Job ID = 9732067 sra ファイルのダウンロード中... Completed: 309189K bytes transferred in 15 seconds (165200K bits/sec), in 1 file, 2 directories. 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... Written 12974231 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675867/SRR5380643.sra Written 12974231 spots total 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: 00:05:57 12974231 reads; of these: 12974231 (100.00%) were paired; of these: 2205192 (17.00%) aligned concordantly 0 times 9940338 (76.62%) aligned concordantly exactly 1 time 828701 (6.39%) aligned concordantly >1 times ---- 2205192 pairs aligned concordantly 0 times; of these: 249587 (11.32%) aligned discordantly 1 time ---- 1955605 pairs aligned 0 times concordantly or discordantly; of these: 3911210 mates make up the pairs; of these: 3458576 (88.43%) aligned 0 times 365136 (9.34%) aligned exactly 1 time 87498 (2.24%) aligned >1 times 86.67% overall alignment rate Time searching: 00:05:57 Overall time: 00:05:57 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] 1435044 / 10875838 = 0.1319 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 @ Sun, 03 Sep 2017 19:34:35: # Command line: callpeak -t SRX2675867.bam -f BAM -g 12100000 -n SRX2675867.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675867.05 # format = BAM # ChIP-seq file = ['SRX2675867.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 @ Sun, 03 Sep 2017 19:34:35: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:34:35: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:34:35: # Command line: callpeak -t SRX2675867.bam -f BAM -g 12100000 -n SRX2675867.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675867.20 # format = BAM # ChIP-seq file = ['SRX2675867.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 @ Sun, 03 Sep 2017 19:34:35: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:34:35: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:34:35: # Command line: callpeak -t SRX2675867.bam -f BAM -g 12100000 -n SRX2675867.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675867.10 # format = BAM # ChIP-seq file = ['SRX2675867.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 @ Sun, 03 Sep 2017 19:34:35: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:34:35: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:34:41: 1000000 INFO @ Sun, 03 Sep 2017 19:34:41: 1000000 INFO @ Sun, 03 Sep 2017 19:34:41: 1000000 INFO @ Sun, 03 Sep 2017 19:34:46: 2000000 INFO @ Sun, 03 Sep 2017 19:34:46: 2000000 INFO @ Sun, 03 Sep 2017 19:34:46: 2000000 INFO @ Sun, 03 Sep 2017 19:34:51: 3000000 INFO @ Sun, 03 Sep 2017 19:34:51: 3000000 INFO @ Sun, 03 Sep 2017 19:34:51: 3000000 INFO @ Sun, 03 Sep 2017 19:34:56: 4000000 INFO @ Sun, 03 Sep 2017 19:34:57: 4000000 INFO @ Sun, 03 Sep 2017 19:34:57: 4000000 INFO @ Sun, 03 Sep 2017 19:35:01: 5000000 INFO @ Sun, 03 Sep 2017 19:35:02: 5000000 INFO @ Sun, 03 Sep 2017 19:35:02: 5000000 INFO @ Sun, 03 Sep 2017 19:35:06: 6000000 INFO @ Sun, 03 Sep 2017 19:35:07: 6000000 INFO @ Sun, 03 Sep 2017 19:35:07: 6000000 INFO @ Sun, 03 Sep 2017 19:35:11: 7000000 INFO @ Sun, 03 Sep 2017 19:35:12: 7000000 INFO @ Sun, 03 Sep 2017 19:35:12: 7000000 INFO @ Sun, 03 Sep 2017 19:35:16: 8000000 INFO @ Sun, 03 Sep 2017 19:35:17: 8000000 INFO @ Sun, 03 Sep 2017 19:35:17: 8000000 INFO @ Sun, 03 Sep 2017 19:35:21: 9000000 INFO @ Sun, 03 Sep 2017 19:35:23: 9000000 INFO @ Sun, 03 Sep 2017 19:35:23: 9000000 INFO @ Sun, 03 Sep 2017 19:35:26: 10000000 INFO @ Sun, 03 Sep 2017 19:35:28: 10000000 INFO @ Sun, 03 Sep 2017 19:35:28: 10000000 INFO @ Sun, 03 Sep 2017 19:35:31: 11000000 INFO @ Sun, 03 Sep 2017 19:35:33: 11000000 INFO @ Sun, 03 Sep 2017 19:35:33: 11000000 INFO @ Sun, 03 Sep 2017 19:35:36: 12000000 INFO @ Sun, 03 Sep 2017 19:35:38: 12000000 INFO @ Sun, 03 Sep 2017 19:35:38: 12000000 INFO @ Sun, 03 Sep 2017 19:35:41: 13000000 INFO @ Sun, 03 Sep 2017 19:35:43: 13000000 INFO @ Sun, 03 Sep 2017 19:35:43: 13000000 INFO @ Sun, 03 Sep 2017 19:35:46: 14000000 INFO @ Sun, 03 Sep 2017 19:35:48: 14000000 INFO @ Sun, 03 Sep 2017 19:35:48: 14000000 INFO @ Sun, 03 Sep 2017 19:35:51: 15000000 INFO @ Sun, 03 Sep 2017 19:35:54: 15000000 INFO @ Sun, 03 Sep 2017 19:35:54: 15000000 INFO @ Sun, 03 Sep 2017 19:35:56: 16000000 INFO @ Sun, 03 Sep 2017 19:35:59: 16000000 INFO @ Sun, 03 Sep 2017 19:35:59: 16000000 INFO @ Sun, 03 Sep 2017 19:36:01: 17000000 INFO @ Sun, 03 Sep 2017 19:36:04: 17000000 INFO @ Sun, 03 Sep 2017 19:36:04: 17000000 INFO @ Sun, 03 Sep 2017 19:36:06: 18000000 INFO @ Sun, 03 Sep 2017 19:36:09: 18000000 INFO @ Sun, 03 Sep 2017 19:36:09: 18000000 INFO @ Sun, 03 Sep 2017 19:36:11: 19000000 INFO @ Sun, 03 Sep 2017 19:36:14: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:36:14: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:36:14: #1 total tags in treatment: 9334600 INFO @ Sun, 03 Sep 2017 19:36:14: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:36:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:36:14: #1 tags after filtering in treatment: 4555250 INFO @ Sun, 03 Sep 2017 19:36:14: #1 Redundant rate of treatment: 0.51 INFO @ Sun, 03 Sep 2017 19:36:14: #1 finished! INFO @ Sun, 03 Sep 2017 19:36:14: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:36:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:36:14: 19000000 INFO @ Sun, 03 Sep 2017 19:36:14: 19000000 INFO @ Sun, 03 Sep 2017 19:36:14: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:36:14: 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 @ Sun, 03 Sep 2017 19:36:14: Process for pairing-model is terminated! cat: SRX2675867.05_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 `SRX2675867.05_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 `SRX2675867.05_*.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 `SRX2675867.05_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 @ Sun, 03 Sep 2017 19:36:17: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:36:17: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:36:17: #1 total tags in treatment: 9334600 INFO @ Sun, 03 Sep 2017 19:36:17: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:36:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:36:17: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:36:17: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:36:17: #1 total tags in treatment: 9334600 INFO @ Sun, 03 Sep 2017 19:36:17: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:36:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:36:18: #1 tags after filtering in treatment: 4555250 INFO @ Sun, 03 Sep 2017 19:36:18: #1 Redundant rate of treatment: 0.51 INFO @ Sun, 03 Sep 2017 19:36:18: #1 finished! INFO @ Sun, 03 Sep 2017 19:36:18: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:36:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:36:18: #1 tags after filtering in treatment: 4555250 INFO @ Sun, 03 Sep 2017 19:36:18: #1 Redundant rate of treatment: 0.51 INFO @ Sun, 03 Sep 2017 19:36:18: #1 finished! INFO @ Sun, 03 Sep 2017 19:36:18: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:36:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:36:18: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:36:18: 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 @ Sun, 03 Sep 2017 19:36:18: Process for pairing-model is terminated! cat: SRX2675867.10_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675867.10_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 `SRX2675867.10_*.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 `SRX2675867.10_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 @ Sun, 03 Sep 2017 19:36:18: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:36:18: 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 @ Sun, 03 Sep 2017 19:36:18: Process for pairing-model is terminated! cat: SRX2675867.20_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675867.20_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 `SRX2675867.20_*.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 `SRX2675867.20_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。