Job ID = 11245178 sra ファイルのダウンロード中... Completed: 29110K bytes transferred in 3 seconds (74672K bits/sec), in 1 file. Completed: 249826K bytes transferred in 5 seconds (376316K 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 622245 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669621/SRR7818210.sra Written 622245 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669621/SRR7818210.sra Read 6779878 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669621/SRR7818211.sra Written 6779878 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669621/SRR7818211.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: 00:05:49 7402123 reads; of these: 7402123 (100.00%) were paired; of these: 837557 (11.32%) aligned concordantly 0 times 5867131 (79.26%) aligned concordantly exactly 1 time 697435 (9.42%) aligned concordantly >1 times ---- 837557 pairs aligned concordantly 0 times; of these: 39359 (4.70%) aligned discordantly 1 time ---- 798198 pairs aligned 0 times concordantly or discordantly; of these: 1596396 mates make up the pairs; of these: 1229572 (77.02%) aligned 0 times 265746 (16.65%) aligned exactly 1 time 101078 (6.33%) aligned >1 times 91.69% overall alignment rate Time searching: 00:05:49 Overall time: 00:05:49 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_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] 1308042 / 6599849 = 0.1982 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 23:52:47: # Command line: callpeak -t SRX4669621.bam -f BAM -g 12100000 -n SRX4669621.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669621.10 # format = BAM # ChIP-seq file = ['SRX4669621.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 23:52:47: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:52:47: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:52:47: # Command line: callpeak -t SRX4669621.bam -f BAM -g 12100000 -n SRX4669621.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669621.05 # format = BAM # ChIP-seq file = ['SRX4669621.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 23:52:47: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:52:47: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:52:47: # Command line: callpeak -t SRX4669621.bam -f BAM -g 12100000 -n SRX4669621.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669621.20 # format = BAM # ChIP-seq file = ['SRX4669621.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 23:52:47: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:52:47: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:52:53: 1000000 INFO @ Tue, 09 Oct 2018 23:52:54: 1000000 INFO @ Tue, 09 Oct 2018 23:52:54: 1000000 INFO @ Tue, 09 Oct 2018 23:53:00: 2000000 INFO @ Tue, 09 Oct 2018 23:53:00: 2000000 INFO @ Tue, 09 Oct 2018 23:53:02: 2000000 INFO @ Tue, 09 Oct 2018 23:53:07: 3000000 INFO @ Tue, 09 Oct 2018 23:53:07: 3000000 INFO @ Tue, 09 Oct 2018 23:53:10: 3000000 INFO @ Tue, 09 Oct 2018 23:53:13: 4000000 INFO @ Tue, 09 Oct 2018 23:53:14: 4000000 INFO @ Tue, 09 Oct 2018 23:53:17: 4000000 INFO @ Tue, 09 Oct 2018 23:53:20: 5000000 INFO @ Tue, 09 Oct 2018 23:53:20: 5000000 INFO @ Tue, 09 Oct 2018 23:53:25: 5000000 INFO @ Tue, 09 Oct 2018 23:53:27: 6000000 INFO @ Tue, 09 Oct 2018 23:53:27: 6000000 INFO @ Tue, 09 Oct 2018 23:53:33: 6000000 INFO @ Tue, 09 Oct 2018 23:53:34: 7000000 INFO @ Tue, 09 Oct 2018 23:53:34: 7000000 INFO @ Tue, 09 Oct 2018 23:53:40: 8000000 INFO @ Tue, 09 Oct 2018 23:53:41: 7000000 INFO @ Tue, 09 Oct 2018 23:53:41: 8000000 INFO @ Tue, 09 Oct 2018 23:53:47: 9000000 INFO @ Tue, 09 Oct 2018 23:53:48: 9000000 INFO @ Tue, 09 Oct 2018 23:53:48: 8000000 INFO @ Tue, 09 Oct 2018 23:53:54: 10000000 INFO @ Tue, 09 Oct 2018 23:53:55: 10000000 INFO @ Tue, 09 Oct 2018 23:53:56: 9000000 INFO @ Tue, 09 Oct 2018 23:54:00: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:54:00: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:54:00: #1 total tags in treatment: 5264026 INFO @ Tue, 09 Oct 2018 23:54:00: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:54:00: #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 23:54:00: #1 tags after filtering in treatment: 4309309 INFO @ Tue, 09 Oct 2018 23:54:00: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 09 Oct 2018 23:54:00: #1 finished! INFO @ Tue, 09 Oct 2018 23:54:00: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:54:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:54:01: #2 number of paired peaks: 31 WARNING @ Tue, 09 Oct 2018 23:54:01: 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 23:54:01: Process for pairing-model is terminated! cat: SRX4669621.10_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 `SRX4669621.10_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 `SRX4669621.10_*.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 `SRX4669621.10_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 @ Tue, 09 Oct 2018 23:54:01: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:54:01: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:54:01: #1 total tags in treatment: 5264026 INFO @ Tue, 09 Oct 2018 23:54:01: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:54:01: #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 23:54:02: #1 tags after filtering in treatment: 4309309 INFO @ Tue, 09 Oct 2018 23:54:02: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 09 Oct 2018 23:54:02: #1 finished! INFO @ Tue, 09 Oct 2018 23:54:02: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:54:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:54:02: #2 number of paired peaks: 31 WARNING @ Tue, 09 Oct 2018 23:54:02: 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 23:54:02: Process for pairing-model is terminated! cat: SRX4669621.05_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 `SRX4669621.05_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 `SRX4669621.05_*.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 `SRX4669621.05_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 23:54:04: 10000000 INFO @ Tue, 09 Oct 2018 23:54:12: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:54:12: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:54:12: #1 total tags in treatment: 5264026 INFO @ Tue, 09 Oct 2018 23:54:12: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:54:12: #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 23:54:12: #1 tags after filtering in treatment: 4309309 INFO @ Tue, 09 Oct 2018 23:54:12: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 09 Oct 2018 23:54:12: #1 finished! INFO @ Tue, 09 Oct 2018 23:54:12: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:54:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:54:12: #2 number of paired peaks: 31 WARNING @ Tue, 09 Oct 2018 23:54:12: 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 23:54:12: Process for pairing-model is terminated! cat: SRX4669621.20_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 `SRX4669621.20_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 `SRX4669621.20_*.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 `SRX4669621.20_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。