Job ID = 10536394 sra ファイルのダウンロード中... Completed: 1087332K bytes transferred in 22 seconds (399825K 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 26925765 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671148/SRR6696900.sra Written 26925765 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: 00:18:12 26925765 reads; of these: 26925765 (100.00%) were paired; of these: 5057467 (18.78%) aligned concordantly 0 times 19338379 (71.82%) aligned concordantly exactly 1 time 2529919 (9.40%) aligned concordantly >1 times ---- 5057467 pairs aligned concordantly 0 times; of these: 75111 (1.49%) aligned discordantly 1 time ---- 4982356 pairs aligned 0 times concordantly or discordantly; of these: 9964712 mates make up the pairs; of these: 9502257 (95.36%) aligned 0 times 384801 (3.86%) aligned exactly 1 time 77654 (0.78%) aligned >1 times 82.35% overall alignment rate Time searching: 00:18:12 Overall time: 00:18:12 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] 16046631 / 21884777 = 0.7332 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 09:43:45: # Command line: callpeak -t SRX3671148.bam -f BAM -g 12100000 -n SRX3671148.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671148.05 # format = BAM # ChIP-seq file = ['SRX3671148.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 09:43:45: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:43:45: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:43:45: # Command line: callpeak -t SRX3671148.bam -f BAM -g 12100000 -n SRX3671148.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671148.10 # format = BAM # ChIP-seq file = ['SRX3671148.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 09:43:45: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:43:45: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:43:45: # Command line: callpeak -t SRX3671148.bam -f BAM -g 12100000 -n SRX3671148.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671148.20 # format = BAM # ChIP-seq file = ['SRX3671148.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 09:43:45: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:43:45: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:43:51: 1000000 INFO @ Thu, 05 Apr 2018 09:43:51: 1000000 INFO @ Thu, 05 Apr 2018 09:43:51: 1000000 INFO @ Thu, 05 Apr 2018 09:43:56: 2000000 INFO @ Thu, 05 Apr 2018 09:43:56: 2000000 INFO @ Thu, 05 Apr 2018 09:43:56: 2000000 INFO @ Thu, 05 Apr 2018 09:44:02: 3000000 INFO @ Thu, 05 Apr 2018 09:44:02: 3000000 INFO @ Thu, 05 Apr 2018 09:44:02: 3000000 INFO @ Thu, 05 Apr 2018 09:44:07: 4000000 INFO @ Thu, 05 Apr 2018 09:44:08: 4000000 INFO @ Thu, 05 Apr 2018 09:44:08: 4000000 INFO @ Thu, 05 Apr 2018 09:44:13: 5000000 INFO @ Thu, 05 Apr 2018 09:44:13: 5000000 INFO @ Thu, 05 Apr 2018 09:44:13: 5000000 INFO @ Thu, 05 Apr 2018 09:44:18: 6000000 INFO @ Thu, 05 Apr 2018 09:44:18: 6000000 INFO @ Thu, 05 Apr 2018 09:44:19: 6000000 INFO @ Thu, 05 Apr 2018 09:44:23: 7000000 INFO @ Thu, 05 Apr 2018 09:44:24: 7000000 INFO @ Thu, 05 Apr 2018 09:44:24: 7000000 INFO @ Thu, 05 Apr 2018 09:44:28: 8000000 INFO @ Thu, 05 Apr 2018 09:44:29: 8000000 INFO @ Thu, 05 Apr 2018 09:44:30: 8000000 INFO @ Thu, 05 Apr 2018 09:44:33: 9000000 INFO @ Thu, 05 Apr 2018 09:44:34: 9000000 INFO @ Thu, 05 Apr 2018 09:44:36: 9000000 INFO @ Thu, 05 Apr 2018 09:44:38: 10000000 INFO @ Thu, 05 Apr 2018 09:44:40: 10000000 INFO @ Thu, 05 Apr 2018 09:44:41: 10000000 INFO @ Thu, 05 Apr 2018 09:44:43: 11000000 INFO @ Thu, 05 Apr 2018 09:44:45: 11000000 INFO @ Thu, 05 Apr 2018 09:44:47: 11000000 INFO @ Thu, 05 Apr 2018 09:44:48: 12000000 INFO @ Thu, 05 Apr 2018 09:44:50: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:44:50: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:44:50: #1 total tags in treatment: 5828105 INFO @ Thu, 05 Apr 2018 09:44:50: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:44:50: #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 09:44:50: #1 tags after filtering in treatment: 4779514 INFO @ Thu, 05 Apr 2018 09:44:50: #1 Redundant rate of treatment: 0.18 INFO @ Thu, 05 Apr 2018 09:44:50: #1 finished! INFO @ Thu, 05 Apr 2018 09:44:50: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:44:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:44:50: #2 number of paired peaks: 25 WARNING @ Thu, 05 Apr 2018 09:44:50: Too few paired peaks (25) 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 09:44:50: Process for pairing-model is terminated! cat: SRX3671148.05_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 `SRX3671148.05_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 `SRX3671148.05_*.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 `SRX3671148.05_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 09:44:51: 12000000 INFO @ Thu, 05 Apr 2018 09:44:52: 12000000 INFO @ Thu, 05 Apr 2018 09:44:52: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:44:52: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:44:52: #1 total tags in treatment: 5828105 INFO @ Thu, 05 Apr 2018 09:44:52: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:44:52: #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 09:44:52: #1 tags after filtering in treatment: 4779514 INFO @ Thu, 05 Apr 2018 09:44:52: #1 Redundant rate of treatment: 0.18 INFO @ Thu, 05 Apr 2018 09:44:52: #1 finished! INFO @ Thu, 05 Apr 2018 09:44:52: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:44:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:44:53: #2 number of paired peaks: 25 WARNING @ Thu, 05 Apr 2018 09:44:53: Too few paired peaks (25) 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 09:44:53: Process for pairing-model is terminated! cat: SRX3671148.10_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 `SRX3671148.10_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 `SRX3671148.10_*.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 `SRX3671148.10_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 09:44:53: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:44:53: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:44:53: #1 total tags in treatment: 5828105 INFO @ Thu, 05 Apr 2018 09:44:53: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:44:53: #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 09:44:53: #1 tags after filtering in treatment: 4779514 INFO @ Thu, 05 Apr 2018 09:44:53: #1 Redundant rate of treatment: 0.18 INFO @ Thu, 05 Apr 2018 09:44:53: #1 finished! INFO @ Thu, 05 Apr 2018 09:44:53: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:44:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:44:54: #2 number of paired peaks: 25 WARNING @ Thu, 05 Apr 2018 09:44:54: Too few paired peaks (25) 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 09:44:54: Process for pairing-model is terminated! cat: SRX3671148.20_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 `SRX3671148.20_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 `SRX3671148.20_*.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 `SRX3671148.20_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。