Job ID = 11633451 sra ファイルのダウンロード中... Completed: 244523K bytes transferred in 5 seconds (364463K 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/ERX1236228/ERR1162821.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236228/ERR1162821.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: 00:03:06 4000000 reads; of these: 4000000 (100.00%) were paired; of these: 532303 (13.31%) aligned concordantly 0 times 3160830 (79.02%) aligned concordantly exactly 1 time 306867 (7.67%) aligned concordantly >1 times ---- 532303 pairs aligned concordantly 0 times; of these: 126100 (23.69%) aligned discordantly 1 time ---- 406203 pairs aligned 0 times concordantly or discordantly; of these: 812406 mates make up the pairs; of these: 751896 (92.55%) aligned 0 times 31822 (3.92%) aligned exactly 1 time 28688 (3.53%) aligned >1 times 90.60% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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] 805144 / 3593065 = 0.2241 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 09:05:28: # Command line: callpeak -t ERX1236228.bam -f BAM -g 12100000 -n ERX1236228.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236228.10 # format = BAM # ChIP-seq file = ['ERX1236228.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 09:05:28: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:05:28: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:05:28: # Command line: callpeak -t ERX1236228.bam -f BAM -g 12100000 -n ERX1236228.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236228.05 # format = BAM # ChIP-seq file = ['ERX1236228.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 09:05:28: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:05:28: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:05:28: # Command line: callpeak -t ERX1236228.bam -f BAM -g 12100000 -n ERX1236228.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236228.20 # format = BAM # ChIP-seq file = ['ERX1236228.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 09:05:28: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:05:28: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:05:33: 1000000 INFO @ Fri, 15 Feb 2019 09:05:33: 1000000 INFO @ Fri, 15 Feb 2019 09:05:33: 1000000 INFO @ Fri, 15 Feb 2019 09:05:39: 2000000 INFO @ Fri, 15 Feb 2019 09:05:39: 2000000 INFO @ Fri, 15 Feb 2019 09:05:39: 2000000 INFO @ Fri, 15 Feb 2019 09:05:45: 3000000 INFO @ Fri, 15 Feb 2019 09:05:45: 3000000 INFO @ Fri, 15 Feb 2019 09:05:45: 3000000 INFO @ Fri, 15 Feb 2019 09:05:50: 4000000 INFO @ Fri, 15 Feb 2019 09:05:51: 4000000 INFO @ Fri, 15 Feb 2019 09:05:51: 4000000 INFO @ Fri, 15 Feb 2019 09:05:56: 5000000 INFO @ Fri, 15 Feb 2019 09:05:57: 5000000 INFO @ Fri, 15 Feb 2019 09:05:58: 5000000 INFO @ Fri, 15 Feb 2019 09:06:00: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:06:00: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:06:00: #1 total tags in treatment: 2689586 INFO @ Fri, 15 Feb 2019 09:06:00: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:06:00: #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 09:06:00: #1 tags after filtering in treatment: 2450233 INFO @ Fri, 15 Feb 2019 09:06:00: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 15 Feb 2019 09:06:00: #1 finished! INFO @ Fri, 15 Feb 2019 09:06:00: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:06:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:06:00: #2 number of paired peaks: 40 WARNING @ Fri, 15 Feb 2019 09:06:00: Too few paired peaks (40) 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 09:06:00: Process for pairing-model is terminated! cat: ERX1236228.05_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `ERX1236228.05_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 `ERX1236228.05_*.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 `ERX1236228.05_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 09:06:01: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:06:01: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:06:01: #1 total tags in treatment: 2689586 INFO @ Fri, 15 Feb 2019 09:06:01: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:06:01: #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 09:06:01: #1 tags after filtering in treatment: 2450233 INFO @ Fri, 15 Feb 2019 09:06:01: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 15 Feb 2019 09:06:01: #1 finished! INFO @ Fri, 15 Feb 2019 09:06:01: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:06:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:06:01: #2 number of paired peaks: 40 WARNING @ Fri, 15 Feb 2019 09:06:01: Too few paired peaks (40) 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 09:06:01: Process for pairing-model is terminated! cat: ERX1236228.20_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `ERX1236228.20_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 `ERX1236228.20_*.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 `ERX1236228.20_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 09:06:02: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:06:02: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:06:02: #1 total tags in treatment: 2689586 INFO @ Fri, 15 Feb 2019 09:06:02: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:06:02: #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 09:06:02: #1 tags after filtering in treatment: 2450233 INFO @ Fri, 15 Feb 2019 09:06:02: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 15 Feb 2019 09:06:02: #1 finished! INFO @ Fri, 15 Feb 2019 09:06:02: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:06:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:06:02: #2 number of paired peaks: 40 WARNING @ Fri, 15 Feb 2019 09:06:02: Too few paired peaks (40) 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 09:06:02: Process for pairing-model is terminated! cat: ERX1236228.10_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 `ERX1236228.10_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 `ERX1236228.10_*.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 `ERX1236228.10_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。