Job ID = 11245037 sra ファイルのダウンロード中... Completed: 438058K bytes transferred in 9 seconds (387803K 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 7026226 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554749/SRR7696422.sra Written 7026226 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554749/SRR7696422.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: 00:04:31 7026226 reads; of these: 7026226 (100.00%) were paired; of these: 1931416 (27.49%) aligned concordantly 0 times 4491570 (63.93%) aligned concordantly exactly 1 time 603240 (8.59%) aligned concordantly >1 times ---- 1931416 pairs aligned concordantly 0 times; of these: 50496 (2.61%) aligned discordantly 1 time ---- 1880920 pairs aligned 0 times concordantly or discordantly; of these: 3761840 mates make up the pairs; of these: 3674696 (97.68%) aligned 0 times 49184 (1.31%) aligned exactly 1 time 37960 (1.01%) aligned >1 times 73.85% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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] 3406407 / 5142100 = 0.6625 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 23:18:40: # Command line: callpeak -t SRX4554749.bam -f BAM -g 12100000 -n SRX4554749.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554749.05 # format = BAM # ChIP-seq file = ['SRX4554749.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 23:18:40: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:18:40: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:18:40: # Command line: callpeak -t SRX4554749.bam -f BAM -g 12100000 -n SRX4554749.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554749.20 # format = BAM # ChIP-seq file = ['SRX4554749.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 23:18:40: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:18:40: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:18:40: # Command line: callpeak -t SRX4554749.bam -f BAM -g 12100000 -n SRX4554749.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554749.10 # format = BAM # ChIP-seq file = ['SRX4554749.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 23:18:40: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:18:40: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:18:46: 1000000 INFO @ Tue, 09 Oct 2018 23:18:46: 1000000 INFO @ Tue, 09 Oct 2018 23:18:47: 1000000 INFO @ Tue, 09 Oct 2018 23:18:53: 2000000 INFO @ Tue, 09 Oct 2018 23:18:53: 2000000 INFO @ Tue, 09 Oct 2018 23:18:53: 2000000 INFO @ Tue, 09 Oct 2018 23:18:59: 3000000 INFO @ Tue, 09 Oct 2018 23:19:00: 3000000 INFO @ Tue, 09 Oct 2018 23:19:00: 3000000 INFO @ Tue, 09 Oct 2018 23:19:03: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:19:03: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:19:03: #1 total tags in treatment: 1713954 INFO @ Tue, 09 Oct 2018 23:19:03: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:19:03: #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 23:19:03: #1 tags after filtering in treatment: 1451346 INFO @ Tue, 09 Oct 2018 23:19:03: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 09 Oct 2018 23:19:03: #1 finished! INFO @ Tue, 09 Oct 2018 23:19:03: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:19:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:19:03: #2 number of paired peaks: 41 WARNING @ Tue, 09 Oct 2018 23:19:03: Too few paired peaks (41) 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 23:19:03: Process for pairing-model is terminated! cat: SRX4554749.05_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 `SRX4554749.05_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 `SRX4554749.05_*.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 `SRX4554749.05_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 23:19:04: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:19:04: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:19:04: #1 total tags in treatment: 1713954 INFO @ Tue, 09 Oct 2018 23:19:04: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:19:04: #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 23:19:04: #1 tags after filtering in treatment: 1451346 INFO @ Tue, 09 Oct 2018 23:19:04: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 09 Oct 2018 23:19:04: #1 finished! INFO @ Tue, 09 Oct 2018 23:19:04: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:19:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:19:04: #2 number of paired peaks: 41 WARNING @ Tue, 09 Oct 2018 23:19:04: Too few paired peaks (41) 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 23:19:04: Process for pairing-model is terminated! INFO @ Tue, 09 Oct 2018 23:19:04: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:19:04: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:19:04: #1 total tags in treatment: 1713954 INFO @ Tue, 09 Oct 2018 23:19:04: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:19:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) cat: SRX4554749.20_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 `SRX4554749.20_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 `SRX4554749.20_*.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 `SRX4554749.20_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 23:19:04: #1 tags after filtering in treatment: 1451346 INFO @ Tue, 09 Oct 2018 23:19:04: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 09 Oct 2018 23:19:04: #1 finished! INFO @ Tue, 09 Oct 2018 23:19:04: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:19:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:19:04: #2 number of paired peaks: 41 WARNING @ Tue, 09 Oct 2018 23:19:04: Too few paired peaks (41) 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 23:19:04: Process for pairing-model is terminated! cat: SRX4554749.10_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 `SRX4554749.10_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 `SRX4554749.10_*.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 `SRX4554749.10_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。