Job ID = 11632955 sra ファイルのダウンロード中... Completed: 218931K bytes transferred in 5 seconds (317078K 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 3101008 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1173893/ERR1094407.sra Written 3101008 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1173893/ERR1094407.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: 00:02:27 3101008 reads; of these: 3101008 (100.00%) were paired; of these: 144726 (4.67%) aligned concordantly 0 times 2663291 (85.88%) aligned concordantly exactly 1 time 292991 (9.45%) aligned concordantly >1 times ---- 144726 pairs aligned concordantly 0 times; of these: 33655 (23.25%) aligned discordantly 1 time ---- 111071 pairs aligned 0 times concordantly or discordantly; of these: 222142 mates make up the pairs; of these: 193888 (87.28%) aligned 0 times 18088 (8.14%) aligned exactly 1 time 10166 (4.58%) aligned >1 times 96.87% overall alignment rate Time searching: 00:02:27 Overall time: 00:02:27 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] 17413 / 2961613 = 0.0059 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 08:01:05: # Command line: callpeak -t ERX1173893.bam -f BAM -g 12100000 -n ERX1173893.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1173893.20 # format = BAM # ChIP-seq file = ['ERX1173893.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 08:01:05: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:01:05: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:01:05: # Command line: callpeak -t ERX1173893.bam -f BAM -g 12100000 -n ERX1173893.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1173893.05 # format = BAM # ChIP-seq file = ['ERX1173893.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 08:01:05: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:01:05: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:01:05: # Command line: callpeak -t ERX1173893.bam -f BAM -g 12100000 -n ERX1173893.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1173893.10 # format = BAM # ChIP-seq file = ['ERX1173893.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 08:01:05: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:01:05: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:01:10: 1000000 INFO @ Fri, 15 Feb 2019 08:01:10: 1000000 INFO @ Fri, 15 Feb 2019 08:01:11: 1000000 INFO @ Fri, 15 Feb 2019 08:01:16: 2000000 INFO @ Fri, 15 Feb 2019 08:01:16: 2000000 INFO @ Fri, 15 Feb 2019 08:01:16: 2000000 INFO @ Fri, 15 Feb 2019 08:01:21: 3000000 INFO @ Fri, 15 Feb 2019 08:01:21: 3000000 INFO @ Fri, 15 Feb 2019 08:01:22: 3000000 INFO @ Fri, 15 Feb 2019 08:01:26: 4000000 INFO @ Fri, 15 Feb 2019 08:01:27: 4000000 INFO @ Fri, 15 Feb 2019 08:01:28: 4000000 INFO @ Fri, 15 Feb 2019 08:01:32: 5000000 INFO @ Fri, 15 Feb 2019 08:01:32: 5000000 INFO @ Fri, 15 Feb 2019 08:01:34: 5000000 INFO @ Fri, 15 Feb 2019 08:01:37: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:01:37: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:01:37: #1 total tags in treatment: 2938887 INFO @ Fri, 15 Feb 2019 08:01:37: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:01:37: #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 08:01:37: #1 tags after filtering in treatment: 2661060 INFO @ Fri, 15 Feb 2019 08:01:37: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 15 Feb 2019 08:01:37: #1 finished! INFO @ Fri, 15 Feb 2019 08:01:37: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:01:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:01:37: #2 number of paired peaks: 36 WARNING @ Fri, 15 Feb 2019 08:01:37: Too few paired peaks (36) 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 08:01:37: Process for pairing-model is terminated! cat: ERX1173893.05_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 `ERX1173893.05_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 `ERX1173893.05_*.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 `ERX1173893.05_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 08:01:38: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:01:38: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:01:38: #1 total tags in treatment: 2938887 INFO @ Fri, 15 Feb 2019 08:01:38: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:01:38: #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 08:01:38: #1 tags after filtering in treatment: 2661060 INFO @ Fri, 15 Feb 2019 08:01:38: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 15 Feb 2019 08:01:38: #1 finished! INFO @ Fri, 15 Feb 2019 08:01:38: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:01:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:01:38: #2 number of paired peaks: 36 WARNING @ Fri, 15 Feb 2019 08:01:38: Too few paired peaks (36) 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 08:01:38: Process for pairing-model is terminated! cat: ERX1173893.10_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 `ERX1173893.10_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 `ERX1173893.10_*.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 `ERX1173893.10_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 08:01:39: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:01:39: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:01:39: #1 total tags in treatment: 2938887 INFO @ Fri, 15 Feb 2019 08:01:39: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:01:39: #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 08:01:39: #1 tags after filtering in treatment: 2661060 INFO @ Fri, 15 Feb 2019 08:01:39: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 15 Feb 2019 08:01:39: #1 finished! INFO @ Fri, 15 Feb 2019 08:01:39: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:01:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:01:40: #2 number of paired peaks: 36 WARNING @ Fri, 15 Feb 2019 08:01:40: Too few paired peaks (36) 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 08:01:40: Process for pairing-model is terminated! cat: ERX1173893.20_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): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `ERX1173893.20_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 `ERX1173893.20_*.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 `ERX1173893.20_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。