Job ID = 9732042 sra ファイルのダウンロード中... Completed: 396898K bytes transferred in 10 seconds (304928K 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 18018712 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675845/SRR5380622.sra Written 18018712 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: 00:09:03 18018712 reads; of these: 18018712 (100.00%) were paired; of these: 3147514 (17.47%) aligned concordantly 0 times 13684742 (75.95%) aligned concordantly exactly 1 time 1186456 (6.58%) aligned concordantly >1 times ---- 3147514 pairs aligned concordantly 0 times; of these: 874450 (27.78%) aligned discordantly 1 time ---- 2273064 pairs aligned 0 times concordantly or discordantly; of these: 4546128 mates make up the pairs; of these: 3819749 (84.02%) aligned 0 times 511755 (11.26%) aligned exactly 1 time 214624 (4.72%) aligned >1 times 89.40% overall alignment rate Time searching: 00:09:03 Overall time: 00:09:03 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] 1765926 / 15504193 = 0.1139 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 19:26:45: # Command line: callpeak -t SRX2675845.bam -f BAM -g 12100000 -n SRX2675845.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675845.05 # format = BAM # ChIP-seq file = ['SRX2675845.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 19:26:45: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:26:45: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:26:45: # Command line: callpeak -t SRX2675845.bam -f BAM -g 12100000 -n SRX2675845.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675845.20 # format = BAM # ChIP-seq file = ['SRX2675845.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 19:26:45: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:26:45: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:26:45: # Command line: callpeak -t SRX2675845.bam -f BAM -g 12100000 -n SRX2675845.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675845.10 # format = BAM # ChIP-seq file = ['SRX2675845.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 19:26:45: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:26:45: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:26:51: 1000000 INFO @ Sun, 03 Sep 2017 19:26:51: 1000000 INFO @ Sun, 03 Sep 2017 19:26:51: 1000000 INFO @ Sun, 03 Sep 2017 19:26:56: 2000000 INFO @ Sun, 03 Sep 2017 19:26:56: 2000000 INFO @ Sun, 03 Sep 2017 19:26:56: 2000000 INFO @ Sun, 03 Sep 2017 19:27:02: 3000000 INFO @ Sun, 03 Sep 2017 19:27:02: 3000000 INFO @ Sun, 03 Sep 2017 19:27:02: 3000000 INFO @ Sun, 03 Sep 2017 19:27:07: 4000000 INFO @ Sun, 03 Sep 2017 19:27:07: 4000000 INFO @ Sun, 03 Sep 2017 19:27:07: 4000000 INFO @ Sun, 03 Sep 2017 19:27:13: 5000000 INFO @ Sun, 03 Sep 2017 19:27:13: 5000000 INFO @ Sun, 03 Sep 2017 19:27:13: 5000000 INFO @ Sun, 03 Sep 2017 19:27:18: 6000000 INFO @ Sun, 03 Sep 2017 19:27:18: 6000000 INFO @ Sun, 03 Sep 2017 19:27:18: 6000000 INFO @ Sun, 03 Sep 2017 19:27:24: 7000000 INFO @ Sun, 03 Sep 2017 19:27:24: 7000000 INFO @ Sun, 03 Sep 2017 19:27:24: 7000000 INFO @ Sun, 03 Sep 2017 19:27:29: 8000000 INFO @ Sun, 03 Sep 2017 19:27:30: 8000000 INFO @ Sun, 03 Sep 2017 19:27:30: 8000000 INFO @ Sun, 03 Sep 2017 19:27:35: 9000000 INFO @ Sun, 03 Sep 2017 19:27:35: 9000000 INFO @ Sun, 03 Sep 2017 19:27:35: 9000000 INFO @ Sun, 03 Sep 2017 19:27:40: 10000000 INFO @ Sun, 03 Sep 2017 19:27:41: 10000000 INFO @ Sun, 03 Sep 2017 19:27:41: 10000000 INFO @ Sun, 03 Sep 2017 19:27:46: 11000000 INFO @ Sun, 03 Sep 2017 19:27:46: 11000000 INFO @ Sun, 03 Sep 2017 19:27:46: 11000000 INFO @ Sun, 03 Sep 2017 19:27:51: 12000000 INFO @ Sun, 03 Sep 2017 19:27:52: 12000000 INFO @ Sun, 03 Sep 2017 19:27:52: 12000000 INFO @ Sun, 03 Sep 2017 19:27:57: 13000000 INFO @ Sun, 03 Sep 2017 19:27:58: 13000000 INFO @ Sun, 03 Sep 2017 19:27:58: 13000000 INFO @ Sun, 03 Sep 2017 19:28:03: 14000000 INFO @ Sun, 03 Sep 2017 19:28:03: 14000000 INFO @ Sun, 03 Sep 2017 19:28:03: 14000000 INFO @ Sun, 03 Sep 2017 19:28:08: 15000000 INFO @ Sun, 03 Sep 2017 19:28:09: 15000000 INFO @ Sun, 03 Sep 2017 19:28:09: 15000000 INFO @ Sun, 03 Sep 2017 19:28:14: 16000000 INFO @ Sun, 03 Sep 2017 19:28:14: 16000000 INFO @ Sun, 03 Sep 2017 19:28:14: 16000000 INFO @ Sun, 03 Sep 2017 19:28:20: 17000000 INFO @ Sun, 03 Sep 2017 19:28:20: 17000000 INFO @ Sun, 03 Sep 2017 19:28:20: 17000000 INFO @ Sun, 03 Sep 2017 19:28:25: 18000000 INFO @ Sun, 03 Sep 2017 19:28:26: 18000000 INFO @ Sun, 03 Sep 2017 19:28:26: 18000000 INFO @ Sun, 03 Sep 2017 19:28:31: 19000000 INFO @ Sun, 03 Sep 2017 19:28:31: 19000000 INFO @ Sun, 03 Sep 2017 19:28:31: 19000000 INFO @ Sun, 03 Sep 2017 19:28:36: 20000000 INFO @ Sun, 03 Sep 2017 19:28:37: 20000000 INFO @ Sun, 03 Sep 2017 19:28:37: 20000000 INFO @ Sun, 03 Sep 2017 19:28:42: 21000000 INFO @ Sun, 03 Sep 2017 19:28:43: 21000000 INFO @ Sun, 03 Sep 2017 19:28:43: 21000000 INFO @ Sun, 03 Sep 2017 19:28:48: 22000000 INFO @ Sun, 03 Sep 2017 19:28:48: 22000000 INFO @ Sun, 03 Sep 2017 19:28:48: 22000000 INFO @ Sun, 03 Sep 2017 19:28:53: 23000000 INFO @ Sun, 03 Sep 2017 19:28:54: 23000000 INFO @ Sun, 03 Sep 2017 19:28:54: 23000000 INFO @ Sun, 03 Sep 2017 19:28:59: 24000000 INFO @ Sun, 03 Sep 2017 19:29:00: 24000000 INFO @ Sun, 03 Sep 2017 19:29:00: 24000000 INFO @ Sun, 03 Sep 2017 19:29:05: 25000000 INFO @ Sun, 03 Sep 2017 19:29:06: 25000000 INFO @ Sun, 03 Sep 2017 19:29:06: 25000000 INFO @ Sun, 03 Sep 2017 19:29:11: 26000000 INFO @ Sun, 03 Sep 2017 19:29:11: 26000000 INFO @ Sun, 03 Sep 2017 19:29:11: 26000000 INFO @ Sun, 03 Sep 2017 19:29:16: 27000000 INFO @ Sun, 03 Sep 2017 19:29:17: 27000000 INFO @ Sun, 03 Sep 2017 19:29:17: 27000000 INFO @ Sun, 03 Sep 2017 19:29:22: 28000000 INFO @ Sun, 03 Sep 2017 19:29:23: 28000000 INFO @ Sun, 03 Sep 2017 19:29:23: 28000000 INFO @ Sun, 03 Sep 2017 19:29:26: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:29:26: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:29:26: #1 total tags in treatment: 13112141 INFO @ Sun, 03 Sep 2017 19:29:26: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:29:26: #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 19:29:26: #1 tags after filtering in treatment: 5427256 INFO @ Sun, 03 Sep 2017 19:29:26: #1 Redundant rate of treatment: 0.59 INFO @ Sun, 03 Sep 2017 19:29:26: #1 finished! INFO @ Sun, 03 Sep 2017 19:29:26: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:29:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:29:27: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:29:27: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:29:27: #1 total tags in treatment: 13112141 INFO @ Sun, 03 Sep 2017 19:29:27: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:29:27: #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 19:29:27: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:29:27: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:29:27: #1 total tags in treatment: 13112141 INFO @ Sun, 03 Sep 2017 19:29:27: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:29:27: #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 19:29:27: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:29:27: 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 19:29:27: Process for pairing-model is terminated! cat: SRX2675845.05_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): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675845.05_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 `SRX2675845.05_*.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 `SRX2675845.05_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 19:29:27: #1 tags after filtering in treatment: 5427256 INFO @ Sun, 03 Sep 2017 19:29:27: #1 tags after filtering in treatment: 5427256 INFO @ Sun, 03 Sep 2017 19:29:27: #1 Redundant rate of treatment: 0.59 INFO @ Sun, 03 Sep 2017 19:29:27: #1 Redundant rate of treatment: 0.59 INFO @ Sun, 03 Sep 2017 19:29:27: #1 finished! INFO @ Sun, 03 Sep 2017 19:29:27: #1 finished! INFO @ Sun, 03 Sep 2017 19:29:27: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:29:27: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:29:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:29:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:29:27: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:29:27: 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 19:29:27: Process for pairing-model is terminated! INFO @ Sun, 03 Sep 2017 19:29:27: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:29:27: 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 19:29:27: Process for pairing-model is terminated! cat: SRX2675845.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX2675845.10_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): 12 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675845.20_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 `SRX2675845.20_*.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 `SRX2675845.20_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 pass1 - making usageList (0 chroms): 14 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675845.10_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 `SRX2675845.10_*.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 `SRX2675845.10_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。