Job ID = 10937431 sra ファイルのダウンロード中... Completed: 469559K bytes transferred in 7 seconds (547411K 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 8664355 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198727/SRR4304457.sra Written 8664355 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198727/SRR4304457.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: 00:06:08 8664355 reads; of these: 8664355 (100.00%) were paired; of these: 441077 (5.09%) aligned concordantly 0 times 7138441 (82.39%) aligned concordantly exactly 1 time 1084837 (12.52%) aligned concordantly >1 times ---- 441077 pairs aligned concordantly 0 times; of these: 161900 (36.71%) aligned discordantly 1 time ---- 279177 pairs aligned 0 times concordantly or discordantly; of these: 558354 mates make up the pairs; of these: 365615 (65.48%) aligned 0 times 118688 (21.26%) aligned exactly 1 time 74051 (13.26%) aligned >1 times 97.89% overall alignment rate Time searching: 00:06:08 Overall time: 00:06:08 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] 233235 / 8305098 = 0.0281 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 @ Fri, 10 Aug 2018 02:15:29: # Command line: callpeak -t SRX2198727.bam -f BAM -g 12100000 -n SRX2198727.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2198727.05 # format = BAM # ChIP-seq file = ['SRX2198727.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 @ Fri, 10 Aug 2018 02:15:29: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:15:29: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:15:29: # Command line: callpeak -t SRX2198727.bam -f BAM -g 12100000 -n SRX2198727.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2198727.20 # format = BAM # ChIP-seq file = ['SRX2198727.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 @ Fri, 10 Aug 2018 02:15:29: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:15:29: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:15:29: # Command line: callpeak -t SRX2198727.bam -f BAM -g 12100000 -n SRX2198727.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2198727.10 # format = BAM # ChIP-seq file = ['SRX2198727.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 @ Fri, 10 Aug 2018 02:15:29: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:15:29: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:15:35: 1000000 INFO @ Fri, 10 Aug 2018 02:15:35: 1000000 INFO @ Fri, 10 Aug 2018 02:15:35: 1000000 INFO @ Fri, 10 Aug 2018 02:15:40: 2000000 INFO @ Fri, 10 Aug 2018 02:15:41: 2000000 INFO @ Fri, 10 Aug 2018 02:15:41: 2000000 INFO @ Fri, 10 Aug 2018 02:15:46: 3000000 INFO @ Fri, 10 Aug 2018 02:15:47: 3000000 INFO @ Fri, 10 Aug 2018 02:15:47: 3000000 INFO @ Fri, 10 Aug 2018 02:15:51: 4000000 INFO @ Fri, 10 Aug 2018 02:15:52: 4000000 INFO @ Fri, 10 Aug 2018 02:15:52: 4000000 INFO @ Fri, 10 Aug 2018 02:15:57: 5000000 INFO @ Fri, 10 Aug 2018 02:15:58: 5000000 INFO @ Fri, 10 Aug 2018 02:15:58: 5000000 INFO @ Fri, 10 Aug 2018 02:16:02: 6000000 INFO @ Fri, 10 Aug 2018 02:16:03: 6000000 INFO @ Fri, 10 Aug 2018 02:16:03: 6000000 INFO @ Fri, 10 Aug 2018 02:16:08: 7000000 INFO @ Fri, 10 Aug 2018 02:16:09: 7000000 INFO @ Fri, 10 Aug 2018 02:16:09: 7000000 INFO @ Fri, 10 Aug 2018 02:16:14: 8000000 INFO @ Fri, 10 Aug 2018 02:16:14: 8000000 INFO @ Fri, 10 Aug 2018 02:16:14: 8000000 INFO @ Fri, 10 Aug 2018 02:16:20: 9000000 INFO @ Fri, 10 Aug 2018 02:16:20: 9000000 INFO @ Fri, 10 Aug 2018 02:16:20: 9000000 INFO @ Fri, 10 Aug 2018 02:16:26: 10000000 INFO @ Fri, 10 Aug 2018 02:16:26: 10000000 INFO @ Fri, 10 Aug 2018 02:16:26: 10000000 INFO @ Fri, 10 Aug 2018 02:16:31: 11000000 INFO @ Fri, 10 Aug 2018 02:16:31: 11000000 INFO @ Fri, 10 Aug 2018 02:16:31: 11000000 INFO @ Fri, 10 Aug 2018 02:16:37: 12000000 INFO @ Fri, 10 Aug 2018 02:16:37: 12000000 INFO @ Fri, 10 Aug 2018 02:16:37: 12000000 INFO @ Fri, 10 Aug 2018 02:16:42: 13000000 INFO @ Fri, 10 Aug 2018 02:16:42: 13000000 INFO @ Fri, 10 Aug 2018 02:16:43: 13000000 INFO @ Fri, 10 Aug 2018 02:16:48: 14000000 INFO @ Fri, 10 Aug 2018 02:16:48: 14000000 INFO @ Fri, 10 Aug 2018 02:16:49: 14000000 INFO @ Fri, 10 Aug 2018 02:16:53: 15000000 INFO @ Fri, 10 Aug 2018 02:16:53: 15000000 INFO @ Fri, 10 Aug 2018 02:16:55: 15000000 INFO @ Fri, 10 Aug 2018 02:16:59: 16000000 INFO @ Fri, 10 Aug 2018 02:16:59: 16000000 INFO @ Fri, 10 Aug 2018 02:17:00: 16000000 INFO @ Fri, 10 Aug 2018 02:17:01: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:17:01: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:17:01: #1 total tags in treatment: 7990554 INFO @ Fri, 10 Aug 2018 02:17:01: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:17:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:17:01: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:17:01: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:17:01: #1 total tags in treatment: 7990554 INFO @ Fri, 10 Aug 2018 02:17:01: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:17:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:17:01: #1 tags after filtering in treatment: 4791889 INFO @ Fri, 10 Aug 2018 02:17:01: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 10 Aug 2018 02:17:01: #1 finished! INFO @ Fri, 10 Aug 2018 02:17:01: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:17:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:17:01: #1 tags after filtering in treatment: 4791889 INFO @ Fri, 10 Aug 2018 02:17:01: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 10 Aug 2018 02:17:01: #1 finished! INFO @ Fri, 10 Aug 2018 02:17:01: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:17:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:17:02: #2 number of paired peaks: 0 WARNING @ Fri, 10 Aug 2018 02:17:02: 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 @ Fri, 10 Aug 2018 02:17:02: Process for pairing-model is terminated! cat: SRX2198727.05_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 `SRX2198727.05_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 `SRX2198727.05_*.xls': そのようなファイルやディレクトリはありません INFO @ Fri, 10 Aug 2018 02:17:02: #2 number of paired peaks: 0 WARNING @ Fri, 10 Aug 2018 02:17:02: 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 @ Fri, 10 Aug 2018 02:17:02: Process for pairing-model is terminated! rm: cannot remove `SRX2198727.05_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 cat: SRX2198727.10_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 `SRX2198727.10_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 `SRX2198727.10_*.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 `SRX2198727.10_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 @ Fri, 10 Aug 2018 02:17:03: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:17:03: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:17:03: #1 total tags in treatment: 7990554 INFO @ Fri, 10 Aug 2018 02:17:03: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:17:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:17:04: #1 tags after filtering in treatment: 4791889 INFO @ Fri, 10 Aug 2018 02:17:04: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 10 Aug 2018 02:17:04: #1 finished! INFO @ Fri, 10 Aug 2018 02:17:04: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:17:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:17:04: #2 number of paired peaks: 0 WARNING @ Fri, 10 Aug 2018 02:17:04: 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 @ Fri, 10 Aug 2018 02:17:04: Process for pairing-model is terminated! cat: SRX2198727.20_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 `SRX2198727.20_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 `SRX2198727.20_*.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 `SRX2198727.20_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。