Job ID = 10536351 sra ファイルのダウンロード中... Completed: 1764780K bytes transferred in 45 seconds (320988K 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... Written 59962227 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3433214/SRR6333855.sra Written 59962227 spots total 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: 00:15:55 59962227 reads; of these: 59962227 (100.00%) were paired; of these: 45205837 (75.39%) aligned concordantly 0 times 13435481 (22.41%) aligned concordantly exactly 1 time 1320909 (2.20%) aligned concordantly >1 times ---- 45205837 pairs aligned concordantly 0 times; of these: 125745 (0.28%) aligned discordantly 1 time ---- 45080092 pairs aligned 0 times concordantly or discordantly; of these: 90160184 mates make up the pairs; of these: 89756067 (99.55%) aligned 0 times 339727 (0.38%) aligned exactly 1 time 64390 (0.07%) aligned >1 times 25.16% overall alignment rate Time searching: 00:15:55 Overall time: 00:15:55 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 16 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] 7828260 / 14778768 = 0.5297 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 @ Thu, 05 Apr 2018 09:13:41: # Command line: callpeak -t SRX3433214.bam -f BAM -g 12100000 -n SRX3433214.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3433214.20 # format = BAM # ChIP-seq file = ['SRX3433214.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 @ Thu, 05 Apr 2018 09:13:41: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:13:41: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:13:41: # Command line: callpeak -t SRX3433214.bam -f BAM -g 12100000 -n SRX3433214.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3433214.05 # format = BAM # ChIP-seq file = ['SRX3433214.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 @ Thu, 05 Apr 2018 09:13:41: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:13:41: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:13:41: # Command line: callpeak -t SRX3433214.bam -f BAM -g 12100000 -n SRX3433214.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3433214.10 # format = BAM # ChIP-seq file = ['SRX3433214.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 @ Thu, 05 Apr 2018 09:13:41: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:13:41: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:13:47: 1000000 INFO @ Thu, 05 Apr 2018 09:13:47: 1000000 INFO @ Thu, 05 Apr 2018 09:13:48: 1000000 INFO @ Thu, 05 Apr 2018 09:13:53: 2000000 INFO @ Thu, 05 Apr 2018 09:13:54: 2000000 INFO @ Thu, 05 Apr 2018 09:13:54: 2000000 INFO @ Thu, 05 Apr 2018 09:13:59: 3000000 INFO @ Thu, 05 Apr 2018 09:14:00: 3000000 INFO @ Thu, 05 Apr 2018 09:14:01: 3000000 INFO @ Thu, 05 Apr 2018 09:14:05: 4000000 INFO @ Thu, 05 Apr 2018 09:14:07: 4000000 INFO @ Thu, 05 Apr 2018 09:14:08: 4000000 INFO @ Thu, 05 Apr 2018 09:14:11: 5000000 INFO @ Thu, 05 Apr 2018 09:14:13: 5000000 INFO @ Thu, 05 Apr 2018 09:14:15: 5000000 INFO @ Thu, 05 Apr 2018 09:14:16: 6000000 INFO @ Thu, 05 Apr 2018 09:14:20: 6000000 INFO @ Thu, 05 Apr 2018 09:14:21: 6000000 INFO @ Thu, 05 Apr 2018 09:14:22: 7000000 INFO @ Thu, 05 Apr 2018 09:14:26: 7000000 INFO @ Thu, 05 Apr 2018 09:14:28: 8000000 INFO @ Thu, 05 Apr 2018 09:14:28: 7000000 INFO @ Thu, 05 Apr 2018 09:14:32: 8000000 INFO @ Thu, 05 Apr 2018 09:14:34: 9000000 INFO @ Thu, 05 Apr 2018 09:14:35: 8000000 INFO @ Thu, 05 Apr 2018 09:14:39: 9000000 INFO @ Thu, 05 Apr 2018 09:14:39: 10000000 INFO @ Thu, 05 Apr 2018 09:14:41: 9000000 INFO @ Thu, 05 Apr 2018 09:14:45: 10000000 INFO @ Thu, 05 Apr 2018 09:14:45: 11000000 INFO @ Thu, 05 Apr 2018 09:14:48: 10000000 INFO @ Thu, 05 Apr 2018 09:14:51: 11000000 INFO @ Thu, 05 Apr 2018 09:14:51: 12000000 INFO @ Thu, 05 Apr 2018 09:14:54: 11000000 INFO @ Thu, 05 Apr 2018 09:14:56: 12000000 INFO @ Thu, 05 Apr 2018 09:14:57: 13000000 INFO @ Thu, 05 Apr 2018 09:15:00: 12000000 INFO @ Thu, 05 Apr 2018 09:15:02: 14000000 INFO @ Thu, 05 Apr 2018 09:15:02: 13000000 INFO @ Thu, 05 Apr 2018 09:15:05: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:15:05: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:15:05: #1 total tags in treatment: 6944329 INFO @ Thu, 05 Apr 2018 09:15:05: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:15:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:15:05: #1 tags after filtering in treatment: 5100023 INFO @ Thu, 05 Apr 2018 09:15:05: #1 Redundant rate of treatment: 0.27 INFO @ Thu, 05 Apr 2018 09:15:05: #1 finished! INFO @ Thu, 05 Apr 2018 09:15:05: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:15:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:15:06: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:15:06: 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 @ Thu, 05 Apr 2018 09:15:06: Process for pairing-model is terminated! cat: SRX3433214.10_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 `SRX3433214.10_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 `SRX3433214.10_*.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 `SRX3433214.10_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 @ Thu, 05 Apr 2018 09:15:07: 13000000 INFO @ Thu, 05 Apr 2018 09:15:08: 14000000 INFO @ Thu, 05 Apr 2018 09:15:11: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:15:11: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:15:11: #1 total tags in treatment: 6944329 INFO @ Thu, 05 Apr 2018 09:15:11: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:15:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:15:12: #1 tags after filtering in treatment: 5100023 INFO @ Thu, 05 Apr 2018 09:15:12: #1 Redundant rate of treatment: 0.27 INFO @ Thu, 05 Apr 2018 09:15:12: #1 finished! INFO @ Thu, 05 Apr 2018 09:15:12: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:15:12: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:15:12: 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 @ Thu, 05 Apr 2018 09:15:12: Process for pairing-model is terminated! cat: SRX3433214.05_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 `SRX3433214.05_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 `SRX3433214.05_*.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 `SRX3433214.05_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 @ Thu, 05 Apr 2018 09:15:13: 14000000 INFO @ Thu, 05 Apr 2018 09:15:16: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:15:16: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:15:16: #1 total tags in treatment: 6944329 INFO @ Thu, 05 Apr 2018 09:15:16: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:15:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:15:16: #1 tags after filtering in treatment: 5100023 INFO @ Thu, 05 Apr 2018 09:15:16: #1 Redundant rate of treatment: 0.27 INFO @ Thu, 05 Apr 2018 09:15:16: #1 finished! INFO @ Thu, 05 Apr 2018 09:15:16: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:15:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:15:16: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:15:16: 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 @ Thu, 05 Apr 2018 09:15:16: Process for pairing-model is terminated! cat: SRX3433214.20_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 `SRX3433214.20_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 `SRX3433214.20_*.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 `SRX3433214.20_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。