Job ID = 11192637 sra ファイルのダウンロード中... Completed: 670389K bytes transferred in 8 seconds (618731K 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... Read 20693443 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1743198/SRR3476612.sra Written 20693443 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1743198/SRR3476612.sra 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:27 20693443 reads; of these: 20693443 (100.00%) were paired; of these: 8273689 (39.98%) aligned concordantly 0 times 10974388 (53.03%) aligned concordantly exactly 1 time 1445366 (6.98%) aligned concordantly >1 times ---- 8273689 pairs aligned concordantly 0 times; of these: 289142 (3.49%) aligned discordantly 1 time ---- 7984547 pairs aligned 0 times concordantly or discordantly; of these: 15969094 mates make up the pairs; of these: 12146928 (76.07%) aligned 0 times 3285212 (20.57%) aligned exactly 1 time 536954 (3.36%) aligned >1 times 70.65% overall alignment rate Time searching: 00:12:28 Overall time: 00:12:28 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 8 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] 7708333 / 12634938 = 0.6101 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 @ Sat, 15 Sep 2018 09:59:18: # Command line: callpeak -t SRX1743198.bam -f BAM -g 12100000 -n SRX1743198.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1743198.10 # format = BAM # ChIP-seq file = ['SRX1743198.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 @ Sat, 15 Sep 2018 09:59:18: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:59:18: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:59:18: # Command line: callpeak -t SRX1743198.bam -f BAM -g 12100000 -n SRX1743198.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1743198.20 # format = BAM # ChIP-seq file = ['SRX1743198.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 @ Sat, 15 Sep 2018 09:59:18: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:59:18: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:59:18: # Command line: callpeak -t SRX1743198.bam -f BAM -g 12100000 -n SRX1743198.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1743198.05 # format = BAM # ChIP-seq file = ['SRX1743198.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 @ Sat, 15 Sep 2018 09:59:18: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:59:18: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:59:25: 1000000 INFO @ Sat, 15 Sep 2018 09:59:25: 1000000 INFO @ Sat, 15 Sep 2018 09:59:25: 1000000 INFO @ Sat, 15 Sep 2018 09:59:32: 2000000 INFO @ Sat, 15 Sep 2018 09:59:32: 2000000 INFO @ Sat, 15 Sep 2018 09:59:32: 2000000 INFO @ Sat, 15 Sep 2018 09:59:38: 3000000 INFO @ Sat, 15 Sep 2018 09:59:38: 3000000 INFO @ Sat, 15 Sep 2018 09:59:40: 3000000 INFO @ Sat, 15 Sep 2018 09:59:45: 4000000 INFO @ Sat, 15 Sep 2018 09:59:45: 4000000 INFO @ Sat, 15 Sep 2018 09:59:48: 4000000 INFO @ Sat, 15 Sep 2018 09:59:51: 5000000 INFO @ Sat, 15 Sep 2018 09:59:52: 5000000 INFO @ Sat, 15 Sep 2018 09:59:56: 5000000 INFO @ Sat, 15 Sep 2018 09:59:57: 6000000 INFO @ Sat, 15 Sep 2018 09:59:59: 6000000 INFO @ Sat, 15 Sep 2018 10:00:03: 7000000 INFO @ Sat, 15 Sep 2018 10:00:04: 6000000 INFO @ Sat, 15 Sep 2018 10:00:06: 7000000 INFO @ Sat, 15 Sep 2018 10:00:09: 8000000 INFO @ Sat, 15 Sep 2018 10:00:12: 7000000 INFO @ Sat, 15 Sep 2018 10:00:13: 8000000 INFO @ Sat, 15 Sep 2018 10:00:16: 9000000 INFO @ Sat, 15 Sep 2018 10:00:20: 8000000 INFO @ Sat, 15 Sep 2018 10:00:20: 9000000 INFO @ Sat, 15 Sep 2018 10:00:22: 10000000 INFO @ Sat, 15 Sep 2018 10:00:27: 10000000 INFO @ Sat, 15 Sep 2018 10:00:28: 9000000 INFO @ Sat, 15 Sep 2018 10:00:28: 11000000 INFO @ Sat, 15 Sep 2018 10:00:34: 11000000 INFO @ Sat, 15 Sep 2018 10:00:34: 12000000 INFO @ Sat, 15 Sep 2018 10:00:36: 10000000 INFO @ Sat, 15 Sep 2018 10:00:40: 13000000 INFO @ Sat, 15 Sep 2018 10:00:42: 12000000 INFO @ Sat, 15 Sep 2018 10:00:44: 11000000 INFO @ Sat, 15 Sep 2018 10:00:45: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:00:45: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:00:45: #1 total tags in treatment: 4843077 INFO @ Sat, 15 Sep 2018 10:00:45: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:00:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:00:45: #1 tags after filtering in treatment: 3904977 INFO @ Sat, 15 Sep 2018 10:00:45: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Sep 2018 10:00:45: #1 finished! INFO @ Sat, 15 Sep 2018 10:00:45: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:00:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:00:45: #2 number of paired peaks: 27 WARNING @ Sat, 15 Sep 2018 10:00:45: Too few paired peaks (27) 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 @ Sat, 15 Sep 2018 10:00:45: Process for pairing-model is terminated! cat: SRX1743198.20_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 `SRX1743198.20_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 `SRX1743198.20_*.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 `SRX1743198.20_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 @ Sat, 15 Sep 2018 10:00:49: 13000000 INFO @ Sat, 15 Sep 2018 10:00:52: 12000000 INFO @ Sat, 15 Sep 2018 10:00:54: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:00:54: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:00:54: #1 total tags in treatment: 4843077 INFO @ Sat, 15 Sep 2018 10:00:54: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:00:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:00:55: #1 tags after filtering in treatment: 3904977 INFO @ Sat, 15 Sep 2018 10:00:55: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Sep 2018 10:00:55: #1 finished! INFO @ Sat, 15 Sep 2018 10:00:55: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:00:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:00:55: #2 number of paired peaks: 27 WARNING @ Sat, 15 Sep 2018 10:00:55: Too few paired peaks (27) 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 @ Sat, 15 Sep 2018 10:00:55: Process for pairing-model is terminated! cat: SRX1743198.05_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 `SRX1743198.05_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 `SRX1743198.05_*.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 `SRX1743198.05_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 @ Sat, 15 Sep 2018 10:00:59: 13000000 INFO @ Sat, 15 Sep 2018 10:01:05: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:01:05: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:01:05: #1 total tags in treatment: 4843077 INFO @ Sat, 15 Sep 2018 10:01:05: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:01:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:01:05: #1 tags after filtering in treatment: 3904977 INFO @ Sat, 15 Sep 2018 10:01:05: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Sep 2018 10:01:05: #1 finished! INFO @ Sat, 15 Sep 2018 10:01:05: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:01:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:01:05: #2 number of paired peaks: 27 WARNING @ Sat, 15 Sep 2018 10:01:05: Too few paired peaks (27) 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 @ Sat, 15 Sep 2018 10:01:05: Process for pairing-model is terminated! cat: SRX1743198.10_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1743198.10_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 `SRX1743198.10_*.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 `SRX1743198.10_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。