Job ID = 11633535 sra ファイルのダウンロード中... Completed: 237226K bytes transferred in 5 seconds (357726K 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/ERX1236312/ERR1162905.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236312/ERR1162905.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: 00:02:54 4000000 reads; of these: 4000000 (100.00%) were paired; of these: 413394 (10.33%) aligned concordantly 0 times 3216324 (80.41%) aligned concordantly exactly 1 time 370282 (9.26%) aligned concordantly >1 times ---- 413394 pairs aligned concordantly 0 times; of these: 5974 (1.45%) aligned discordantly 1 time ---- 407420 pairs aligned 0 times concordantly or discordantly; of these: 814840 mates make up the pairs; of these: 802166 (98.44%) aligned 0 times 9070 (1.11%) aligned exactly 1 time 3604 (0.44%) aligned >1 times 89.97% overall alignment rate Time searching: 00:02:54 Overall time: 00:02:55 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] 1356164 / 3591870 = 0.3776 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 09:06:10: # Command line: callpeak -t ERX1236312.bam -f BAM -g 12100000 -n ERX1236312.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236312.05 # format = BAM # ChIP-seq file = ['ERX1236312.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 09:06:10: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:06:10: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:06:10: # Command line: callpeak -t ERX1236312.bam -f BAM -g 12100000 -n ERX1236312.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236312.20 # format = BAM # ChIP-seq file = ['ERX1236312.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 09:06:10: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:06:10: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:06:10: # Command line: callpeak -t ERX1236312.bam -f BAM -g 12100000 -n ERX1236312.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236312.10 # format = BAM # ChIP-seq file = ['ERX1236312.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 09:06:10: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:06:10: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:06:17: 1000000 INFO @ Fri, 15 Feb 2019 09:06:17: 1000000 INFO @ Fri, 15 Feb 2019 09:06:17: 1000000 INFO @ Fri, 15 Feb 2019 09:06:24: 2000000 INFO @ Fri, 15 Feb 2019 09:06:24: 2000000 INFO @ Fri, 15 Feb 2019 09:06:25: 2000000 INFO @ Fri, 15 Feb 2019 09:06:30: 3000000 INFO @ Fri, 15 Feb 2019 09:06:30: 3000000 INFO @ Fri, 15 Feb 2019 09:06:31: 3000000 INFO @ Fri, 15 Feb 2019 09:06:36: 4000000 INFO @ Fri, 15 Feb 2019 09:06:36: 4000000 INFO @ Fri, 15 Feb 2019 09:06:37: 4000000 INFO @ Fri, 15 Feb 2019 09:06:39: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:06:39: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:06:39: #1 total tags in treatment: 2232220 INFO @ Fri, 15 Feb 2019 09:06:39: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:06:39: #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 09:06:39: #1 tags after filtering in treatment: 2009930 INFO @ Fri, 15 Feb 2019 09:06:39: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 15 Feb 2019 09:06:39: #1 finished! INFO @ Fri, 15 Feb 2019 09:06:39: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:06:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:06:39: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:06:39: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:06:39: #1 total tags in treatment: 2232220 INFO @ Fri, 15 Feb 2019 09:06:39: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:06:39: #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 09:06:39: #1 tags after filtering in treatment: 2009930 INFO @ Fri, 15 Feb 2019 09:06:39: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 15 Feb 2019 09:06:39: #1 finished! INFO @ Fri, 15 Feb 2019 09:06:39: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:06:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:06:39: #2 number of paired peaks: 96 WARNING @ Fri, 15 Feb 2019 09:06:39: Too few paired peaks (96) 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 09:06:39: Process for pairing-model is terminated! cat: ERX1236312.05_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): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `ERX1236312.05_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 `ERX1236312.05_*.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 `ERX1236312.05_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 09:06:39: #2 number of paired peaks: 96 WARNING @ Fri, 15 Feb 2019 09:06:39: Too few paired peaks (96) 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 09:06:39: Process for pairing-model is terminated! cat: ERX1236312.20_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 `ERX1236312.20_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 `ERX1236312.20_*.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 `ERX1236312.20_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 INFO @ Fri, 15 Feb 2019 09:06:40: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:06:40: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:06:40: #1 total tags in treatment: 2232220 INFO @ Fri, 15 Feb 2019 09:06:40: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:06:40: #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 09:06:40: #1 tags after filtering in treatment: 2009930 INFO @ Fri, 15 Feb 2019 09:06:40: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 15 Feb 2019 09:06:40: #1 finished! INFO @ Fri, 15 Feb 2019 09:06:40: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:06:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:06:40: #2 number of paired peaks: 96 WARNING @ Fri, 15 Feb 2019 09:06:40: Too few paired peaks (96) 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 09:06:40: Process for pairing-model is terminated! cat: ERX1236312.10_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `ERX1236312.10_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 `ERX1236312.10_*.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 `ERX1236312.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。