Job ID = 11633422 sra ファイルのダウンロード中... Completed: 249708K bytes transferred in 5 seconds (354064K 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 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236199/ERR1162792.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236199/ERR1162792.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: 00:03:04 4000000 reads; of these: 4000000 (100.00%) were paired; of these: 539362 (13.48%) aligned concordantly 0 times 3000312 (75.01%) aligned concordantly exactly 1 time 460326 (11.51%) aligned concordantly >1 times ---- 539362 pairs aligned concordantly 0 times; of these: 23445 (4.35%) aligned discordantly 1 time ---- 515917 pairs aligned 0 times concordantly or discordantly; of these: 1031834 mates make up the pairs; of these: 1000625 (96.98%) aligned 0 times 15589 (1.51%) aligned exactly 1 time 15620 (1.51%) aligned >1 times 87.49% overall alignment rate Time searching: 00:03:04 Overall time: 00:03:04 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] 354024 / 3482470 = 0.1017 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, 15 Feb 2019 08:57:01: # Command line: callpeak -t ERX1236199.bam -f BAM -g 12100000 -n ERX1236199.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236199.10 # format = BAM # ChIP-seq file = ['ERX1236199.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, 15 Feb 2019 08:57:01: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:57:01: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:57:01: # Command line: callpeak -t ERX1236199.bam -f BAM -g 12100000 -n ERX1236199.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236199.20 # format = BAM # ChIP-seq file = ['ERX1236199.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, 15 Feb 2019 08:57:01: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:57:01: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:57:01: # Command line: callpeak -t ERX1236199.bam -f BAM -g 12100000 -n ERX1236199.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236199.05 # format = BAM # ChIP-seq file = ['ERX1236199.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, 15 Feb 2019 08:57:01: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:57:01: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:57:06: 1000000 INFO @ Fri, 15 Feb 2019 08:57:06: 1000000 INFO @ Fri, 15 Feb 2019 08:57:07: 1000000 INFO @ Fri, 15 Feb 2019 08:57:12: 2000000 INFO @ Fri, 15 Feb 2019 08:57:12: 2000000 INFO @ Fri, 15 Feb 2019 08:57:12: 2000000 INFO @ Fri, 15 Feb 2019 08:57:17: 3000000 INFO @ Fri, 15 Feb 2019 08:57:17: 3000000 INFO @ Fri, 15 Feb 2019 08:57:18: 3000000 INFO @ Fri, 15 Feb 2019 08:57:22: 4000000 INFO @ Fri, 15 Feb 2019 08:57:22: 4000000 INFO @ Fri, 15 Feb 2019 08:57:24: 4000000 INFO @ Fri, 15 Feb 2019 08:57:27: 5000000 INFO @ Fri, 15 Feb 2019 08:57:28: 5000000 INFO @ Fri, 15 Feb 2019 08:57:29: 5000000 INFO @ Fri, 15 Feb 2019 08:57:32: 6000000 INFO @ Fri, 15 Feb 2019 08:57:33: 6000000 INFO @ Fri, 15 Feb 2019 08:57:34: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:57:34: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:57:34: #1 total tags in treatment: 3108196 INFO @ Fri, 15 Feb 2019 08:57:34: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:57:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 08:57:34: #1 tags after filtering in treatment: 2690480 INFO @ Fri, 15 Feb 2019 08:57:34: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 15 Feb 2019 08:57:34: #1 finished! INFO @ Fri, 15 Feb 2019 08:57:34: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:57:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:57:34: #2 number of paired peaks: 67 WARNING @ Fri, 15 Feb 2019 08:57:34: Too few paired peaks (67) 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, 15 Feb 2019 08:57:34: Process for pairing-model is terminated! cat: ERX1236199.05_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `ERX1236199.05_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 `ERX1236199.05_*.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 `ERX1236199.05_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 @ Fri, 15 Feb 2019 08:57:35: 6000000 INFO @ Fri, 15 Feb 2019 08:57:35: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:57:35: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:57:35: #1 total tags in treatment: 3108196 INFO @ Fri, 15 Feb 2019 08:57:35: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:57:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 08:57:35: #1 tags after filtering in treatment: 2690480 INFO @ Fri, 15 Feb 2019 08:57:35: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 15 Feb 2019 08:57:35: #1 finished! INFO @ Fri, 15 Feb 2019 08:57:35: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:57:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:57:35: #2 number of paired peaks: 67 WARNING @ Fri, 15 Feb 2019 08:57:35: Too few paired peaks (67) 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, 15 Feb 2019 08:57:35: Process for pairing-model is terminated! cat: ERX1236199.10_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `ERX1236199.10_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 `ERX1236199.10_*.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 `ERX1236199.10_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, 15 Feb 2019 08:57:36: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:57:36: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:57:36: #1 total tags in treatment: 3108196 INFO @ Fri, 15 Feb 2019 08:57:36: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:57:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 08:57:36: #1 tags after filtering in treatment: 2690480 INFO @ Fri, 15 Feb 2019 08:57:36: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 15 Feb 2019 08:57:36: #1 finished! INFO @ Fri, 15 Feb 2019 08:57:36: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:57:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:57:37: #2 number of paired peaks: 67 WARNING @ Fri, 15 Feb 2019 08:57:37: Too few paired peaks (67) 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, 15 Feb 2019 08:57:37: Process for pairing-model is terminated! cat: ERX1236199.20_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `ERX1236199.20_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 `ERX1236199.20_*.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 `ERX1236199.20_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。