Job ID = 11245151 sra ファイルのダウンロード中... Completed: 370681K bytes transferred in 6 seconds (440306K 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 7487439 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669603/SRR7818186.sra Written 7487439 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669603/SRR7818186.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: 00:05:59 7487439 reads; of these: 7487439 (100.00%) were paired; of these: 925432 (12.36%) aligned concordantly 0 times 5757895 (76.90%) aligned concordantly exactly 1 time 804112 (10.74%) aligned concordantly >1 times ---- 925432 pairs aligned concordantly 0 times; of these: 48902 (5.28%) aligned discordantly 1 time ---- 876530 pairs aligned 0 times concordantly or discordantly; of these: 1753060 mates make up the pairs; of these: 1400587 (79.89%) aligned 0 times 251073 (14.32%) aligned exactly 1 time 101400 (5.78%) aligned >1 times 90.65% overall alignment rate Time searching: 00:05:59 Overall time: 00:05:59 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] 84423 / 6586463 = 0.0128 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 23:45:49: # Command line: callpeak -t SRX4669603.bam -f BAM -g 12100000 -n SRX4669603.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669603.20 # format = BAM # ChIP-seq file = ['SRX4669603.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 23:45:49: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:45:49: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:45:49: # Command line: callpeak -t SRX4669603.bam -f BAM -g 12100000 -n SRX4669603.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669603.05 # format = BAM # ChIP-seq file = ['SRX4669603.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 23:45:49: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:45:49: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:45:49: # Command line: callpeak -t SRX4669603.bam -f BAM -g 12100000 -n SRX4669603.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669603.10 # format = BAM # ChIP-seq file = ['SRX4669603.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 23:45:49: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:45:49: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:45:54: 1000000 INFO @ Tue, 09 Oct 2018 23:45:54: 1000000 INFO @ Tue, 09 Oct 2018 23:45:55: 1000000 INFO @ Tue, 09 Oct 2018 23:46:00: 2000000 INFO @ Tue, 09 Oct 2018 23:46:00: 2000000 INFO @ Tue, 09 Oct 2018 23:46:01: 2000000 INFO @ Tue, 09 Oct 2018 23:46:05: 3000000 INFO @ Tue, 09 Oct 2018 23:46:05: 3000000 INFO @ Tue, 09 Oct 2018 23:46:07: 3000000 INFO @ Tue, 09 Oct 2018 23:46:10: 4000000 INFO @ Tue, 09 Oct 2018 23:46:10: 4000000 INFO @ Tue, 09 Oct 2018 23:46:13: 4000000 INFO @ Tue, 09 Oct 2018 23:46:16: 5000000 INFO @ Tue, 09 Oct 2018 23:46:16: 5000000 INFO @ Tue, 09 Oct 2018 23:46:19: 5000000 INFO @ Tue, 09 Oct 2018 23:46:21: 6000000 INFO @ Tue, 09 Oct 2018 23:46:21: 6000000 INFO @ Tue, 09 Oct 2018 23:46:25: 6000000 INFO @ Tue, 09 Oct 2018 23:46:27: 7000000 INFO @ Tue, 09 Oct 2018 23:46:27: 7000000 INFO @ Tue, 09 Oct 2018 23:46:31: 7000000 INFO @ Tue, 09 Oct 2018 23:46:32: 8000000 INFO @ Tue, 09 Oct 2018 23:46:32: 8000000 INFO @ Tue, 09 Oct 2018 23:46:37: 8000000 INFO @ Tue, 09 Oct 2018 23:46:37: 9000000 INFO @ Tue, 09 Oct 2018 23:46:38: 9000000 INFO @ Tue, 09 Oct 2018 23:46:43: 10000000 INFO @ Tue, 09 Oct 2018 23:46:43: 9000000 INFO @ Tue, 09 Oct 2018 23:46:43: 10000000 INFO @ Tue, 09 Oct 2018 23:46:48: 11000000 INFO @ Tue, 09 Oct 2018 23:46:49: 11000000 INFO @ Tue, 09 Oct 2018 23:46:49: 10000000 INFO @ Tue, 09 Oct 2018 23:46:54: 12000000 INFO @ Tue, 09 Oct 2018 23:46:54: 12000000 INFO @ Tue, 09 Oct 2018 23:46:55: 11000000 INFO @ Tue, 09 Oct 2018 23:46:59: 13000000 INFO @ Tue, 09 Oct 2018 23:47:00: 13000000 INFO @ Tue, 09 Oct 2018 23:47:01: 12000000 INFO @ Tue, 09 Oct 2018 23:47:01: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:47:01: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:47:01: #1 total tags in treatment: 6478071 INFO @ Tue, 09 Oct 2018 23:47:01: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:47:01: #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 23:47:02: #1 tags after filtering in treatment: 5175564 INFO @ Tue, 09 Oct 2018 23:47:02: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 09 Oct 2018 23:47:02: #1 finished! INFO @ Tue, 09 Oct 2018 23:47:02: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:47:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:47:02: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:47:02: Too few paired peaks (0) 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 23:47:02: Process for pairing-model is terminated! cat: SRX4669603.05_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 `SRX4669603.05_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 `SRX4669603.05_*.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 `SRX4669603.05_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 23:47:02: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:47:02: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:47:02: #1 total tags in treatment: 6478071 INFO @ Tue, 09 Oct 2018 23:47:02: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:47:02: #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 23:47:02: #1 tags after filtering in treatment: 5175564 INFO @ Tue, 09 Oct 2018 23:47:02: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 09 Oct 2018 23:47:02: #1 finished! INFO @ Tue, 09 Oct 2018 23:47:02: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:47:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:47:03: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:47:03: Too few paired peaks (0) 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 23:47:03: Process for pairing-model is terminated! cat: SRX4669603.20_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 `SRX4669603.20_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 `SRX4669603.20_*.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 `SRX4669603.20_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 23:47:07: 13000000 INFO @ Tue, 09 Oct 2018 23:47:09: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:47:09: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:47:09: #1 total tags in treatment: 6478071 INFO @ Tue, 09 Oct 2018 23:47:09: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:47:09: #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 23:47:09: #1 tags after filtering in treatment: 5175564 INFO @ Tue, 09 Oct 2018 23:47:09: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 09 Oct 2018 23:47:09: #1 finished! INFO @ Tue, 09 Oct 2018 23:47:09: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:47:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:47:09: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:47:09: Too few paired peaks (0) 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 23:47:09: Process for pairing-model is terminated! cat: SRX4669603.10_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 `SRX4669603.10_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 `SRX4669603.10_*.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 `SRX4669603.10_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。