Job ID = 10937697 sra ファイルのダウンロード中... Completed: 220243K bytes transferred in 20 seconds (87684K 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 7293708 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3467910/SRR6372873.sra Written 7293708 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3467910/SRR6372873.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: 00:14:28 7293708 reads; of these: 7293708 (100.00%) were paired; of these: 2349347 (32.21%) aligned concordantly 0 times 2130447 (29.21%) aligned concordantly exactly 1 time 2813914 (38.58%) aligned concordantly >1 times ---- 2349347 pairs aligned concordantly 0 times; of these: 38887 (1.66%) aligned discordantly 1 time ---- 2310460 pairs aligned 0 times concordantly or discordantly; of these: 4620920 mates make up the pairs; of these: 4254939 (92.08%) aligned 0 times 131863 (2.85%) aligned exactly 1 time 234118 (5.07%) aligned >1 times 70.83% overall alignment rate Time searching: 00:14:28 Overall time: 00:14:28 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] 215882 / 4966835 = 0.0435 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, 10 Aug 2018 03:09:44: # Command line: callpeak -t SRX3467910.bam -f BAM -g 12100000 -n SRX3467910.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3467910.05 # format = BAM # ChIP-seq file = ['SRX3467910.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, 10 Aug 2018 03:09:44: #1 read tag files... INFO @ Fri, 10 Aug 2018 03:09:44: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 03:09:44: # Command line: callpeak -t SRX3467910.bam -f BAM -g 12100000 -n SRX3467910.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3467910.20 # format = BAM # ChIP-seq file = ['SRX3467910.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, 10 Aug 2018 03:09:44: #1 read tag files... INFO @ Fri, 10 Aug 2018 03:09:44: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 03:09:44: # Command line: callpeak -t SRX3467910.bam -f BAM -g 12100000 -n SRX3467910.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3467910.10 # format = BAM # ChIP-seq file = ['SRX3467910.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, 10 Aug 2018 03:09:44: #1 read tag files... INFO @ Fri, 10 Aug 2018 03:09:44: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 03:09:50: 1000000 INFO @ Fri, 10 Aug 2018 03:09:50: 1000000 INFO @ Fri, 10 Aug 2018 03:09:50: 1000000 INFO @ Fri, 10 Aug 2018 03:09:56: 2000000 INFO @ Fri, 10 Aug 2018 03:09:56: 2000000 INFO @ Fri, 10 Aug 2018 03:09:56: 2000000 INFO @ Fri, 10 Aug 2018 03:10:01: 3000000 INFO @ Fri, 10 Aug 2018 03:10:01: 3000000 INFO @ Fri, 10 Aug 2018 03:10:02: 3000000 INFO @ Fri, 10 Aug 2018 03:10:07: 4000000 INFO @ Fri, 10 Aug 2018 03:10:07: 4000000 INFO @ Fri, 10 Aug 2018 03:10:08: 4000000 INFO @ Fri, 10 Aug 2018 03:10:13: 5000000 INFO @ Fri, 10 Aug 2018 03:10:13: 5000000 INFO @ Fri, 10 Aug 2018 03:10:14: 5000000 INFO @ Fri, 10 Aug 2018 03:10:18: 6000000 INFO @ Fri, 10 Aug 2018 03:10:19: 6000000 INFO @ Fri, 10 Aug 2018 03:10:20: 6000000 INFO @ Fri, 10 Aug 2018 03:10:24: 7000000 INFO @ Fri, 10 Aug 2018 03:10:24: 7000000 INFO @ Fri, 10 Aug 2018 03:10:26: 7000000 INFO @ Fri, 10 Aug 2018 03:10:30: 8000000 INFO @ Fri, 10 Aug 2018 03:10:30: 8000000 INFO @ Fri, 10 Aug 2018 03:10:33: 8000000 INFO @ Fri, 10 Aug 2018 03:10:36: 9000000 INFO @ Fri, 10 Aug 2018 03:10:36: 9000000 INFO @ Fri, 10 Aug 2018 03:10:39: 9000000 INFO @ Fri, 10 Aug 2018 03:10:41: #1 tag size is determined as 36 bps INFO @ Fri, 10 Aug 2018 03:10:41: #1 tag size = 36 INFO @ Fri, 10 Aug 2018 03:10:41: #1 total tags in treatment: 4729101 INFO @ Fri, 10 Aug 2018 03:10:41: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 03:10:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 03:10:41: #1 tags after filtering in treatment: 2315789 INFO @ Fri, 10 Aug 2018 03:10:41: #1 Redundant rate of treatment: 0.51 INFO @ Fri, 10 Aug 2018 03:10:41: #1 finished! INFO @ Fri, 10 Aug 2018 03:10:41: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 03:10:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 03:10:41: #2 number of paired peaks: 86 WARNING @ Fri, 10 Aug 2018 03:10:41: Too few paired peaks (86) 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, 10 Aug 2018 03:10:41: Process for pairing-model is terminated! cat: SRX3467910.20_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 `SRX3467910.20_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 `SRX3467910.20_*.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 `SRX3467910.20_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, 10 Aug 2018 03:10:42: #1 tag size is determined as 36 bps INFO @ Fri, 10 Aug 2018 03:10:42: #1 tag size = 36 INFO @ Fri, 10 Aug 2018 03:10:42: #1 total tags in treatment: 4729101 INFO @ Fri, 10 Aug 2018 03:10:42: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 03:10:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 03:10:42: #1 tags after filtering in treatment: 2315789 INFO @ Fri, 10 Aug 2018 03:10:42: #1 Redundant rate of treatment: 0.51 INFO @ Fri, 10 Aug 2018 03:10:42: #1 finished! INFO @ Fri, 10 Aug 2018 03:10:42: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 03:10:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 03:10:42: #2 number of paired peaks: 86 WARNING @ Fri, 10 Aug 2018 03:10:42: Too few paired peaks (86) 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, 10 Aug 2018 03:10:42: Process for pairing-model is terminated! cat: SRX3467910.05_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 `SRX3467910.05_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 `SRX3467910.05_*.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 `SRX3467910.05_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, 10 Aug 2018 03:10:44: #1 tag size is determined as 36 bps INFO @ Fri, 10 Aug 2018 03:10:44: #1 tag size = 36 INFO @ Fri, 10 Aug 2018 03:10:44: #1 total tags in treatment: 4729101 INFO @ Fri, 10 Aug 2018 03:10:44: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 03:10:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 03:10:44: #1 tags after filtering in treatment: 2315789 INFO @ Fri, 10 Aug 2018 03:10:44: #1 Redundant rate of treatment: 0.51 INFO @ Fri, 10 Aug 2018 03:10:44: #1 finished! INFO @ Fri, 10 Aug 2018 03:10:44: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 03:10:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 03:10:45: #2 number of paired peaks: 86 WARNING @ Fri, 10 Aug 2018 03:10:45: Too few paired peaks (86) 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, 10 Aug 2018 03:10:45: Process for pairing-model is terminated! cat: SRX3467910.10_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 `SRX3467910.10_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 `SRX3467910.10_*.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 `SRX3467910.10_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。