRX3709388.05_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3709388.05_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 `SRX3709388.05_*.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 `SRX3709388.05_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。