Job ID = 11192887 sra ファイルのダウンロード中... Completed: 1044914K bytes transferred in 40 seconds (212375K 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 14560585 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2771765/SRR5488920.sra Written 14560585 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2771765/SRR5488920.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: 00:13:05 14560585 reads; of these: 14560585 (100.00%) were paired; of these: 3272457 (22.47%) aligned concordantly 0 times 7730904 (53.09%) aligned concordantly exactly 1 time 3557224 (24.43%) aligned concordantly >1 times ---- 3272457 pairs aligned concordantly 0 times; of these: 17390 (0.53%) aligned discordantly 1 time ---- 3255067 pairs aligned 0 times concordantly or discordantly; of these: 6510134 mates make up the pairs; of these: 6204902 (95.31%) aligned 0 times 231571 (3.56%) aligned exactly 1 time 73661 (1.13%) aligned >1 times 78.69% overall alignment rate Time searching: 00:13:05 Overall time: 00:13:05 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 12 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] 4404820 / 11290551 = 0.3901 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 @ Sat, 15 Sep 2018 10:38:47: # Command line: callpeak -t SRX2771765.bam -f BAM -g 12100000 -n SRX2771765.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2771765.20 # format = BAM # ChIP-seq file = ['SRX2771765.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 @ Sat, 15 Sep 2018 10:38:47: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:38:47: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:38:47: # Command line: callpeak -t SRX2771765.bam -f BAM -g 12100000 -n SRX2771765.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2771765.05 # format = BAM # ChIP-seq file = ['SRX2771765.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 @ Sat, 15 Sep 2018 10:38:47: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:38:47: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:38:47: # Command line: callpeak -t SRX2771765.bam -f BAM -g 12100000 -n SRX2771765.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2771765.10 # format = BAM # ChIP-seq file = ['SRX2771765.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 @ Sat, 15 Sep 2018 10:38:47: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:38:47: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:38:53: 1000000 INFO @ Sat, 15 Sep 2018 10:38:53: 1000000 INFO @ Sat, 15 Sep 2018 10:38:53: 1000000 INFO @ Sat, 15 Sep 2018 10:38:59: 2000000 INFO @ Sat, 15 Sep 2018 10:39:00: 2000000 INFO @ Sat, 15 Sep 2018 10:39:00: 2000000 INFO @ Sat, 15 Sep 2018 10:39:06: 3000000 INFO @ Sat, 15 Sep 2018 10:39:06: 3000000 INFO @ Sat, 15 Sep 2018 10:39:07: 3000000 INFO @ Sat, 15 Sep 2018 10:39:12: 4000000 INFO @ Sat, 15 Sep 2018 10:39:13: 4000000 INFO @ Sat, 15 Sep 2018 10:39:13: 4000000 INFO @ Sat, 15 Sep 2018 10:39:19: 5000000 INFO @ Sat, 15 Sep 2018 10:39:19: 5000000 INFO @ Sat, 15 Sep 2018 10:39:20: 5000000 INFO @ Sat, 15 Sep 2018 10:39:25: 6000000 INFO @ Sat, 15 Sep 2018 10:39:26: 6000000 INFO @ Sat, 15 Sep 2018 10:39:27: 6000000 INFO @ Sat, 15 Sep 2018 10:39:32: 7000000 INFO @ Sat, 15 Sep 2018 10:39:33: 7000000 INFO @ Sat, 15 Sep 2018 10:39:34: 7000000 INFO @ Sat, 15 Sep 2018 10:39:37: 8000000 INFO @ Sat, 15 Sep 2018 10:39:40: 8000000 INFO @ Sat, 15 Sep 2018 10:39:41: 8000000 INFO @ Sat, 15 Sep 2018 10:39:43: 9000000 INFO @ Sat, 15 Sep 2018 10:39:47: 9000000 INFO @ Sat, 15 Sep 2018 10:39:48: 9000000 INFO @ Sat, 15 Sep 2018 10:39:50: 10000000 INFO @ Sat, 15 Sep 2018 10:39:54: 10000000 INFO @ Sat, 15 Sep 2018 10:39:55: 10000000 INFO @ Sat, 15 Sep 2018 10:39:56: 11000000 INFO @ Sat, 15 Sep 2018 10:40:00: 11000000 INFO @ Sat, 15 Sep 2018 10:40:02: 12000000 INFO @ Sat, 15 Sep 2018 10:40:02: 11000000 INFO @ Sat, 15 Sep 2018 10:40:07: 12000000 INFO @ Sat, 15 Sep 2018 10:40:08: 13000000 INFO @ Sat, 15 Sep 2018 10:40:09: 12000000 INFO @ Sat, 15 Sep 2018 10:40:14: 14000000 INFO @ Sat, 15 Sep 2018 10:40:14: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:40:14: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:40:14: #1 total tags in treatment: 6883896 INFO @ Sat, 15 Sep 2018 10:40:14: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:40:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:40:14: #1 tags after filtering in treatment: 4390855 INFO @ Sat, 15 Sep 2018 10:40:14: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 15 Sep 2018 10:40:14: #1 finished! INFO @ Sat, 15 Sep 2018 10:40:14: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:40:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:40:14: 13000000 INFO @ Sat, 15 Sep 2018 10:40:15: #2 number of paired peaks: 28 WARNING @ Sat, 15 Sep 2018 10:40:15: Too few paired peaks (28) 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 @ Sat, 15 Sep 2018 10:40:15: Process for pairing-model is terminated! cat: SRX2771765.05_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 `SRX2771765.05_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 `SRX2771765.05_*.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 `SRX2771765.05_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 @ Sat, 15 Sep 2018 10:40:16: 13000000 INFO @ Sat, 15 Sep 2018 10:40:22: 14000000 INFO @ Sat, 15 Sep 2018 10:40:23: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:40:23: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:40:23: #1 total tags in treatment: 6883896 INFO @ Sat, 15 Sep 2018 10:40:23: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:40:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:40:23: #1 tags after filtering in treatment: 4390855 INFO @ Sat, 15 Sep 2018 10:40:23: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 15 Sep 2018 10:40:23: #1 finished! INFO @ Sat, 15 Sep 2018 10:40:23: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:40:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:40:23: #2 number of paired peaks: 28 WARNING @ Sat, 15 Sep 2018 10:40:23: Too few paired peaks (28) 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 @ Sat, 15 Sep 2018 10:40:23: Process for pairing-model is terminated! cat: SRX2771765.20_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 `SRX2771765.20_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 `SRX2771765.20_*.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 `SRX2771765.20_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 @ Sat, 15 Sep 2018 10:40:24: 14000000 INFO @ Sat, 15 Sep 2018 10:40:25: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:40:25: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:40:25: #1 total tags in treatment: 6883896 INFO @ Sat, 15 Sep 2018 10:40:25: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:40:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:40:25: #1 tags after filtering in treatment: 4390855 INFO @ Sat, 15 Sep 2018 10:40:25: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 15 Sep 2018 10:40:25: #1 finished! INFO @ Sat, 15 Sep 2018 10:40:25: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:40:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:40:25: #2 number of paired peaks: 28 WARNING @ Sat, 15 Sep 2018 10:40:25: Too few paired peaks (28) 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 @ Sat, 15 Sep 2018 10:40:25: Process for pairing-model is terminated! cat: SRX2771765.10_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 `SRX2771765.10_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 `SRX2771765.10_*.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 `SRX2771765.10_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。