Job ID = 9732087 sra ファイルのダウンロード中... Completed: 340235K bytes transferred in 11 seconds (251039K 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 14715509 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675877/SRR5380653.sra Written 14715509 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: 00:06:28 14715509 reads; of these: 14715509 (100.00%) were paired; of these: 3381272 (22.98%) aligned concordantly 0 times 10163733 (69.07%) aligned concordantly exactly 1 time 1170504 (7.95%) aligned concordantly >1 times ---- 3381272 pairs aligned concordantly 0 times; of these: 622546 (18.41%) aligned discordantly 1 time ---- 2758726 pairs aligned 0 times concordantly or discordantly; of these: 5517452 mates make up the pairs; of these: 4848216 (87.87%) aligned 0 times 459831 (8.33%) aligned exactly 1 time 209405 (3.80%) aligned >1 times 83.53% overall alignment rate Time searching: 00:06:28 Overall time: 00:06:28 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] 1734079 / 11749790 = 0.1476 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 19:37:51: # Command line: callpeak -t SRX2675877.bam -f BAM -g 12100000 -n SRX2675877.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675877.10 # format = BAM # ChIP-seq file = ['SRX2675877.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 19:37:51: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:37:51: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:37:51: # Command line: callpeak -t SRX2675877.bam -f BAM -g 12100000 -n SRX2675877.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675877.05 # format = BAM # ChIP-seq file = ['SRX2675877.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 19:37:51: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:37:51: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:37:51: # Command line: callpeak -t SRX2675877.bam -f BAM -g 12100000 -n SRX2675877.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675877.20 # format = BAM # ChIP-seq file = ['SRX2675877.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 19:37:51: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:37:51: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:37:56: 1000000 INFO @ Sun, 03 Sep 2017 19:37:56: 1000000 INFO @ Sun, 03 Sep 2017 19:37:56: 1000000 INFO @ Sun, 03 Sep 2017 19:38:01: 2000000 INFO @ Sun, 03 Sep 2017 19:38:01: 2000000 INFO @ Sun, 03 Sep 2017 19:38:01: 2000000 INFO @ Sun, 03 Sep 2017 19:38:06: 3000000 INFO @ Sun, 03 Sep 2017 19:38:06: 3000000 INFO @ Sun, 03 Sep 2017 19:38:06: 3000000 INFO @ Sun, 03 Sep 2017 19:38:11: 4000000 INFO @ Sun, 03 Sep 2017 19:38:11: 4000000 INFO @ Sun, 03 Sep 2017 19:38:11: 4000000 INFO @ Sun, 03 Sep 2017 19:38:15: 5000000 INFO @ Sun, 03 Sep 2017 19:38:15: 5000000 INFO @ Sun, 03 Sep 2017 19:38:16: 5000000 INFO @ Sun, 03 Sep 2017 19:38:20: 6000000 INFO @ Sun, 03 Sep 2017 19:38:20: 6000000 INFO @ Sun, 03 Sep 2017 19:38:21: 6000000 INFO @ Sun, 03 Sep 2017 19:38:25: 7000000 INFO @ Sun, 03 Sep 2017 19:38:25: 7000000 INFO @ Sun, 03 Sep 2017 19:38:26: 7000000 INFO @ Sun, 03 Sep 2017 19:38:30: 8000000 INFO @ Sun, 03 Sep 2017 19:38:30: 8000000 INFO @ Sun, 03 Sep 2017 19:38:31: 8000000 INFO @ Sun, 03 Sep 2017 19:38:35: 9000000 INFO @ Sun, 03 Sep 2017 19:38:35: 9000000 INFO @ Sun, 03 Sep 2017 19:38:36: 9000000 INFO @ Sun, 03 Sep 2017 19:38:40: 10000000 INFO @ Sun, 03 Sep 2017 19:38:40: 10000000 INFO @ Sun, 03 Sep 2017 19:38:41: 10000000 INFO @ Sun, 03 Sep 2017 19:38:44: 11000000 INFO @ Sun, 03 Sep 2017 19:38:44: 11000000 INFO @ Sun, 03 Sep 2017 19:38:46: 11000000 INFO @ Sun, 03 Sep 2017 19:38:49: 12000000 INFO @ Sun, 03 Sep 2017 19:38:49: 12000000 INFO @ Sun, 03 Sep 2017 19:38:51: 12000000 INFO @ Sun, 03 Sep 2017 19:38:54: 13000000 INFO @ Sun, 03 Sep 2017 19:38:54: 13000000 INFO @ Sun, 03 Sep 2017 19:38:56: 13000000 INFO @ Sun, 03 Sep 2017 19:38:59: 14000000 INFO @ Sun, 03 Sep 2017 19:38:59: 14000000 INFO @ Sun, 03 Sep 2017 19:39:01: 14000000 INFO @ Sun, 03 Sep 2017 19:39:03: 15000000 INFO @ Sun, 03 Sep 2017 19:39:04: 15000000 INFO @ Sun, 03 Sep 2017 19:39:06: 15000000 INFO @ Sun, 03 Sep 2017 19:39:08: 16000000 INFO @ Sun, 03 Sep 2017 19:39:08: 16000000 INFO @ Sun, 03 Sep 2017 19:39:11: 16000000 INFO @ Sun, 03 Sep 2017 19:39:13: 17000000 INFO @ Sun, 03 Sep 2017 19:39:13: 17000000 INFO @ Sun, 03 Sep 2017 19:39:16: 17000000 INFO @ Sun, 03 Sep 2017 19:39:18: 18000000 INFO @ Sun, 03 Sep 2017 19:39:18: 18000000 INFO @ Sun, 03 Sep 2017 19:39:21: 18000000 INFO @ Sun, 03 Sep 2017 19:39:23: 19000000 INFO @ Sun, 03 Sep 2017 19:39:23: 19000000 INFO @ Sun, 03 Sep 2017 19:39:26: 19000000 INFO @ Sun, 03 Sep 2017 19:39:28: 20000000 INFO @ Sun, 03 Sep 2017 19:39:28: 20000000 INFO @ Sun, 03 Sep 2017 19:39:30: 20000000 INFO @ Sun, 03 Sep 2017 19:39:32: 21000000 INFO @ Sun, 03 Sep 2017 19:39:33: 21000000 INFO @ Sun, 03 Sep 2017 19:39:33: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:39:33: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:39:33: #1 total tags in treatment: 9609313 INFO @ Sun, 03 Sep 2017 19:39:33: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:39:33: #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 19:39:33: #1 tags after filtering in treatment: 4530278 INFO @ Sun, 03 Sep 2017 19:39:33: #1 Redundant rate of treatment: 0.53 INFO @ Sun, 03 Sep 2017 19:39:33: #1 finished! INFO @ Sun, 03 Sep 2017 19:39:33: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:39:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:39:33: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:39:33: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:39:33: #1 total tags in treatment: 9609313 INFO @ Sun, 03 Sep 2017 19:39:33: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:39:33: #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 19:39:33: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:39:33: 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 19:39:33: Process for pairing-model is terminated! INFO @ Sun, 03 Sep 2017 19:39:33: #1 tags after filtering in treatment: 4530278 INFO @ Sun, 03 Sep 2017 19:39:33: #1 Redundant rate of treatment: 0.53 INFO @ Sun, 03 Sep 2017 19:39:33: #1 finished! INFO @ Sun, 03 Sep 2017 19:39:34: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:39:34: #2 looking for paired plus/minus strand peaks... cat: SRX2675877.20_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): 7 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675877.20_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 `SRX2675877.20_*.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 `SRX2675877.20_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 @ Sun, 03 Sep 2017 19:39:34: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:39:34: 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 19:39:34: Process for pairing-model is terminated! cat: SRX2675877.05_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): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675877.05_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 `SRX2675877.05_*.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 `SRX2675877.05_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 19:39:35: 21000000 INFO @ Sun, 03 Sep 2017 19:39:36: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:39:36: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:39:36: #1 total tags in treatment: 9609313 INFO @ Sun, 03 Sep 2017 19:39:36: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:39:36: #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 19:39:36: #1 tags after filtering in treatment: 4530278 INFO @ Sun, 03 Sep 2017 19:39:36: #1 Redundant rate of treatment: 0.53 INFO @ Sun, 03 Sep 2017 19:39:36: #1 finished! INFO @ Sun, 03 Sep 2017 19:39:36: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:39:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:39:36: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:39:36: 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 19:39:36: Process for pairing-model is terminated! cat: SRX2675877.10_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): 7 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675877.10_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 `SRX2675877.10_*.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 `SRX2675877.10_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。