Job ID = 10536530 sra ファイルのダウンロード中... Completed: 1200100K bytes transferred in 37 seconds (263283K 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 32694898 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671222/SRR6696974.sra Written 32694898 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: 00:20:56 32694898 reads; of these: 32694898 (100.00%) were paired; of these: 8907654 (27.24%) aligned concordantly 0 times 20671541 (63.23%) aligned concordantly exactly 1 time 3115703 (9.53%) aligned concordantly >1 times ---- 8907654 pairs aligned concordantly 0 times; of these: 35005 (0.39%) aligned discordantly 1 time ---- 8872649 pairs aligned 0 times concordantly or discordantly; of these: 17745298 mates make up the pairs; of these: 17518662 (98.72%) aligned 0 times 181052 (1.02%) aligned exactly 1 time 45584 (0.26%) aligned >1 times 73.21% overall alignment rate Time searching: 00:20:56 Overall time: 00:20:56 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 20 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] 14028494 / 23795538 = 0.5895 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 10:34:38: # Command line: callpeak -t SRX3671222.bam -f BAM -g 12100000 -n SRX3671222.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671222.20 # format = BAM # ChIP-seq file = ['SRX3671222.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 10:34:38: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:34:38: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:34:38: # Command line: callpeak -t SRX3671222.bam -f BAM -g 12100000 -n SRX3671222.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671222.05 # format = BAM # ChIP-seq file = ['SRX3671222.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 10:34:38: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:34:38: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:34:38: # Command line: callpeak -t SRX3671222.bam -f BAM -g 12100000 -n SRX3671222.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671222.10 # format = BAM # ChIP-seq file = ['SRX3671222.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 10:34:38: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:34:38: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:34:44: 1000000 INFO @ Thu, 05 Apr 2018 10:34:45: 1000000 INFO @ Thu, 05 Apr 2018 10:34:45: 1000000 INFO @ Thu, 05 Apr 2018 10:34:50: 2000000 INFO @ Thu, 05 Apr 2018 10:34:52: 2000000 INFO @ Thu, 05 Apr 2018 10:34:52: 2000000 INFO @ Thu, 05 Apr 2018 10:34:56: 3000000 INFO @ Thu, 05 Apr 2018 10:34:59: 3000000 INFO @ Thu, 05 Apr 2018 10:34:59: 3000000 INFO @ Thu, 05 Apr 2018 10:35:02: 4000000 INFO @ Thu, 05 Apr 2018 10:35:06: 4000000 INFO @ Thu, 05 Apr 2018 10:35:06: 4000000 INFO @ Thu, 05 Apr 2018 10:35:08: 5000000 INFO @ Thu, 05 Apr 2018 10:35:13: 5000000 INFO @ Thu, 05 Apr 2018 10:35:13: 5000000 INFO @ Thu, 05 Apr 2018 10:35:14: 6000000 INFO @ Thu, 05 Apr 2018 10:35:20: 6000000 INFO @ Thu, 05 Apr 2018 10:35:20: 6000000 INFO @ Thu, 05 Apr 2018 10:35:20: 7000000 INFO @ Thu, 05 Apr 2018 10:35:26: 8000000 INFO @ Thu, 05 Apr 2018 10:35:27: 7000000 INFO @ Thu, 05 Apr 2018 10:35:27: 7000000 INFO @ Thu, 05 Apr 2018 10:35:32: 9000000 INFO @ Thu, 05 Apr 2018 10:35:33: 8000000 INFO @ Thu, 05 Apr 2018 10:35:33: 8000000 INFO @ Thu, 05 Apr 2018 10:35:38: 10000000 INFO @ Thu, 05 Apr 2018 10:35:40: 9000000 INFO @ Thu, 05 Apr 2018 10:35:40: 9000000 INFO @ Thu, 05 Apr 2018 10:35:44: 11000000 INFO @ Thu, 05 Apr 2018 10:35:47: 10000000 INFO @ Thu, 05 Apr 2018 10:35:47: 10000000 INFO @ Thu, 05 Apr 2018 10:35:50: 12000000 INFO @ Thu, 05 Apr 2018 10:35:54: 11000000 INFO @ Thu, 05 Apr 2018 10:35:54: 11000000 INFO @ Thu, 05 Apr 2018 10:35:56: 13000000 INFO @ Thu, 05 Apr 2018 10:36:01: 12000000 INFO @ Thu, 05 Apr 2018 10:36:01: 12000000 INFO @ Thu, 05 Apr 2018 10:36:02: 14000000 INFO @ Thu, 05 Apr 2018 10:36:08: 13000000 INFO @ Thu, 05 Apr 2018 10:36:08: 13000000 INFO @ Thu, 05 Apr 2018 10:36:08: 15000000 INFO @ Thu, 05 Apr 2018 10:36:14: 16000000 INFO @ Thu, 05 Apr 2018 10:36:14: 14000000 INFO @ Thu, 05 Apr 2018 10:36:14: 14000000 INFO @ Thu, 05 Apr 2018 10:36:20: 17000000 INFO @ Thu, 05 Apr 2018 10:36:21: 15000000 INFO @ Thu, 05 Apr 2018 10:36:21: 15000000 INFO @ Thu, 05 Apr 2018 10:36:26: 18000000 INFO @ Thu, 05 Apr 2018 10:36:28: 16000000 INFO @ Thu, 05 Apr 2018 10:36:28: 16000000 INFO @ Thu, 05 Apr 2018 10:36:32: 19000000 INFO @ Thu, 05 Apr 2018 10:36:35: 17000000 INFO @ Thu, 05 Apr 2018 10:36:35: 17000000 INFO @ Thu, 05 Apr 2018 10:36:36: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:36:36: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:36:36: #1 total tags in treatment: 9764647 INFO @ Thu, 05 Apr 2018 10:36:36: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:36:36: #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 10:36:37: #1 tags after filtering in treatment: 5046343 INFO @ Thu, 05 Apr 2018 10:36:37: #1 Redundant rate of treatment: 0.48 INFO @ Thu, 05 Apr 2018 10:36:37: #1 finished! INFO @ Thu, 05 Apr 2018 10:36:37: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:36:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:36:37: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:36:37: 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 10:36:37: Process for pairing-model is terminated! cat: SRX3671222.20_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 `SRX3671222.20_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 `SRX3671222.20_*.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 `SRX3671222.20_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 @ Thu, 05 Apr 2018 10:36:42: 18000000 INFO @ Thu, 05 Apr 2018 10:36:42: 18000000 INFO @ Thu, 05 Apr 2018 10:36:48: 19000000 INFO @ Thu, 05 Apr 2018 10:36:48: 19000000 INFO @ Thu, 05 Apr 2018 10:36:54: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:36:54: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:36:54: #1 total tags in treatment: 9764647 INFO @ Thu, 05 Apr 2018 10:36:54: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:36:54: #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 10:36:54: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:36:54: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:36:54: #1 total tags in treatment: 9764647 INFO @ Thu, 05 Apr 2018 10:36:54: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:36:54: #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 10:36:54: #1 tags after filtering in treatment: 5046343 INFO @ Thu, 05 Apr 2018 10:36:54: #1 Redundant rate of treatment: 0.48 INFO @ Thu, 05 Apr 2018 10:36:54: #1 finished! INFO @ Thu, 05 Apr 2018 10:36:54: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:36:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:36:54: #1 tags after filtering in treatment: 5046343 INFO @ Thu, 05 Apr 2018 10:36:54: #1 Redundant rate of treatment: 0.48 INFO @ Thu, 05 Apr 2018 10:36:54: #1 finished! INFO @ Thu, 05 Apr 2018 10:36:54: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:36:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:36:54: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:36:54: 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 10:36:54: Process for pairing-model is terminated! cat: SRX3671222.05_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 `SRX3671222.05_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 `SRX3671222.05_*.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 `SRX3671222.05_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 10:36:54: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:36:54: 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 10:36:54: Process for pairing-model is terminated! cat: SRX3671222.10_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 `SRX3671222.10_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 `SRX3671222.10_*.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 `SRX3671222.10_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。