Job ID = 11245145 sra ファイルのダウンロード中... Completed: 27700K bytes transferred in 3 seconds (71261K bits/sec), in 1 file. Completed: 223945K bytes transferred in 5 seconds (338065K 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 590239 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669595/SRR7818170.sra Written 590239 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669595/SRR7818170.sra Read 5990394 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669595/SRR7818171.sra Written 5990394 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669595/SRR7818171.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 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: 00:04:53 6580633 reads; of these: 6580633 (100.00%) were paired; of these: 592873 (9.01%) aligned concordantly 0 times 5222716 (79.36%) aligned concordantly exactly 1 time 765044 (11.63%) aligned concordantly >1 times ---- 592873 pairs aligned concordantly 0 times; of these: 22327 (3.77%) aligned discordantly 1 time ---- 570546 pairs aligned 0 times concordantly or discordantly; of these: 1141092 mates make up the pairs; of these: 973280 (85.29%) aligned 0 times 93561 (8.20%) aligned exactly 1 time 74251 (6.51%) aligned >1 times 92.60% overall alignment rate Time searching: 00:04:53 Overall time: 00:04:54 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_sort_core] merging from 8 files... [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] 1138248 / 6005193 = 0.1895 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 @ Tue, 09 Oct 2018 23:41:56: # Command line: callpeak -t SRX4669595.bam -f BAM -g 12100000 -n SRX4669595.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669595.10 # format = BAM # ChIP-seq file = ['SRX4669595.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 @ Tue, 09 Oct 2018 23:41:56: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:41:56: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:41:56: # Command line: callpeak -t SRX4669595.bam -f BAM -g 12100000 -n SRX4669595.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669595.20 # format = BAM # ChIP-seq file = ['SRX4669595.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 @ Tue, 09 Oct 2018 23:41:56: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:41:56: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:41:56: # Command line: callpeak -t SRX4669595.bam -f BAM -g 12100000 -n SRX4669595.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669595.05 # format = BAM # ChIP-seq file = ['SRX4669595.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 @ Tue, 09 Oct 2018 23:41:56: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:41:56: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:42:02: 1000000 INFO @ Tue, 09 Oct 2018 23:42:02: 1000000 INFO @ Tue, 09 Oct 2018 23:42:02: 1000000 INFO @ Tue, 09 Oct 2018 23:42:07: 2000000 INFO @ Tue, 09 Oct 2018 23:42:08: 2000000 INFO @ Tue, 09 Oct 2018 23:42:08: 2000000 INFO @ Tue, 09 Oct 2018 23:42:13: 3000000 INFO @ Tue, 09 Oct 2018 23:42:13: 3000000 INFO @ Tue, 09 Oct 2018 23:42:14: 3000000 INFO @ Tue, 09 Oct 2018 23:42:18: 4000000 INFO @ Tue, 09 Oct 2018 23:42:19: 4000000 INFO @ Tue, 09 Oct 2018 23:42:20: 4000000 INFO @ Tue, 09 Oct 2018 23:42:24: 5000000 INFO @ Tue, 09 Oct 2018 23:42:25: 5000000 INFO @ Tue, 09 Oct 2018 23:42:26: 5000000 INFO @ Tue, 09 Oct 2018 23:42:29: 6000000 INFO @ Tue, 09 Oct 2018 23:42:31: 6000000 INFO @ Tue, 09 Oct 2018 23:42:33: 6000000 INFO @ Tue, 09 Oct 2018 23:42:34: 7000000 INFO @ Tue, 09 Oct 2018 23:42:38: 7000000 INFO @ Tue, 09 Oct 2018 23:42:39: 7000000 INFO @ Tue, 09 Oct 2018 23:42:40: 8000000 INFO @ Tue, 09 Oct 2018 23:42:44: 8000000 INFO @ Tue, 09 Oct 2018 23:42:45: 8000000 INFO @ Tue, 09 Oct 2018 23:42:46: 9000000 INFO @ Tue, 09 Oct 2018 23:42:50: 9000000 INFO @ Tue, 09 Oct 2018 23:42:51: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:42:51: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:42:51: #1 total tags in treatment: 4853275 INFO @ Tue, 09 Oct 2018 23:42:51: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:42:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:42:51: #1 tags after filtering in treatment: 3960106 INFO @ Tue, 09 Oct 2018 23:42:51: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 09 Oct 2018 23:42:51: #1 finished! INFO @ Tue, 09 Oct 2018 23:42:51: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:42:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:42:51: #2 number of paired peaks: 31 WARNING @ Tue, 09 Oct 2018 23:42:51: Too few paired peaks (31) 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 @ Tue, 09 Oct 2018 23:42:51: Process for pairing-model is terminated! cat: SRX4669595.05_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 `SRX4669595.05_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 `SRX4669595.05_*.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 `SRX4669595.05_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 @ Tue, 09 Oct 2018 23:42:51: 9000000 INFO @ Tue, 09 Oct 2018 23:42:55: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:42:55: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:42:55: #1 total tags in treatment: 4853275 INFO @ Tue, 09 Oct 2018 23:42:55: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:42:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:42:55: #1 tags after filtering in treatment: 3960106 INFO @ Tue, 09 Oct 2018 23:42:55: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 09 Oct 2018 23:42:55: #1 finished! INFO @ Tue, 09 Oct 2018 23:42:55: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:42:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:42:56: #2 number of paired peaks: 31 WARNING @ Tue, 09 Oct 2018 23:42:56: Too few paired peaks (31) 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 @ Tue, 09 Oct 2018 23:42:56: Process for pairing-model is terminated! cat: SRX4669595.20_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 `SRX4669595.20_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 `SRX4669595.20_*.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 `SRX4669595.20_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 @ Tue, 09 Oct 2018 23:42:57: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:42:57: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:42:57: #1 total tags in treatment: 4853275 INFO @ Tue, 09 Oct 2018 23:42:57: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:42:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:42:57: #1 tags after filtering in treatment: 3960106 INFO @ Tue, 09 Oct 2018 23:42:57: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 09 Oct 2018 23:42:57: #1 finished! INFO @ Tue, 09 Oct 2018 23:42:57: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:42:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:42:57: #2 number of paired peaks: 31 WARNING @ Tue, 09 Oct 2018 23:42:57: Too few paired peaks (31) 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 @ Tue, 09 Oct 2018 23:42:57: Process for pairing-model is terminated! cat: SRX4669595.10_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): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669595.10_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 `SRX4669595.10_*.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 `SRX4669595.10_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。