Job ID = 9732100 sra ファイルのダウンロード中... Completed: 389382K bytes transferred in 11 seconds (282562K bits/sec), in 1 file, 2 directories. 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 16780792 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675891/SRR5380667.sra Written 16780792 spots total 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: 00:07:07 16780792 reads; of these: 16780792 (100.00%) were paired; of these: 5256806 (31.33%) aligned concordantly 0 times 10258611 (61.13%) aligned concordantly exactly 1 time 1265375 (7.54%) aligned concordantly >1 times ---- 5256806 pairs aligned concordantly 0 times; of these: 730446 (13.90%) aligned discordantly 1 time ---- 4526360 pairs aligned 0 times concordantly or discordantly; of these: 9052720 mates make up the pairs; of these: 8203866 (90.62%) aligned 0 times 586173 (6.48%) aligned exactly 1 time 262681 (2.90%) aligned >1 times 75.56% overall alignment rate Time searching: 00:07:08 Overall time: 00:07:08 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] 1693535 / 11989674 = 0.1412 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 @ Sun, 03 Sep 2017 19:46:55: # Command line: callpeak -t SRX2675891.bam -f BAM -g 12100000 -n SRX2675891.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675891.05 # format = BAM # ChIP-seq file = ['SRX2675891.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 @ Sun, 03 Sep 2017 19:46:55: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:46:55: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:46:55: # Command line: callpeak -t SRX2675891.bam -f BAM -g 12100000 -n SRX2675891.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675891.20 # format = BAM # ChIP-seq file = ['SRX2675891.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 @ Sun, 03 Sep 2017 19:46:55: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:46:55: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:46:55: # Command line: callpeak -t SRX2675891.bam -f BAM -g 12100000 -n SRX2675891.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675891.10 # format = BAM # ChIP-seq file = ['SRX2675891.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 @ Sun, 03 Sep 2017 19:46:55: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:46:55: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:46:59: 1000000 INFO @ Sun, 03 Sep 2017 19:47:00: 1000000 INFO @ Sun, 03 Sep 2017 19:47:00: 1000000 INFO @ Sun, 03 Sep 2017 19:47:04: 2000000 INFO @ Sun, 03 Sep 2017 19:47:04: 2000000 INFO @ Sun, 03 Sep 2017 19:47:05: 2000000 INFO @ Sun, 03 Sep 2017 19:47:09: 3000000 INFO @ Sun, 03 Sep 2017 19:47:09: 3000000 INFO @ Sun, 03 Sep 2017 19:47:10: 3000000 INFO @ Sun, 03 Sep 2017 19:47:14: 4000000 INFO @ Sun, 03 Sep 2017 19:47:14: 4000000 INFO @ Sun, 03 Sep 2017 19:47:15: 4000000 INFO @ Sun, 03 Sep 2017 19:47:19: 5000000 INFO @ Sun, 03 Sep 2017 19:47:19: 5000000 INFO @ Sun, 03 Sep 2017 19:47:20: 5000000 INFO @ Sun, 03 Sep 2017 19:47:24: 6000000 INFO @ Sun, 03 Sep 2017 19:47:24: 6000000 INFO @ Sun, 03 Sep 2017 19:47:25: 6000000 INFO @ Sun, 03 Sep 2017 19:47:28: 7000000 INFO @ Sun, 03 Sep 2017 19:47:29: 7000000 INFO @ Sun, 03 Sep 2017 19:47:30: 7000000 INFO @ Sun, 03 Sep 2017 19:47:33: 8000000 INFO @ Sun, 03 Sep 2017 19:47:35: 8000000 INFO @ Sun, 03 Sep 2017 19:47:35: 8000000 INFO @ Sun, 03 Sep 2017 19:47:38: 9000000 INFO @ Sun, 03 Sep 2017 19:47:40: 9000000 INFO @ Sun, 03 Sep 2017 19:47:40: 9000000 INFO @ Sun, 03 Sep 2017 19:47:43: 10000000 INFO @ Sun, 03 Sep 2017 19:47:45: 10000000 INFO @ Sun, 03 Sep 2017 19:47:45: 10000000 INFO @ Sun, 03 Sep 2017 19:47:48: 11000000 INFO @ Sun, 03 Sep 2017 19:47:50: 11000000 INFO @ Sun, 03 Sep 2017 19:47:50: 11000000 INFO @ Sun, 03 Sep 2017 19:47:53: 12000000 INFO @ Sun, 03 Sep 2017 19:47:55: 12000000 INFO @ Sun, 03 Sep 2017 19:47:55: 12000000 INFO @ Sun, 03 Sep 2017 19:47:57: 13000000 INFO @ Sun, 03 Sep 2017 19:48:00: 13000000 INFO @ Sun, 03 Sep 2017 19:48:00: 13000000 INFO @ Sun, 03 Sep 2017 19:48:02: 14000000 INFO @ Sun, 03 Sep 2017 19:48:05: 14000000 INFO @ Sun, 03 Sep 2017 19:48:05: 14000000 INFO @ Sun, 03 Sep 2017 19:48:07: 15000000 INFO @ Sun, 03 Sep 2017 19:48:10: 15000000 INFO @ Sun, 03 Sep 2017 19:48:10: 15000000 INFO @ Sun, 03 Sep 2017 19:48:12: 16000000 INFO @ Sun, 03 Sep 2017 19:48:15: 16000000 INFO @ Sun, 03 Sep 2017 19:48:15: 16000000 INFO @ Sun, 03 Sep 2017 19:48:17: 17000000 INFO @ Sun, 03 Sep 2017 19:48:20: 17000000 INFO @ Sun, 03 Sep 2017 19:48:20: 17000000 INFO @ Sun, 03 Sep 2017 19:48:22: 18000000 INFO @ Sun, 03 Sep 2017 19:48:25: 18000000 INFO @ Sun, 03 Sep 2017 19:48:25: 18000000 INFO @ Sun, 03 Sep 2017 19:48:27: 19000000 INFO @ Sun, 03 Sep 2017 19:48:29: 19000000 INFO @ Sun, 03 Sep 2017 19:48:30: 19000000 INFO @ Sun, 03 Sep 2017 19:48:31: 20000000 INFO @ Sun, 03 Sep 2017 19:48:34: 20000000 INFO @ Sun, 03 Sep 2017 19:48:35: 20000000 INFO @ Sun, 03 Sep 2017 19:48:36: 21000000 INFO @ Sun, 03 Sep 2017 19:48:39: 21000000 INFO @ Sun, 03 Sep 2017 19:48:40: 21000000 INFO @ Sun, 03 Sep 2017 19:48:41: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:48:41: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:48:41: #1 total tags in treatment: 9842668 INFO @ Sun, 03 Sep 2017 19:48:41: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:48:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:48:41: #1 tags after filtering in treatment: 4615754 INFO @ Sun, 03 Sep 2017 19:48:41: #1 Redundant rate of treatment: 0.53 INFO @ Sun, 03 Sep 2017 19:48:41: #1 finished! INFO @ Sun, 03 Sep 2017 19:48:41: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:48:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:48:42: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:48:42: 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 @ Sun, 03 Sep 2017 19:48:42: Process for pairing-model is terminated! cat: SRX2675891.20_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675891.20_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 `SRX2675891.20_*.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 `SRX2675891.20_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 @ Sun, 03 Sep 2017 19:48:44: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:48:44: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:48:44: #1 total tags in treatment: 9842668 INFO @ Sun, 03 Sep 2017 19:48:44: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:48:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:48:44: #1 tags after filtering in treatment: 4615754 INFO @ Sun, 03 Sep 2017 19:48:44: #1 Redundant rate of treatment: 0.53 INFO @ Sun, 03 Sep 2017 19:48:44: #1 finished! INFO @ Sun, 03 Sep 2017 19:48:44: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:48:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:48:45: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:48:45: 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 @ Sun, 03 Sep 2017 19:48:45: Process for pairing-model is terminated! cat: SRX2675891.10_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675891.10_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 `SRX2675891.10_*.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 `SRX2675891.10_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 @ Sun, 03 Sep 2017 19:48:45: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:48:45: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:48:45: #1 total tags in treatment: 9842668 INFO @ Sun, 03 Sep 2017 19:48:45: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:48:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:48:45: #1 tags after filtering in treatment: 4615754 INFO @ Sun, 03 Sep 2017 19:48:45: #1 Redundant rate of treatment: 0.53 INFO @ Sun, 03 Sep 2017 19:48:45: #1 finished! INFO @ Sun, 03 Sep 2017 19:48:45: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:48:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:48:45: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:48:45: 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 @ Sun, 03 Sep 2017 19:48:45: Process for pairing-model is terminated! cat: SRX2675891.05_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675891.05_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 `SRX2675891.05_*.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 `SRX2675891.05_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。