Job ID = 11193130 sra ファイルのダウンロード中... Completed: 632196K bytes transferred in 24 seconds (214630K 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 19084962 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337722/SRR7467881.sra Written 19084962 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337722/SRR7467881.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: 00:04:49 19084962 reads; of these: 19084962 (100.00%) were paired; of these: 17673040 (92.60%) aligned concordantly 0 times 1183395 (6.20%) aligned concordantly exactly 1 time 228527 (1.20%) aligned concordantly >1 times ---- 17673040 pairs aligned concordantly 0 times; of these: 845292 (4.78%) aligned discordantly 1 time ---- 16827748 pairs aligned 0 times concordantly or discordantly; of these: 33655496 mates make up the pairs; of these: 31112796 (92.44%) aligned 0 times 1850514 (5.50%) aligned exactly 1 time 692186 (2.06%) aligned >1 times 18.49% overall alignment rate Time searching: 00:04:49 Overall time: 00:04:49 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] 569692 / 2058156 = 0.2768 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 @ Sat, 15 Sep 2018 11:07:58: # Command line: callpeak -t SRX4337722.bam -f BAM -g 12100000 -n SRX4337722.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4337722.20 # format = BAM # ChIP-seq file = ['SRX4337722.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 @ Sat, 15 Sep 2018 11:07:58: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:07:58: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:07:58: # Command line: callpeak -t SRX4337722.bam -f BAM -g 12100000 -n SRX4337722.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4337722.05 # format = BAM # ChIP-seq file = ['SRX4337722.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 @ Sat, 15 Sep 2018 11:07:58: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:07:58: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:07:58: # Command line: callpeak -t SRX4337722.bam -f BAM -g 12100000 -n SRX4337722.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4337722.10 # format = BAM # ChIP-seq file = ['SRX4337722.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 @ Sat, 15 Sep 2018 11:07:58: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:07:58: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:08:04: 1000000 INFO @ Sat, 15 Sep 2018 11:08:04: 1000000 INFO @ Sat, 15 Sep 2018 11:08:04: 1000000 INFO @ Sat, 15 Sep 2018 11:08:09: 2000000 INFO @ Sat, 15 Sep 2018 11:08:10: 2000000 INFO @ Sat, 15 Sep 2018 11:08:10: 2000000 INFO @ Sat, 15 Sep 2018 11:08:15: 3000000 INFO @ Sat, 15 Sep 2018 11:08:16: 3000000 INFO @ Sat, 15 Sep 2018 11:08:16: 3000000 INFO @ Sat, 15 Sep 2018 11:08:20: 4000000 INFO @ Sat, 15 Sep 2018 11:08:21: 4000000 INFO @ Sat, 15 Sep 2018 11:08:21: 4000000 INFO @ Sat, 15 Sep 2018 11:08:26: 5000000 INFO @ Sat, 15 Sep 2018 11:08:27: 5000000 INFO @ Sat, 15 Sep 2018 11:08:27: 5000000 INFO @ Sat, 15 Sep 2018 11:08:31: #1 tag size is determined as 44 bps INFO @ Sat, 15 Sep 2018 11:08:31: #1 tag size = 44 INFO @ Sat, 15 Sep 2018 11:08:31: #1 total tags in treatment: 1015942 INFO @ Sat, 15 Sep 2018 11:08:31: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:08:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:08:31: #1 tags after filtering in treatment: 883697 INFO @ Sat, 15 Sep 2018 11:08:31: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Sep 2018 11:08:31: #1 finished! INFO @ Sat, 15 Sep 2018 11:08:31: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:08:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:08:31: #2 number of paired peaks: 70 WARNING @ Sat, 15 Sep 2018 11:08:31: Too few paired peaks (70) 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 @ Sat, 15 Sep 2018 11:08:31: Process for pairing-model is terminated! cat: SRX4337722.10_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4337722.10_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 `SRX4337722.10_*.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 `SRX4337722.10_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 @ Sat, 15 Sep 2018 11:08:32: #1 tag size is determined as 44 bps INFO @ Sat, 15 Sep 2018 11:08:32: #1 tag size = 44 INFO @ Sat, 15 Sep 2018 11:08:32: #1 total tags in treatment: 1015942 INFO @ Sat, 15 Sep 2018 11:08:32: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:08:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:08:32: #1 tags after filtering in treatment: 883697 INFO @ Sat, 15 Sep 2018 11:08:32: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Sep 2018 11:08:32: #1 finished! INFO @ Sat, 15 Sep 2018 11:08:32: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:08:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:08:32: #2 number of paired peaks: 70 WARNING @ Sat, 15 Sep 2018 11:08:32: Too few paired peaks (70) 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 @ Sat, 15 Sep 2018 11:08:32: Process for pairing-model is terminated! cat: SRX4337722.05_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): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4337722.05_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 `SRX4337722.05_*.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 `SRX4337722.05_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 @ Sat, 15 Sep 2018 11:08:32: #1 tag size is determined as 44 bps INFO @ Sat, 15 Sep 2018 11:08:32: #1 tag size = 44 INFO @ Sat, 15 Sep 2018 11:08:32: #1 total tags in treatment: 1015942 INFO @ Sat, 15 Sep 2018 11:08:32: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:08:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:08:32: #1 tags after filtering in treatment: 883697 INFO @ Sat, 15 Sep 2018 11:08:32: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Sep 2018 11:08:32: #1 finished! INFO @ Sat, 15 Sep 2018 11:08:32: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:08:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:08:32: #2 number of paired peaks: 70 WARNING @ Sat, 15 Sep 2018 11:08:32: Too few paired peaks (70) 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 @ Sat, 15 Sep 2018 11:08:32: Process for pairing-model is terminated! cat: SRX4337722.20_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): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4337722.20_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 `SRX4337722.20_*.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 `SRX4337722.20_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。