Job ID = 11632797 sra ファイルのダウンロード中... Completed: 280072K bytes transferred in 6 seconds (367157K 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/ERX1173754/ERR1094268.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1173754/ERR1094268.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: 00:02:57 4000000 reads; of these: 4000000 (100.00%) were paired; of these: 185091 (4.63%) aligned concordantly 0 times 3481298 (87.03%) aligned concordantly exactly 1 time 333611 (8.34%) aligned concordantly >1 times ---- 185091 pairs aligned concordantly 0 times; of these: 13045 (7.05%) aligned discordantly 1 time ---- 172046 pairs aligned 0 times concordantly or discordantly; of these: 344092 mates make up the pairs; of these: 327955 (95.31%) aligned 0 times 11859 (3.45%) aligned exactly 1 time 4278 (1.24%) aligned >1 times 95.90% overall alignment rate Time searching: 00:02:57 Overall time: 00:02:57 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] 42731 / 3825404 = 0.0112 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 07:44:12: # Command line: callpeak -t ERX1173754.bam -f BAM -g 12100000 -n ERX1173754.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1173754.05 # format = BAM # ChIP-seq file = ['ERX1173754.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 07:44:12: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:44:12: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:44:12: # Command line: callpeak -t ERX1173754.bam -f BAM -g 12100000 -n ERX1173754.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1173754.20 # format = BAM # ChIP-seq file = ['ERX1173754.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 07:44:12: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:44:12: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:44:12: # Command line: callpeak -t ERX1173754.bam -f BAM -g 12100000 -n ERX1173754.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1173754.10 # format = BAM # ChIP-seq file = ['ERX1173754.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 07:44:12: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:44:12: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:44:18: 1000000 INFO @ Fri, 15 Feb 2019 07:44:18: 1000000 INFO @ Fri, 15 Feb 2019 07:44:18: 1000000 INFO @ Fri, 15 Feb 2019 07:44:24: 2000000 INFO @ Fri, 15 Feb 2019 07:44:24: 2000000 INFO @ Fri, 15 Feb 2019 07:44:24: 2000000 INFO @ Fri, 15 Feb 2019 07:44:30: 3000000 INFO @ Fri, 15 Feb 2019 07:44:30: 3000000 INFO @ Fri, 15 Feb 2019 07:44:31: 3000000 INFO @ Fri, 15 Feb 2019 07:44:36: 4000000 INFO @ Fri, 15 Feb 2019 07:44:36: 4000000 INFO @ Fri, 15 Feb 2019 07:44:37: 4000000 INFO @ Fri, 15 Feb 2019 07:44:41: 5000000 INFO @ Fri, 15 Feb 2019 07:44:42: 5000000 INFO @ Fri, 15 Feb 2019 07:44:43: 5000000 INFO @ Fri, 15 Feb 2019 07:44:47: 6000000 INFO @ Fri, 15 Feb 2019 07:44:49: 6000000 INFO @ Fri, 15 Feb 2019 07:44:50: 6000000 INFO @ Fri, 15 Feb 2019 07:44:53: 7000000 INFO @ Fri, 15 Feb 2019 07:44:55: 7000000 INFO @ Fri, 15 Feb 2019 07:44:56: 7000000 INFO @ Fri, 15 Feb 2019 07:44:57: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:44:57: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:44:57: #1 total tags in treatment: 3772217 INFO @ Fri, 15 Feb 2019 07:44:57: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:44:57: #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 07:44:57: #1 tags after filtering in treatment: 3327155 INFO @ Fri, 15 Feb 2019 07:44:57: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 15 Feb 2019 07:44:57: #1 finished! INFO @ Fri, 15 Feb 2019 07:44:57: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:44:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:44:57: #2 number of paired peaks: 14 WARNING @ Fri, 15 Feb 2019 07:44:57: Too few paired peaks (14) 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 07:44:57: Process for pairing-model is terminated! cat: ERX1173754.20_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 `ERX1173754.20_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 `ERX1173754.20_*.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 `ERX1173754.20_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 07:44:59: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:44:59: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:44:59: #1 total tags in treatment: 3772217 INFO @ Fri, 15 Feb 2019 07:44:59: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:44:59: #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 07:44:59: #1 tags after filtering in treatment: 3327155 INFO @ Fri, 15 Feb 2019 07:44:59: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 15 Feb 2019 07:44:59: #1 finished! INFO @ Fri, 15 Feb 2019 07:44:59: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:44:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:44:59: #2 number of paired peaks: 14 WARNING @ Fri, 15 Feb 2019 07:44:59: Too few paired peaks (14) 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 07:44:59: Process for pairing-model is terminated! cat: ERX1173754.05_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 `ERX1173754.05_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 `ERX1173754.05_*.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 `ERX1173754.05_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 07:45:00: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:45:00: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:45:00: #1 total tags in treatment: 3772217 INFO @ Fri, 15 Feb 2019 07:45:00: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:45:00: #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 07:45:00: #1 tags after filtering in treatment: 3327155 INFO @ Fri, 15 Feb 2019 07:45:00: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 15 Feb 2019 07:45:00: #1 finished! INFO @ Fri, 15 Feb 2019 07:45:00: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:45:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:45:00: #2 number of paired peaks: 14 WARNING @ Fri, 15 Feb 2019 07:45:00: Too few paired peaks (14) 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 07:45:00: Process for pairing-model is terminated! cat: ERX1173754.10_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 `ERX1173754.10_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 `ERX1173754.10_*.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 `ERX1173754.10_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。