Job ID = 11633528 sra ファイルのダウンロード中... Completed: 247735K bytes transferred in 4 seconds (414332K 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/ERX1236305/ERR1162898.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236305/ERR1162898.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: 00:02:39 4000000 reads; of these: 4000000 (100.00%) were paired; of these: 855557 (21.39%) aligned concordantly 0 times 2833084 (70.83%) aligned concordantly exactly 1 time 311359 (7.78%) aligned concordantly >1 times ---- 855557 pairs aligned concordantly 0 times; of these: 38081 (4.45%) aligned discordantly 1 time ---- 817476 pairs aligned 0 times concordantly or discordantly; of these: 1634952 mates make up the pairs; of these: 1613853 (98.71%) aligned 0 times 12521 (0.77%) aligned exactly 1 time 8578 (0.52%) aligned >1 times 79.83% overall alignment rate Time searching: 00:02:39 Overall time: 00:02:39 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] 1379056 / 3181774 = 0.4334 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 09:04:55: # Command line: callpeak -t ERX1236305.bam -f BAM -g 12100000 -n ERX1236305.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236305.10 # format = BAM # ChIP-seq file = ['ERX1236305.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 09:04:55: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:04:55: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:04:55: # Command line: callpeak -t ERX1236305.bam -f BAM -g 12100000 -n ERX1236305.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236305.05 # format = BAM # ChIP-seq file = ['ERX1236305.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 09:04:55: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:04:55: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:04:55: # Command line: callpeak -t ERX1236305.bam -f BAM -g 12100000 -n ERX1236305.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236305.20 # format = BAM # ChIP-seq file = ['ERX1236305.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 09:04:55: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:04:55: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:05:01: 1000000 INFO @ Fri, 15 Feb 2019 09:05:02: 1000000 INFO @ Fri, 15 Feb 2019 09:05:02: 1000000 INFO @ Fri, 15 Feb 2019 09:05:08: 2000000 INFO @ Fri, 15 Feb 2019 09:05:08: 2000000 INFO @ Fri, 15 Feb 2019 09:05:08: 2000000 INFO @ Fri, 15 Feb 2019 09:05:14: 3000000 INFO @ Fri, 15 Feb 2019 09:05:15: 3000000 INFO @ Fri, 15 Feb 2019 09:05:15: 3000000 INFO @ Fri, 15 Feb 2019 09:05:18: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:05:18: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:05:18: #1 total tags in treatment: 1778453 INFO @ Fri, 15 Feb 2019 09:05:18: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:05:18: #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 09:05:18: #1 tags after filtering in treatment: 1635961 INFO @ Fri, 15 Feb 2019 09:05:18: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 15 Feb 2019 09:05:18: #1 finished! INFO @ Fri, 15 Feb 2019 09:05:18: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:05:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:05:19: #2 number of paired peaks: 77 WARNING @ Fri, 15 Feb 2019 09:05:19: Too few paired peaks (77) 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 09:05:19: Process for pairing-model is terminated! cat: ERX1236305.10_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 `ERX1236305.10_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 `ERX1236305.10_*.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 `ERX1236305.10_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 09:05:19: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:05:19: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:05:19: #1 total tags in treatment: 1778453 INFO @ Fri, 15 Feb 2019 09:05:19: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:05:19: #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 09:05:19: #1 tags after filtering in treatment: 1635961 INFO @ Fri, 15 Feb 2019 09:05:19: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 15 Feb 2019 09:05:19: #1 finished! INFO @ Fri, 15 Feb 2019 09:05:19: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:05:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:05:19: #2 number of paired peaks: 77 WARNING @ Fri, 15 Feb 2019 09:05:19: Too few paired peaks (77) 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 09:05:19: Process for pairing-model is terminated! cat: ERX1236305.05_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 `ERX1236305.05_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 `ERX1236305.05_*.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 `ERX1236305.05_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 09:05:19: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:05:19: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:05:19: #1 total tags in treatment: 1778453 INFO @ Fri, 15 Feb 2019 09:05:19: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:05:19: #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 09:05:19: #1 tags after filtering in treatment: 1635961 INFO @ Fri, 15 Feb 2019 09:05:19: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 15 Feb 2019 09:05:19: #1 finished! INFO @ Fri, 15 Feb 2019 09:05:19: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:05:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:05:20: #2 number of paired peaks: 77 WARNING @ Fri, 15 Feb 2019 09:05:20: Too few paired peaks (77) 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 09:05:20: Process for pairing-model is terminated! cat: ERX1236305.20_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 `ERX1236305.20_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 `ERX1236305.20_*.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 `ERX1236305.20_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。