Job ID = 11633152 sra ファイルのダウンロード中... Completed: 209800K bytes transferred in 5 seconds (317843K 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 3407986 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1174088/ERR1094602.sra Written 3407986 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1174088/ERR1094602.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: 00:02:24 3407986 reads; of these: 3407986 (100.00%) were paired; of these: 278357 (8.17%) aligned concordantly 0 times 2909159 (85.36%) aligned concordantly exactly 1 time 220470 (6.47%) aligned concordantly >1 times ---- 278357 pairs aligned concordantly 0 times; of these: 19446 (6.99%) aligned discordantly 1 time ---- 258911 pairs aligned 0 times concordantly or discordantly; of these: 517822 mates make up the pairs; of these: 496471 (95.88%) aligned 0 times 16059 (3.10%) aligned exactly 1 time 5292 (1.02%) aligned >1 times 92.72% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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] 232441 / 3147478 = 0.0738 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 08:26:20: # Command line: callpeak -t ERX1174088.bam -f BAM -g 12100000 -n ERX1174088.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1174088.05 # format = BAM # ChIP-seq file = ['ERX1174088.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 08:26:20: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:26:20: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:26:20: # Command line: callpeak -t ERX1174088.bam -f BAM -g 12100000 -n ERX1174088.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1174088.20 # format = BAM # ChIP-seq file = ['ERX1174088.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 08:26:20: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:26:20: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:26:20: # Command line: callpeak -t ERX1174088.bam -f BAM -g 12100000 -n ERX1174088.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1174088.10 # format = BAM # ChIP-seq file = ['ERX1174088.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 08:26:20: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:26:20: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:26:26: 1000000 INFO @ Fri, 15 Feb 2019 08:26:26: 1000000 INFO @ Fri, 15 Feb 2019 08:26:28: 1000000 INFO @ Fri, 15 Feb 2019 08:26:32: 2000000 INFO @ Fri, 15 Feb 2019 08:26:32: 2000000 INFO @ Fri, 15 Feb 2019 08:26:36: 2000000 INFO @ Fri, 15 Feb 2019 08:26:39: 3000000 INFO @ Fri, 15 Feb 2019 08:26:39: 3000000 INFO @ Fri, 15 Feb 2019 08:26:43: 3000000 INFO @ Fri, 15 Feb 2019 08:26:45: 4000000 INFO @ Fri, 15 Feb 2019 08:26:45: 4000000 INFO @ Fri, 15 Feb 2019 08:26:49: 4000000 INFO @ Fri, 15 Feb 2019 08:26:51: 5000000 INFO @ Fri, 15 Feb 2019 08:26:51: 5000000 INFO @ Fri, 15 Feb 2019 08:26:55: 5000000 INFO @ Fri, 15 Feb 2019 08:26:56: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:26:56: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:26:56: #1 total tags in treatment: 2898418 INFO @ Fri, 15 Feb 2019 08:26:56: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:26:56: #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 08:26:56: #1 tags after filtering in treatment: 2641489 INFO @ Fri, 15 Feb 2019 08:26:56: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 15 Feb 2019 08:26:56: #1 finished! INFO @ Fri, 15 Feb 2019 08:26:56: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:26:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:26:56: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:26:56: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:26:56: #1 total tags in treatment: 2898418 INFO @ Fri, 15 Feb 2019 08:26:56: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:26:56: #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 08:26:56: #2 number of paired peaks: 34 WARNING @ Fri, 15 Feb 2019 08:26:56: Too few paired peaks (34) 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 08:26:56: Process for pairing-model is terminated! cat: ERX1174088.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Fri, 15 Feb 2019 08:26:57: #1 tags after filtering in treatment: 2641489 INFO @ Fri, 15 Feb 2019 08:26:57: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 15 Feb 2019 08:26:57: #1 finished! INFO @ Fri, 15 Feb 2019 08:26:57: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:26:57: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `ERX1174088.20_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 `ERX1174088.20_*.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 `ERX1174088.20_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 08:26:57: #2 number of paired peaks: 34 WARNING @ Fri, 15 Feb 2019 08:26:57: Too few paired peaks (34) 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 08:26:57: Process for pairing-model is terminated! cat: ERX1174088.05_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 `ERX1174088.05_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 `ERX1174088.05_*.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 `ERX1174088.05_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 08:27:00: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:27:00: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:27:00: #1 total tags in treatment: 2898418 INFO @ Fri, 15 Feb 2019 08:27:00: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:27:00: #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 08:27:00: #1 tags after filtering in treatment: 2641489 INFO @ Fri, 15 Feb 2019 08:27:00: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 15 Feb 2019 08:27:00: #1 finished! INFO @ Fri, 15 Feb 2019 08:27:00: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:27:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:27:00: #2 number of paired peaks: 34 WARNING @ Fri, 15 Feb 2019 08:27:00: Too few paired peaks (34) 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 08:27:00: Process for pairing-model is terminated! cat: ERX1174088.10_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 `ERX1174088.10_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 `ERX1174088.10_*.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 `ERX1174088.10_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。