Job ID = 10937392 sra ファイルのダウンロード中... Completed: 591428K bytes transferred in 8 seconds (582804K 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 8263103 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198717/SRR4304447.sra Written 8263103 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198717/SRR4304447.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: 00:06:43 8263103 reads; of these: 8263103 (100.00%) were paired; of these: 560757 (6.79%) aligned concordantly 0 times 5941599 (71.91%) aligned concordantly exactly 1 time 1760747 (21.31%) aligned concordantly >1 times ---- 560757 pairs aligned concordantly 0 times; of these: 113598 (20.26%) aligned discordantly 1 time ---- 447159 pairs aligned 0 times concordantly or discordantly; of these: 894318 mates make up the pairs; of these: 636523 (71.17%) aligned 0 times 159910 (17.88%) aligned exactly 1 time 97885 (10.95%) aligned >1 times 96.15% overall alignment rate Time searching: 00:06:43 Overall time: 00:06:43 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] 1079982 / 7798007 = 0.1385 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 02:05:39: # Command line: callpeak -t SRX2198717.bam -f BAM -g 12100000 -n SRX2198717.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2198717.20 # format = BAM # ChIP-seq file = ['SRX2198717.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 02:05:39: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:05:39: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:05:39: # Command line: callpeak -t SRX2198717.bam -f BAM -g 12100000 -n SRX2198717.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2198717.05 # format = BAM # ChIP-seq file = ['SRX2198717.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 02:05:39: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:05:39: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:05:39: # Command line: callpeak -t SRX2198717.bam -f BAM -g 12100000 -n SRX2198717.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2198717.10 # format = BAM # ChIP-seq file = ['SRX2198717.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 02:05:39: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:05:39: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:05:45: 1000000 INFO @ Fri, 10 Aug 2018 02:05:45: 1000000 INFO @ Fri, 10 Aug 2018 02:05:45: 1000000 INFO @ Fri, 10 Aug 2018 02:05:50: 2000000 INFO @ Fri, 10 Aug 2018 02:05:51: 2000000 INFO @ Fri, 10 Aug 2018 02:05:51: 2000000 INFO @ Fri, 10 Aug 2018 02:05:56: 3000000 INFO @ Fri, 10 Aug 2018 02:05:56: 3000000 INFO @ Fri, 10 Aug 2018 02:05:57: 3000000 INFO @ Fri, 10 Aug 2018 02:06:01: 4000000 INFO @ Fri, 10 Aug 2018 02:06:02: 4000000 INFO @ Fri, 10 Aug 2018 02:06:02: 4000000 INFO @ Fri, 10 Aug 2018 02:06:06: 5000000 INFO @ Fri, 10 Aug 2018 02:06:08: 5000000 INFO @ Fri, 10 Aug 2018 02:06:08: 5000000 INFO @ Fri, 10 Aug 2018 02:06:12: 6000000 INFO @ Fri, 10 Aug 2018 02:06:14: 6000000 INFO @ Fri, 10 Aug 2018 02:06:15: 6000000 INFO @ Fri, 10 Aug 2018 02:06:17: 7000000 INFO @ Fri, 10 Aug 2018 02:06:19: 7000000 INFO @ Fri, 10 Aug 2018 02:06:21: 7000000 INFO @ Fri, 10 Aug 2018 02:06:22: 8000000 INFO @ Fri, 10 Aug 2018 02:06:25: 8000000 INFO @ Fri, 10 Aug 2018 02:06:27: 8000000 INFO @ Fri, 10 Aug 2018 02:06:28: 9000000 INFO @ Fri, 10 Aug 2018 02:06:31: 9000000 INFO @ Fri, 10 Aug 2018 02:06:33: 9000000 INFO @ Fri, 10 Aug 2018 02:06:33: 10000000 INFO @ Fri, 10 Aug 2018 02:06:37: 10000000 INFO @ Fri, 10 Aug 2018 02:06:38: 11000000 INFO @ Fri, 10 Aug 2018 02:06:39: 10000000 INFO @ Fri, 10 Aug 2018 02:06:43: 11000000 INFO @ Fri, 10 Aug 2018 02:06:44: 12000000 INFO @ Fri, 10 Aug 2018 02:06:45: 11000000 INFO @ Fri, 10 Aug 2018 02:06:48: 12000000 INFO @ Fri, 10 Aug 2018 02:06:49: 13000000 INFO @ Fri, 10 Aug 2018 02:06:51: 12000000 INFO @ Fri, 10 Aug 2018 02:06:53: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 02:06:53: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 02:06:53: #1 total tags in treatment: 6662628 INFO @ Fri, 10 Aug 2018 02:06:53: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:06:53: #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 02:06:53: #1 tags after filtering in treatment: 4717583 INFO @ Fri, 10 Aug 2018 02:06:53: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 10 Aug 2018 02:06:53: #1 finished! INFO @ Fri, 10 Aug 2018 02:06:53: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:06:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:06:53: #2 number of paired peaks: 29 WARNING @ Fri, 10 Aug 2018 02:06:53: Too few paired peaks (29) 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 02:06:53: Process for pairing-model is terminated! cat: SRX2198717.05_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 `SRX2198717.05_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 `SRX2198717.05_*.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 `SRX2198717.05_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 @ Fri, 10 Aug 2018 02:06:54: 13000000 INFO @ Fri, 10 Aug 2018 02:06:57: 13000000 INFO @ Fri, 10 Aug 2018 02:06:58: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 02:06:58: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 02:06:58: #1 total tags in treatment: 6662628 INFO @ Fri, 10 Aug 2018 02:06:58: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:06:58: #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 02:06:58: #1 tags after filtering in treatment: 4717583 INFO @ Fri, 10 Aug 2018 02:06:58: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 10 Aug 2018 02:06:58: #1 finished! INFO @ Fri, 10 Aug 2018 02:06:58: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:06:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:06:59: #2 number of paired peaks: 29 WARNING @ Fri, 10 Aug 2018 02:06:59: Too few paired peaks (29) 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 02:06:59: Process for pairing-model is terminated! cat: SRX2198717.10_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 `SRX2198717.10_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 `SRX2198717.10_*.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 `SRX2198717.10_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 02:07:01: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 02:07:01: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 02:07:01: #1 total tags in treatment: 6662628 INFO @ Fri, 10 Aug 2018 02:07:01: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:07:01: #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 02:07:01: #1 tags after filtering in treatment: 4717583 INFO @ Fri, 10 Aug 2018 02:07:01: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 10 Aug 2018 02:07:01: #1 finished! INFO @ Fri, 10 Aug 2018 02:07:01: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:07:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:07:01: #2 number of paired peaks: 29 WARNING @ Fri, 10 Aug 2018 02:07:01: Too few paired peaks (29) 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 02:07:01: Process for pairing-model is terminated! cat: SRX2198717.20_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 `SRX2198717.20_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 `SRX2198717.20_*.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 `SRX2198717.20_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。