Job ID = 9732052 sra ファイルのダウンロード中... Completed: 363591K bytes transferred in 14 seconds (209286K 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 16585091 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675853/SRR5380629.sra Written 16585091 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: 00:07:43 16585091 reads; of these: 16585091 (100.00%) were paired; of these: 3117026 (18.79%) aligned concordantly 0 times 12287411 (74.09%) aligned concordantly exactly 1 time 1180654 (7.12%) aligned concordantly >1 times ---- 3117026 pairs aligned concordantly 0 times; of these: 965255 (30.97%) aligned discordantly 1 time ---- 2151771 pairs aligned 0 times concordantly or discordantly; of these: 4303542 mates make up the pairs; of these: 3607603 (83.83%) aligned 0 times 449052 (10.43%) aligned exactly 1 time 246887 (5.74%) aligned >1 times 89.12% overall alignment rate Time searching: 00:07:43 Overall time: 00:07:43 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] 2064939 / 14280726 = 0.1446 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 19:26:08: # Command line: callpeak -t SRX2675853.bam -f BAM -g 12100000 -n SRX2675853.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675853.05 # format = BAM # ChIP-seq file = ['SRX2675853.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 19:26:08: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:26:08: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:26:08: # Command line: callpeak -t SRX2675853.bam -f BAM -g 12100000 -n SRX2675853.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675853.20 # format = BAM # ChIP-seq file = ['SRX2675853.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 19:26:08: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:26:08: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:26:08: # Command line: callpeak -t SRX2675853.bam -f BAM -g 12100000 -n SRX2675853.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675853.10 # format = BAM # ChIP-seq file = ['SRX2675853.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 19:26:08: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:26:08: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:26:13: 1000000 INFO @ Sun, 03 Sep 2017 19:26:13: 1000000 INFO @ Sun, 03 Sep 2017 19:26:13: 1000000 INFO @ Sun, 03 Sep 2017 19:26:18: 2000000 INFO @ Sun, 03 Sep 2017 19:26:18: 2000000 INFO @ Sun, 03 Sep 2017 19:26:18: 2000000 INFO @ Sun, 03 Sep 2017 19:26:23: 3000000 INFO @ Sun, 03 Sep 2017 19:26:23: 3000000 INFO @ Sun, 03 Sep 2017 19:26:24: 3000000 INFO @ Sun, 03 Sep 2017 19:26:27: 4000000 INFO @ Sun, 03 Sep 2017 19:26:28: 4000000 INFO @ Sun, 03 Sep 2017 19:26:29: 4000000 INFO @ Sun, 03 Sep 2017 19:26:32: 5000000 INFO @ Sun, 03 Sep 2017 19:26:33: 5000000 INFO @ Sun, 03 Sep 2017 19:26:35: 5000000 INFO @ Sun, 03 Sep 2017 19:26:37: 6000000 INFO @ Sun, 03 Sep 2017 19:26:38: 6000000 INFO @ Sun, 03 Sep 2017 19:26:40: 6000000 INFO @ Sun, 03 Sep 2017 19:26:42: 7000000 INFO @ Sun, 03 Sep 2017 19:26:43: 7000000 INFO @ Sun, 03 Sep 2017 19:26:45: 7000000 INFO @ Sun, 03 Sep 2017 19:26:47: 8000000 INFO @ Sun, 03 Sep 2017 19:26:48: 8000000 INFO @ Sun, 03 Sep 2017 19:26:51: 8000000 INFO @ Sun, 03 Sep 2017 19:26:52: 9000000 INFO @ Sun, 03 Sep 2017 19:26:53: 9000000 INFO @ Sun, 03 Sep 2017 19:26:56: 9000000 INFO @ Sun, 03 Sep 2017 19:26:56: 10000000 INFO @ Sun, 03 Sep 2017 19:26:58: 10000000 INFO @ Sun, 03 Sep 2017 19:27:01: 11000000 INFO @ Sun, 03 Sep 2017 19:27:02: 10000000 INFO @ Sun, 03 Sep 2017 19:27:03: 11000000 INFO @ Sun, 03 Sep 2017 19:27:06: 12000000 INFO @ Sun, 03 Sep 2017 19:27:07: 11000000 INFO @ Sun, 03 Sep 2017 19:27:07: 12000000 INFO @ Sun, 03 Sep 2017 19:27:11: 13000000 INFO @ Sun, 03 Sep 2017 19:27:12: 13000000 INFO @ Sun, 03 Sep 2017 19:27:12: 12000000 INFO @ Sun, 03 Sep 2017 19:27:15: 14000000 INFO @ Sun, 03 Sep 2017 19:27:17: 14000000 INFO @ Sun, 03 Sep 2017 19:27:18: 13000000 INFO @ Sun, 03 Sep 2017 19:27:20: 15000000 INFO @ Sun, 03 Sep 2017 19:27:22: 15000000 INFO @ Sun, 03 Sep 2017 19:27:23: 14000000 INFO @ Sun, 03 Sep 2017 19:27:25: 16000000 INFO @ Sun, 03 Sep 2017 19:27:27: 16000000 INFO @ Sun, 03 Sep 2017 19:27:29: 15000000 INFO @ Sun, 03 Sep 2017 19:27:30: 17000000 INFO @ Sun, 03 Sep 2017 19:27:32: 17000000 INFO @ Sun, 03 Sep 2017 19:27:34: 16000000 INFO @ Sun, 03 Sep 2017 19:27:35: 18000000 INFO @ Sun, 03 Sep 2017 19:27:37: 18000000 INFO @ Sun, 03 Sep 2017 19:27:39: 19000000 INFO @ Sun, 03 Sep 2017 19:27:40: 17000000 INFO @ Sun, 03 Sep 2017 19:27:42: 19000000 INFO @ Sun, 03 Sep 2017 19:27:44: 20000000 INFO @ Sun, 03 Sep 2017 19:27:45: 18000000 INFO @ Sun, 03 Sep 2017 19:27:47: 20000000 INFO @ Sun, 03 Sep 2017 19:27:49: 21000000 INFO @ Sun, 03 Sep 2017 19:27:51: 19000000 INFO @ Sun, 03 Sep 2017 19:27:52: 21000000 INFO @ Sun, 03 Sep 2017 19:27:54: 22000000 INFO @ Sun, 03 Sep 2017 19:27:56: 20000000 INFO @ Sun, 03 Sep 2017 19:27:57: 22000000 INFO @ Sun, 03 Sep 2017 19:27:58: 23000000 INFO @ Sun, 03 Sep 2017 19:28:02: 21000000 INFO @ Sun, 03 Sep 2017 19:28:02: 23000000 INFO @ Sun, 03 Sep 2017 19:28:03: 24000000 INFO @ Sun, 03 Sep 2017 19:28:07: 24000000 INFO @ Sun, 03 Sep 2017 19:28:07: 22000000 INFO @ Sun, 03 Sep 2017 19:28:08: 25000000 INFO @ Sun, 03 Sep 2017 19:28:10: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:28:10: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:28:10: #1 total tags in treatment: 11418840 INFO @ Sun, 03 Sep 2017 19:28:10: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:28:10: #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 19:28:10: #1 tags after filtering in treatment: 4829698 INFO @ Sun, 03 Sep 2017 19:28:10: #1 Redundant rate of treatment: 0.58 INFO @ Sun, 03 Sep 2017 19:28:10: #1 finished! INFO @ Sun, 03 Sep 2017 19:28:10: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:28:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:28:11: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:28:11: 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 19:28:11: Process for pairing-model is terminated! cat: SRX2675853.05_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675853.05_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 `SRX2675853.05_*.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 `SRX2675853.05_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 @ Sun, 03 Sep 2017 19:28:12: 25000000 INFO @ Sun, 03 Sep 2017 19:28:13: 23000000 INFO @ Sun, 03 Sep 2017 19:28:14: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:28:14: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:28:14: #1 total tags in treatment: 11418840 INFO @ Sun, 03 Sep 2017 19:28:14: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:28:14: #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 19:28:15: #1 tags after filtering in treatment: 4829698 INFO @ Sun, 03 Sep 2017 19:28:15: #1 Redundant rate of treatment: 0.58 INFO @ Sun, 03 Sep 2017 19:28:15: #1 finished! INFO @ Sun, 03 Sep 2017 19:28:15: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:28:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:28:15: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:28:15: 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 19:28:15: Process for pairing-model is terminated! cat: SRX2675853.10_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675853.10_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 `SRX2675853.10_*.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 `SRX2675853.10_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 19:28:17: 24000000 INFO @ Sun, 03 Sep 2017 19:28:22: 25000000 INFO @ Sun, 03 Sep 2017 19:28:24: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:28:24: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:28:24: #1 total tags in treatment: 11418840 INFO @ Sun, 03 Sep 2017 19:28:24: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:28:24: #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 19:28:25: #1 tags after filtering in treatment: 4829698 INFO @ Sun, 03 Sep 2017 19:28:25: #1 Redundant rate of treatment: 0.58 INFO @ Sun, 03 Sep 2017 19:28:25: #1 finished! INFO @ Sun, 03 Sep 2017 19:28:25: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:28:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:28:25: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:28:25: 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 19:28:25: Process for pairing-model is terminated! cat: SRX2675853.20_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 `SRX2675853.20_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 `SRX2675853.20_*.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 `SRX2675853.20_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。