Job ID = 10536405 sra ファイルのダウンロード中... Completed: 987881K bytes transferred in 19 seconds (415634K 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 21225678 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671152/SRR6696904.sra Written 21225678 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: 00:13:41 21225678 reads; of these: 21225678 (100.00%) were paired; of these: 5436219 (25.61%) aligned concordantly 0 times 13882592 (65.40%) aligned concordantly exactly 1 time 1906867 (8.98%) aligned concordantly >1 times ---- 5436219 pairs aligned concordantly 0 times; of these: 44594 (0.82%) aligned discordantly 1 time ---- 5391625 pairs aligned 0 times concordantly or discordantly; of these: 10783250 mates make up the pairs; of these: 10399788 (96.44%) aligned 0 times 322570 (2.99%) aligned exactly 1 time 60892 (0.56%) aligned >1 times 75.50% overall alignment rate Time searching: 00:13:41 Overall time: 00:13:41 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] 8815975 / 15801405 = 0.5579 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 09:38:34: # Command line: callpeak -t SRX3671152.bam -f BAM -g 12100000 -n SRX3671152.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671152.10 # format = BAM # ChIP-seq file = ['SRX3671152.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 09:38:34: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:38:34: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:38:34: # Command line: callpeak -t SRX3671152.bam -f BAM -g 12100000 -n SRX3671152.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671152.05 # format = BAM # ChIP-seq file = ['SRX3671152.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 09:38:34: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:38:34: # Command line: callpeak -t SRX3671152.bam -f BAM -g 12100000 -n SRX3671152.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671152.20 # format = BAM # ChIP-seq file = ['SRX3671152.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 09:38:34: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:38:34: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:38:34: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:38:41: 1000000 INFO @ Thu, 05 Apr 2018 09:38:41: 1000000 INFO @ Thu, 05 Apr 2018 09:38:41: 1000000 INFO @ Thu, 05 Apr 2018 09:38:48: 2000000 INFO @ Thu, 05 Apr 2018 09:38:48: 2000000 INFO @ Thu, 05 Apr 2018 09:38:50: 2000000 INFO @ Thu, 05 Apr 2018 09:38:56: 3000000 INFO @ Thu, 05 Apr 2018 09:38:56: 3000000 INFO @ Thu, 05 Apr 2018 09:38:58: 3000000 INFO @ Thu, 05 Apr 2018 09:39:03: 4000000 INFO @ Thu, 05 Apr 2018 09:39:03: 4000000 INFO @ Thu, 05 Apr 2018 09:39:07: 4000000 INFO @ Thu, 05 Apr 2018 09:39:10: 5000000 INFO @ Thu, 05 Apr 2018 09:39:10: 5000000 INFO @ Thu, 05 Apr 2018 09:39:15: 5000000 INFO @ Thu, 05 Apr 2018 09:39:18: 6000000 INFO @ Thu, 05 Apr 2018 09:39:18: 6000000 INFO @ Thu, 05 Apr 2018 09:39:23: 6000000 INFO @ Thu, 05 Apr 2018 09:39:25: 7000000 INFO @ Thu, 05 Apr 2018 09:39:25: 7000000 INFO @ Thu, 05 Apr 2018 09:39:31: 7000000 INFO @ Thu, 05 Apr 2018 09:39:32: 8000000 INFO @ Thu, 05 Apr 2018 09:39:33: 8000000 INFO @ Thu, 05 Apr 2018 09:39:38: 8000000 INFO @ Thu, 05 Apr 2018 09:39:40: 9000000 INFO @ Thu, 05 Apr 2018 09:39:40: 9000000 INFO @ Thu, 05 Apr 2018 09:39:45: 9000000 INFO @ Thu, 05 Apr 2018 09:39:47: 10000000 INFO @ Thu, 05 Apr 2018 09:39:48: 10000000 INFO @ Thu, 05 Apr 2018 09:39:53: 10000000 INFO @ Thu, 05 Apr 2018 09:39:54: 11000000 INFO @ Thu, 05 Apr 2018 09:39:55: 11000000 INFO @ Thu, 05 Apr 2018 09:40:00: 11000000 INFO @ Thu, 05 Apr 2018 09:40:01: 12000000 INFO @ Thu, 05 Apr 2018 09:40:02: 12000000 INFO @ Thu, 05 Apr 2018 09:40:07: 12000000 INFO @ Thu, 05 Apr 2018 09:40:07: 13000000 INFO @ Thu, 05 Apr 2018 09:40:10: 13000000 INFO @ Thu, 05 Apr 2018 09:40:13: 14000000 INFO @ Thu, 05 Apr 2018 09:40:14: 13000000 INFO @ Thu, 05 Apr 2018 09:40:17: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:40:17: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:40:17: #1 total tags in treatment: 6977415 INFO @ Thu, 05 Apr 2018 09:40:17: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:40:17: #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 09:40:17: 14000000 INFO @ Thu, 05 Apr 2018 09:40:17: #1 tags after filtering in treatment: 5617987 INFO @ Thu, 05 Apr 2018 09:40:17: #1 Redundant rate of treatment: 0.19 INFO @ Thu, 05 Apr 2018 09:40:17: #1 finished! INFO @ Thu, 05 Apr 2018 09:40:17: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:40:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:40:17: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:40:17: 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 09:40:17: Process for pairing-model is terminated! cat: SRX3671152.10_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 `SRX3671152.10_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 `SRX3671152.10_*.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 `SRX3671152.10_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 09:40:19: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:40:19: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:40:19: #1 total tags in treatment: 6977415 INFO @ Thu, 05 Apr 2018 09:40:19: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:40:19: #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 09:40:20: #1 tags after filtering in treatment: 5617987 INFO @ Thu, 05 Apr 2018 09:40:20: #1 Redundant rate of treatment: 0.19 INFO @ Thu, 05 Apr 2018 09:40:20: #1 finished! INFO @ Thu, 05 Apr 2018 09:40:20: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:40:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:40:20: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:40:20: 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 09:40:20: Process for pairing-model is terminated! cat: SRX3671152.20_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 `SRX3671152.20_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 `SRX3671152.20_*.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 `SRX3671152.20_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 09:40:20: 14000000 INFO @ Thu, 05 Apr 2018 09:40:23: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:40:23: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:40:23: #1 total tags in treatment: 6977415 INFO @ Thu, 05 Apr 2018 09:40:23: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:40:23: #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 09:40:23: #1 tags after filtering in treatment: 5617987 INFO @ Thu, 05 Apr 2018 09:40:23: #1 Redundant rate of treatment: 0.19 INFO @ Thu, 05 Apr 2018 09:40:23: #1 finished! INFO @ Thu, 05 Apr 2018 09:40:23: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:40:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:40:23: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:40:23: 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 09:40:23: Process for pairing-model is terminated! cat: SRX3671152.05_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 `SRX3671152.05_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 `SRX3671152.05_*.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 `SRX3671152.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。