Job ID = 10536520 sra ファイルのダウンロード中... Completed: 979969K bytes transferred in 27 seconds (290583K 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 24994286 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671213/SRR6696965.sra Written 24994286 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: 00:17:04 24994286 reads; of these: 24994286 (100.00%) were paired; of these: 4366424 (17.47%) aligned concordantly 0 times 17793871 (71.19%) aligned concordantly exactly 1 time 2833991 (11.34%) aligned concordantly >1 times ---- 4366424 pairs aligned concordantly 0 times; of these: 45735 (1.05%) aligned discordantly 1 time ---- 4320689 pairs aligned 0 times concordantly or discordantly; of these: 8641378 mates make up the pairs; of these: 8406520 (97.28%) aligned 0 times 177931 (2.06%) aligned exactly 1 time 56927 (0.66%) aligned >1 times 83.18% overall alignment rate Time searching: 00:17:04 Overall time: 00:17:04 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] 8263678 / 20647162 = 0.4002 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 10:27:35: # Command line: callpeak -t SRX3671213.bam -f BAM -g 12100000 -n SRX3671213.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671213.10 # format = BAM # ChIP-seq file = ['SRX3671213.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 10:27:35: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:27:35: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:27:35: # Command line: callpeak -t SRX3671213.bam -f BAM -g 12100000 -n SRX3671213.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671213.05 # format = BAM # ChIP-seq file = ['SRX3671213.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 10:27:35: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:27:35: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:27:35: # Command line: callpeak -t SRX3671213.bam -f BAM -g 12100000 -n SRX3671213.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671213.20 # format = BAM # ChIP-seq file = ['SRX3671213.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 10:27:35: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:27:35: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:27:41: 1000000 INFO @ Thu, 05 Apr 2018 10:27:41: 1000000 INFO @ Thu, 05 Apr 2018 10:27:41: 1000000 INFO @ Thu, 05 Apr 2018 10:27:48: 2000000 INFO @ Thu, 05 Apr 2018 10:27:48: 2000000 INFO @ Thu, 05 Apr 2018 10:27:48: 2000000 INFO @ Thu, 05 Apr 2018 10:27:54: 3000000 INFO @ Thu, 05 Apr 2018 10:27:54: 3000000 INFO @ Thu, 05 Apr 2018 10:27:54: 3000000 INFO @ Thu, 05 Apr 2018 10:28:00: 4000000 INFO @ Thu, 05 Apr 2018 10:28:00: 4000000 INFO @ Thu, 05 Apr 2018 10:28:01: 4000000 INFO @ Thu, 05 Apr 2018 10:28:07: 5000000 INFO @ Thu, 05 Apr 2018 10:28:07: 5000000 INFO @ Thu, 05 Apr 2018 10:28:07: 5000000 INFO @ Thu, 05 Apr 2018 10:28:13: 6000000 INFO @ Thu, 05 Apr 2018 10:28:13: 6000000 INFO @ Thu, 05 Apr 2018 10:28:14: 6000000 INFO @ Thu, 05 Apr 2018 10:28:20: 7000000 INFO @ Thu, 05 Apr 2018 10:28:20: 7000000 INFO @ Thu, 05 Apr 2018 10:28:20: 7000000 INFO @ Thu, 05 Apr 2018 10:28:26: 8000000 INFO @ Thu, 05 Apr 2018 10:28:26: 8000000 INFO @ Thu, 05 Apr 2018 10:28:26: 8000000 INFO @ Thu, 05 Apr 2018 10:28:33: 9000000 INFO @ Thu, 05 Apr 2018 10:28:33: 9000000 INFO @ Thu, 05 Apr 2018 10:28:33: 9000000 INFO @ Thu, 05 Apr 2018 10:28:39: 10000000 INFO @ Thu, 05 Apr 2018 10:28:39: 10000000 INFO @ Thu, 05 Apr 2018 10:28:39: 10000000 INFO @ Thu, 05 Apr 2018 10:28:45: 11000000 INFO @ Thu, 05 Apr 2018 10:28:45: 11000000 INFO @ Thu, 05 Apr 2018 10:28:46: 11000000 INFO @ Thu, 05 Apr 2018 10:28:52: 12000000 INFO @ Thu, 05 Apr 2018 10:28:52: 12000000 INFO @ Thu, 05 Apr 2018 10:28:52: 12000000 INFO @ Thu, 05 Apr 2018 10:28:58: 13000000 INFO @ Thu, 05 Apr 2018 10:28:59: 13000000 INFO @ Thu, 05 Apr 2018 10:28:59: 13000000 INFO @ Thu, 05 Apr 2018 10:29:04: 14000000 INFO @ Thu, 05 Apr 2018 10:29:05: 14000000 INFO @ Thu, 05 Apr 2018 10:29:05: 14000000 INFO @ Thu, 05 Apr 2018 10:29:11: 15000000 INFO @ Thu, 05 Apr 2018 10:29:11: 15000000 INFO @ Thu, 05 Apr 2018 10:29:11: 15000000 INFO @ Thu, 05 Apr 2018 10:29:17: 16000000 INFO @ Thu, 05 Apr 2018 10:29:18: 16000000 INFO @ Thu, 05 Apr 2018 10:29:18: 16000000 INFO @ Thu, 05 Apr 2018 10:29:23: 17000000 INFO @ Thu, 05 Apr 2018 10:29:24: 17000000 INFO @ Thu, 05 Apr 2018 10:29:25: 17000000 INFO @ Thu, 05 Apr 2018 10:29:30: 18000000 INFO @ Thu, 05 Apr 2018 10:29:30: 18000000 INFO @ Thu, 05 Apr 2018 10:29:32: 18000000 INFO @ Thu, 05 Apr 2018 10:29:36: 19000000 INFO @ Thu, 05 Apr 2018 10:29:37: 19000000 INFO @ Thu, 05 Apr 2018 10:29:39: 19000000 INFO @ Thu, 05 Apr 2018 10:29:42: 20000000 INFO @ Thu, 05 Apr 2018 10:29:45: 20000000 INFO @ Thu, 05 Apr 2018 10:29:46: 20000000 INFO @ Thu, 05 Apr 2018 10:29:48: 21000000 INFO @ Thu, 05 Apr 2018 10:29:52: 21000000 INFO @ Thu, 05 Apr 2018 10:29:53: 21000000 INFO @ Thu, 05 Apr 2018 10:29:54: 22000000 INFO @ Thu, 05 Apr 2018 10:29:59: 22000000 INFO @ Thu, 05 Apr 2018 10:30:00: 22000000 INFO @ Thu, 05 Apr 2018 10:30:00: 23000000 INFO @ Thu, 05 Apr 2018 10:30:05: 23000000 INFO @ Thu, 05 Apr 2018 10:30:06: 24000000 INFO @ Thu, 05 Apr 2018 10:30:07: 23000000 INFO @ Thu, 05 Apr 2018 10:30:12: 25000000 INFO @ Thu, 05 Apr 2018 10:30:12: 24000000 INFO @ Thu, 05 Apr 2018 10:30:13: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:30:13: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:30:13: #1 total tags in treatment: 12370454 INFO @ Thu, 05 Apr 2018 10:30:13: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:30:13: #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 10:30:13: #1 tags after filtering in treatment: 5694744 INFO @ Thu, 05 Apr 2018 10:30:13: #1 Redundant rate of treatment: 0.54 INFO @ Thu, 05 Apr 2018 10:30:13: #1 finished! INFO @ Thu, 05 Apr 2018 10:30:13: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:30:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:30:13: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:30:13: 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 10:30:13: Process for pairing-model is terminated! cat: SRX3671213.05_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 `SRX3671213.05_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 `SRX3671213.05_*.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 `SRX3671213.05_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 10:30:14: 24000000 INFO @ Thu, 05 Apr 2018 10:30:19: 25000000 INFO @ Thu, 05 Apr 2018 10:30:20: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:30:20: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:30:20: #1 total tags in treatment: 12370454 INFO @ Thu, 05 Apr 2018 10:30:20: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:30:20: #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 10:30:20: #1 tags after filtering in treatment: 5694744 INFO @ Thu, 05 Apr 2018 10:30:20: #1 Redundant rate of treatment: 0.54 INFO @ Thu, 05 Apr 2018 10:30:20: #1 finished! INFO @ Thu, 05 Apr 2018 10:30:20: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:30:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:30:20: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:30:20: 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 10:30:20: Process for pairing-model is terminated! cat: SRX3671213.10_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 `SRX3671213.10_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 `SRX3671213.10_*.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 `SRX3671213.10_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 10:30:21: 25000000 INFO @ Thu, 05 Apr 2018 10:30:21: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:30:21: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:30:21: #1 total tags in treatment: 12370454 INFO @ Thu, 05 Apr 2018 10:30:21: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:30:21: #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 10:30:22: #1 tags after filtering in treatment: 5694744 INFO @ Thu, 05 Apr 2018 10:30:22: #1 Redundant rate of treatment: 0.54 INFO @ Thu, 05 Apr 2018 10:30:22: #1 finished! INFO @ Thu, 05 Apr 2018 10:30:22: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:30:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:30:22: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:30:22: 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 10:30:22: Process for pairing-model is terminated! cat: SRX3671213.20_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 `SRX3671213.20_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 `SRX3671213.20_*.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 `SRX3671213.20_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。