Job ID = 11632862 sra ファイルのダウンロード中... Completed: 84239K bytes transferred in 4 seconds (156500K 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 1266178 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1173815/ERR1094329.sra Written 1266178 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1173815/ERR1094329.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: 00:01:02 1266178 reads; of these: 1266178 (100.00%) were paired; of these: 79559 (6.28%) aligned concordantly 0 times 1065166 (84.12%) aligned concordantly exactly 1 time 121453 (9.59%) aligned concordantly >1 times ---- 79559 pairs aligned concordantly 0 times; of these: 23615 (29.68%) aligned discordantly 1 time ---- 55944 pairs aligned 0 times concordantly or discordantly; of these: 111888 mates make up the pairs; of these: 95479 (85.33%) aligned 0 times 9288 (8.30%) aligned exactly 1 time 7121 (6.36%) aligned >1 times 96.23% overall alignment rate Time searching: 00:01:02 Overall time: 00:01:02 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] 29750 / 1196096 = 0.0249 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 07:48:58: # Command line: callpeak -t ERX1173815.bam -f BAM -g 12100000 -n ERX1173815.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1173815.05 # format = BAM # ChIP-seq file = ['ERX1173815.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 07:48:58: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:48:58: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:48:58: # Command line: callpeak -t ERX1173815.bam -f BAM -g 12100000 -n ERX1173815.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1173815.20 # format = BAM # ChIP-seq file = ['ERX1173815.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 07:48:58: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:48:58: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:48:58: # Command line: callpeak -t ERX1173815.bam -f BAM -g 12100000 -n ERX1173815.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1173815.10 # format = BAM # ChIP-seq file = ['ERX1173815.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 07:48:58: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:48:58: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:49:05: 1000000 INFO @ Fri, 15 Feb 2019 07:49:05: 1000000 INFO @ Fri, 15 Feb 2019 07:49:05: 1000000 INFO @ Fri, 15 Feb 2019 07:49:12: 2000000 INFO @ Fri, 15 Feb 2019 07:49:13: 2000000 INFO @ Fri, 15 Feb 2019 07:49:13: 2000000 INFO @ Fri, 15 Feb 2019 07:49:14: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:49:14: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:49:14: #1 total tags in treatment: 1156972 INFO @ Fri, 15 Feb 2019 07:49:14: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:49:14: #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 07:49:14: #1 tags after filtering in treatment: 1105686 INFO @ Fri, 15 Feb 2019 07:49:14: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 15 Feb 2019 07:49:14: #1 finished! INFO @ Fri, 15 Feb 2019 07:49:14: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:49:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:49:14: #2 number of paired peaks: 27 WARNING @ Fri, 15 Feb 2019 07:49:14: Too few paired peaks (27) 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 07:49:14: Process for pairing-model is terminated! cat: ERX1173815.20_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 `ERX1173815.20_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 `ERX1173815.20_*.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 `ERX1173815.20_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 07:49:16: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:49:16: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:49:16: #1 total tags in treatment: 1156972 INFO @ Fri, 15 Feb 2019 07:49:16: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:49:16: #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 07:49:16: #1 tags after filtering in treatment: 1105686 INFO @ Fri, 15 Feb 2019 07:49:16: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 15 Feb 2019 07:49:16: #1 finished! INFO @ Fri, 15 Feb 2019 07:49:16: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:49:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:49:16: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:49:16: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:49:16: #1 total tags in treatment: 1156972 INFO @ Fri, 15 Feb 2019 07:49:16: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:49:16: #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 07:49:16: #2 number of paired peaks: 27 WARNING @ Fri, 15 Feb 2019 07:49:16: Too few paired peaks (27) 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 07:49:16: Process for pairing-model is terminated! INFO @ Fri, 15 Feb 2019 07:49:16: #1 tags after filtering in treatment: 1105686 INFO @ Fri, 15 Feb 2019 07:49:16: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 15 Feb 2019 07:49:16: #1 finished! INFO @ Fri, 15 Feb 2019 07:49:16: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:49:16: #2 looking for paired plus/minus strand peaks... cat: ERX1173815.05_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): 7 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `ERX1173815.05_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 `ERX1173815.05_*.xls': そのようなファイルやディレクトリはありません INFO @ Fri, 15 Feb 2019 07:49:16: #2 number of paired peaks: 27 WARNING @ Fri, 15 Feb 2019 07:49:16: Too few paired peaks (27) 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 07:49:16: Process for pairing-model is terminated! rm: cannot remove `ERX1173815.05_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 cat: ERX1173815.10_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): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `ERX1173815.10_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 `ERX1173815.10_*.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 `ERX1173815.10_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。