Job ID = 11192834 sra ファイルのダウンロード中... Completed: 837262K bytes transferred in 19 seconds (359128K 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 21782782 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1972002/SRR3946117.sra Written 21782782 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1972002/SRR3946117.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:58 21782782 reads; of these: 21782782 (100.00%) were paired; of these: 10623719 (48.77%) aligned concordantly 0 times 9868307 (45.30%) aligned concordantly exactly 1 time 1290756 (5.93%) aligned concordantly >1 times ---- 10623719 pairs aligned concordantly 0 times; of these: 163014 (1.53%) aligned discordantly 1 time ---- 10460705 pairs aligned 0 times concordantly or discordantly; of these: 20921410 mates make up the pairs; of these: 12764735 (61.01%) aligned 0 times 6909594 (33.03%) aligned exactly 1 time 1247081 (5.96%) aligned >1 times 70.70% overall alignment rate Time searching: 00:12:58 Overall time: 00:12:58 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 12 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] 6736636 / 11264392 = 0.5980 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 10:20:15: # Command line: callpeak -t SRX1972002.bam -f BAM -g 12100000 -n SRX1972002.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1972002.05 # format = BAM # ChIP-seq file = ['SRX1972002.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 10:20:15: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:20:15: # Command line: callpeak -t SRX1972002.bam -f BAM -g 12100000 -n SRX1972002.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1972002.20 # format = BAM # ChIP-seq file = ['SRX1972002.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 10:20:15: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:20:15: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:20:15: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:20:15: # Command line: callpeak -t SRX1972002.bam -f BAM -g 12100000 -n SRX1972002.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1972002.10 # format = BAM # ChIP-seq file = ['SRX1972002.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 10:20:15: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:20:15: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:20:20: 1000000 INFO @ Sat, 15 Sep 2018 10:20:20: 1000000 INFO @ Sat, 15 Sep 2018 10:20:20: 1000000 INFO @ Sat, 15 Sep 2018 10:20:25: 2000000 INFO @ Sat, 15 Sep 2018 10:20:26: 2000000 INFO @ Sat, 15 Sep 2018 10:20:26: 2000000 INFO @ Sat, 15 Sep 2018 10:20:29: 3000000 INFO @ Sat, 15 Sep 2018 10:20:31: 3000000 INFO @ Sat, 15 Sep 2018 10:20:31: 3000000 INFO @ Sat, 15 Sep 2018 10:20:34: 4000000 INFO @ Sat, 15 Sep 2018 10:20:37: 4000000 INFO @ Sat, 15 Sep 2018 10:20:37: 4000000 INFO @ Sat, 15 Sep 2018 10:20:39: 5000000 INFO @ Sat, 15 Sep 2018 10:20:42: 5000000 INFO @ Sat, 15 Sep 2018 10:20:42: 5000000 INFO @ Sat, 15 Sep 2018 10:20:44: 6000000 INFO @ Sat, 15 Sep 2018 10:20:47: 6000000 INFO @ Sat, 15 Sep 2018 10:20:47: 6000000 INFO @ Sat, 15 Sep 2018 10:20:49: 7000000 INFO @ Sat, 15 Sep 2018 10:20:53: 7000000 INFO @ Sat, 15 Sep 2018 10:20:53: 7000000 INFO @ Sat, 15 Sep 2018 10:20:54: 8000000 INFO @ Sat, 15 Sep 2018 10:20:58: 8000000 INFO @ Sat, 15 Sep 2018 10:20:58: 8000000 INFO @ Sat, 15 Sep 2018 10:20:59: 9000000 INFO @ Sat, 15 Sep 2018 10:21:04: 10000000 INFO @ Sat, 15 Sep 2018 10:21:04: 9000000 INFO @ Sat, 15 Sep 2018 10:21:04: 9000000 INFO @ Sat, 15 Sep 2018 10:21:08: 11000000 INFO @ Sat, 15 Sep 2018 10:21:09: 10000000 INFO @ Sat, 15 Sep 2018 10:21:09: 10000000 INFO @ Sat, 15 Sep 2018 10:21:13: 12000000 INFO @ Sat, 15 Sep 2018 10:21:15: 11000000 INFO @ Sat, 15 Sep 2018 10:21:15: 11000000 INFO @ Sat, 15 Sep 2018 10:21:18: 13000000 INFO @ Sat, 15 Sep 2018 10:21:20: 12000000 INFO @ Sat, 15 Sep 2018 10:21:20: 12000000 INFO @ Sat, 15 Sep 2018 10:21:23: 14000000 INFO @ Sat, 15 Sep 2018 10:21:25: 13000000 INFO @ Sat, 15 Sep 2018 10:21:25: 13000000 INFO @ Sat, 15 Sep 2018 10:21:28: 15000000 INFO @ Sat, 15 Sep 2018 10:21:31: 14000000 INFO @ Sat, 15 Sep 2018 10:21:31: 14000000 INFO @ Sat, 15 Sep 2018 10:21:33: 16000000 INFO @ Sat, 15 Sep 2018 10:21:36: 15000000 INFO @ Sat, 15 Sep 2018 10:21:36: 15000000 INFO @ Sat, 15 Sep 2018 10:21:38: 17000000 INFO @ Sat, 15 Sep 2018 10:21:40: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:21:40: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:21:40: #1 total tags in treatment: 4470637 INFO @ Sat, 15 Sep 2018 10:21:40: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:21:40: #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 10:21:40: #1 tags after filtering in treatment: 2793290 INFO @ Sat, 15 Sep 2018 10:21:40: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Sep 2018 10:21:40: #1 finished! INFO @ Sat, 15 Sep 2018 10:21:40: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:21:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:21:40: #2 number of paired peaks: 34 WARNING @ Sat, 15 Sep 2018 10:21:40: Too few paired peaks (34) 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 10:21:40: Process for pairing-model is terminated! cat: SRX1972002.10_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 `SRX1972002.10_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 `SRX1972002.10_*.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 `SRX1972002.10_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 @ Sat, 15 Sep 2018 10:21:42: 16000000 INFO @ Sat, 15 Sep 2018 10:21:42: 16000000 INFO @ Sat, 15 Sep 2018 10:21:47: 17000000 INFO @ Sat, 15 Sep 2018 10:21:47: 17000000 INFO @ Sat, 15 Sep 2018 10:21:49: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:21:49: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:21:49: #1 total tags in treatment: 4470637 INFO @ Sat, 15 Sep 2018 10:21:49: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:21:49: #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 10:21:49: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:21:49: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:21:49: #1 total tags in treatment: 4470637 INFO @ Sat, 15 Sep 2018 10:21:49: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:21:49: #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 10:21:49: #1 tags after filtering in treatment: 2793290 INFO @ Sat, 15 Sep 2018 10:21:49: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Sep 2018 10:21:49: #1 finished! INFO @ Sat, 15 Sep 2018 10:21:49: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:21:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:21:49: #1 tags after filtering in treatment: 2793290 INFO @ Sat, 15 Sep 2018 10:21:49: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Sep 2018 10:21:49: #1 finished! INFO @ Sat, 15 Sep 2018 10:21:49: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:21:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:21:49: #2 number of paired peaks: 34 WARNING @ Sat, 15 Sep 2018 10:21:49: Too few paired peaks (34) 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 10:21:49: Process for pairing-model is terminated! cat: SRX1972002.05_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1972002.05_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 `SRX1972002.05_*.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 `SRX1972002.05_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 10:21:49: #2 number of paired peaks: 34 WARNING @ Sat, 15 Sep 2018 10:21:49: Too few paired peaks (34) 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 10:21:49: Process for pairing-model is terminated! cat: SRX1972002.20_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 `SRX1972002.20_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 `SRX1972002.20_*.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 `SRX1972002.20_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。