Job ID = 10254445 sra ファイルのダウンロード中... Completed: 206352K bytes transferred in 6 seconds (252890K bits/sec), in 1 file. Completed: 272632K bytes transferred in 11 seconds (188074K 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 3186827 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3353383/SRR6246240.sra Written 3186827 spots total Written 4288916 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3353383/SRR6246241.sra Written 4288916 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 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: 00:06:10 7475743 reads; of these: 7475743 (100.00%) were paired; of these: 2352110 (31.46%) aligned concordantly 0 times 4716102 (63.09%) aligned concordantly exactly 1 time 407531 (5.45%) aligned concordantly >1 times ---- 2352110 pairs aligned concordantly 0 times; of these: 778047 (33.08%) aligned discordantly 1 time ---- 1574063 pairs aligned 0 times concordantly or discordantly; of these: 3148126 mates make up the pairs; of these: 1834135 (58.26%) aligned 0 times 1108268 (35.20%) aligned exactly 1 time 205723 (6.53%) aligned >1 times 87.73% overall alignment rate Time searching: 00:06:10 Overall time: 00:06:10 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] 161310 / 5604290 = 0.0288 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, 06 Dec 2017 18:13:26: # Command line: callpeak -t SRX3353383.bam -f BAM -g 12100000 -n SRX3353383.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3353383.05 # format = BAM # ChIP-seq file = ['SRX3353383.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, 06 Dec 2017 18:13:26: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:13:26: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:13:26: # Command line: callpeak -t SRX3353383.bam -f BAM -g 12100000 -n SRX3353383.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3353383.10 # format = BAM # ChIP-seq file = ['SRX3353383.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, 06 Dec 2017 18:13:26: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:13:26: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:13:26: # Command line: callpeak -t SRX3353383.bam -f BAM -g 12100000 -n SRX3353383.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3353383.20 # format = BAM # ChIP-seq file = ['SRX3353383.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, 06 Dec 2017 18:13:26: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:13:26: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:13:32: 1000000 INFO @ Wed, 06 Dec 2017 18:13:32: 1000000 INFO @ Wed, 06 Dec 2017 18:13:32: 1000000 INFO @ Wed, 06 Dec 2017 18:13:38: 2000000 INFO @ Wed, 06 Dec 2017 18:13:39: 2000000 INFO @ Wed, 06 Dec 2017 18:13:39: 2000000 INFO @ Wed, 06 Dec 2017 18:13:44: 3000000 INFO @ Wed, 06 Dec 2017 18:13:46: 3000000 INFO @ Wed, 06 Dec 2017 18:13:46: 3000000 INFO @ Wed, 06 Dec 2017 18:13:51: 4000000 INFO @ Wed, 06 Dec 2017 18:13:52: 4000000 INFO @ Wed, 06 Dec 2017 18:13:52: 4000000 INFO @ Wed, 06 Dec 2017 18:13:57: 5000000 INFO @ Wed, 06 Dec 2017 18:13:59: 5000000 INFO @ Wed, 06 Dec 2017 18:13:59: 5000000 INFO @ Wed, 06 Dec 2017 18:14:03: 6000000 INFO @ Wed, 06 Dec 2017 18:14:06: 6000000 INFO @ Wed, 06 Dec 2017 18:14:06: 6000000 INFO @ Wed, 06 Dec 2017 18:14:09: 7000000 INFO @ Wed, 06 Dec 2017 18:14:13: 7000000 INFO @ Wed, 06 Dec 2017 18:14:13: 7000000 INFO @ Wed, 06 Dec 2017 18:14:15: 8000000 INFO @ Wed, 06 Dec 2017 18:14:19: 8000000 INFO @ Wed, 06 Dec 2017 18:14:19: 8000000 INFO @ Wed, 06 Dec 2017 18:14:21: 9000000 INFO @ Wed, 06 Dec 2017 18:14:26: 9000000 INFO @ Wed, 06 Dec 2017 18:14:26: 9000000 INFO @ Wed, 06 Dec 2017 18:14:28: 10000000 INFO @ Wed, 06 Dec 2017 18:14:33: 10000000 INFO @ Wed, 06 Dec 2017 18:14:33: 10000000 INFO @ Wed, 06 Dec 2017 18:14:34: 11000000 INFO @ Wed, 06 Dec 2017 18:14:39: 11000000 INFO @ Wed, 06 Dec 2017 18:14:39: 11000000 INFO @ Wed, 06 Dec 2017 18:14:40: 12000000 INFO @ Wed, 06 Dec 2017 18:14:45: #1 tag size is determined as 51 bps INFO @ Wed, 06 Dec 2017 18:14:45: #1 tag size = 51 INFO @ Wed, 06 Dec 2017 18:14:45: #1 total tags in treatment: 4965850 INFO @ Wed, 06 Dec 2017 18:14:45: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:14:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:14:46: #1 tags after filtering in treatment: 4148644 INFO @ Wed, 06 Dec 2017 18:14:46: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 06 Dec 2017 18:14:46: #1 finished! INFO @ Wed, 06 Dec 2017 18:14:46: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:14:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:14:46: #2 number of paired peaks: 5 WARNING @ Wed, 06 Dec 2017 18:14:46: Too few paired peaks (5) 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, 06 Dec 2017 18:14:46: Process for pairing-model is terminated! cat: SRX3353383.05_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 `SRX3353383.05_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 `SRX3353383.05_*.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 `SRX3353383.05_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 @ Wed, 06 Dec 2017 18:14:46: 12000000 INFO @ Wed, 06 Dec 2017 18:14:46: 12000000 INFO @ Wed, 06 Dec 2017 18:14:51: #1 tag size is determined as 51 bps INFO @ Wed, 06 Dec 2017 18:14:51: #1 tag size = 51 INFO @ Wed, 06 Dec 2017 18:14:51: #1 total tags in treatment: 4965850 INFO @ Wed, 06 Dec 2017 18:14:51: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:14:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:14:51: #1 tag size is determined as 51 bps INFO @ Wed, 06 Dec 2017 18:14:51: #1 tag size = 51 INFO @ Wed, 06 Dec 2017 18:14:51: #1 total tags in treatment: 4965850 INFO @ Wed, 06 Dec 2017 18:14:51: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:14:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:14:51: #1 tags after filtering in treatment: 4148644 INFO @ Wed, 06 Dec 2017 18:14:51: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 06 Dec 2017 18:14:51: #1 finished! INFO @ Wed, 06 Dec 2017 18:14:51: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:14:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:14:51: #1 tags after filtering in treatment: 4148644 INFO @ Wed, 06 Dec 2017 18:14:51: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 06 Dec 2017 18:14:51: #1 finished! INFO @ Wed, 06 Dec 2017 18:14:51: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:14:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:14:52: #2 number of paired peaks: 5 WARNING @ Wed, 06 Dec 2017 18:14:52: Too few paired peaks (5) 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, 06 Dec 2017 18:14:52: Process for pairing-model is terminated! cat: SRX3353383.10_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 `SRX3353383.10_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 `SRX3353383.10_*.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 `SRX3353383.10_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, 06 Dec 2017 18:14:52: #2 number of paired peaks: 5 WARNING @ Wed, 06 Dec 2017 18:14:52: Too few paired peaks (5) 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, 06 Dec 2017 18:14:52: Process for pairing-model is terminated! cat: SRX3353383.20_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 `SRX3353383.20_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 `SRX3353383.20_*.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 `SRX3353383.20_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。