Job ID = 10536368 sra ファイルのダウンロード中... Completed: 960588K bytes transferred in 23 seconds (341655K 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... Written 26535820 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3433230/SRR6333871.sra Written 26535820 spots total 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: 00:19:25 26535820 reads; of these: 26535820 (100.00%) were paired; of these: 4465135 (16.83%) aligned concordantly 0 times 20356130 (76.71%) aligned concordantly exactly 1 time 1714555 (6.46%) aligned concordantly >1 times ---- 4465135 pairs aligned concordantly 0 times; of these: 855505 (19.16%) aligned discordantly 1 time ---- 3609630 pairs aligned 0 times concordantly or discordantly; of these: 7219260 mates make up the pairs; of these: 4624937 (64.06%) aligned 0 times 2255268 (31.24%) aligned exactly 1 time 339055 (4.70%) aligned >1 times 91.29% overall alignment rate Time searching: 00:19:25 Overall time: 00:19:25 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 20 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] 4966671 / 22154686 = 0.2242 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 @ Thu, 05 Apr 2018 09:30:27: # Command line: callpeak -t SRX3433230.bam -f BAM -g 12100000 -n SRX3433230.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3433230.10 # format = BAM # ChIP-seq file = ['SRX3433230.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 @ Thu, 05 Apr 2018 09:30:27: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:30:27: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:30:27: # Command line: callpeak -t SRX3433230.bam -f BAM -g 12100000 -n SRX3433230.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3433230.20 # format = BAM # ChIP-seq file = ['SRX3433230.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 @ Thu, 05 Apr 2018 09:30:27: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:30:27: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:30:27: # Command line: callpeak -t SRX3433230.bam -f BAM -g 12100000 -n SRX3433230.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3433230.05 # format = BAM # ChIP-seq file = ['SRX3433230.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 @ Thu, 05 Apr 2018 09:30:27: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:30:27: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:30:32: 1000000 INFO @ Thu, 05 Apr 2018 09:30:32: 1000000 INFO @ Thu, 05 Apr 2018 09:30:32: 1000000 INFO @ Thu, 05 Apr 2018 09:30:37: 2000000 INFO @ Thu, 05 Apr 2018 09:30:37: 2000000 INFO @ Thu, 05 Apr 2018 09:30:37: 2000000 INFO @ Thu, 05 Apr 2018 09:30:42: 3000000 INFO @ Thu, 05 Apr 2018 09:30:42: 3000000 INFO @ Thu, 05 Apr 2018 09:30:42: 3000000 INFO @ Thu, 05 Apr 2018 09:30:47: 4000000 INFO @ Thu, 05 Apr 2018 09:30:47: 4000000 INFO @ Thu, 05 Apr 2018 09:30:47: 4000000 INFO @ Thu, 05 Apr 2018 09:30:52: 5000000 INFO @ Thu, 05 Apr 2018 09:30:52: 5000000 INFO @ Thu, 05 Apr 2018 09:30:52: 5000000 INFO @ Thu, 05 Apr 2018 09:30:57: 6000000 INFO @ Thu, 05 Apr 2018 09:30:57: 6000000 INFO @ Thu, 05 Apr 2018 09:30:57: 6000000 INFO @ Thu, 05 Apr 2018 09:31:02: 7000000 INFO @ Thu, 05 Apr 2018 09:31:02: 7000000 INFO @ Thu, 05 Apr 2018 09:31:02: 7000000 INFO @ Thu, 05 Apr 2018 09:31:07: 8000000 INFO @ Thu, 05 Apr 2018 09:31:07: 8000000 INFO @ Thu, 05 Apr 2018 09:31:07: 8000000 INFO @ Thu, 05 Apr 2018 09:31:11: 9000000 INFO @ Thu, 05 Apr 2018 09:31:12: 9000000 INFO @ Thu, 05 Apr 2018 09:31:12: 9000000 INFO @ Thu, 05 Apr 2018 09:31:16: 10000000 INFO @ Thu, 05 Apr 2018 09:31:17: 10000000 INFO @ Thu, 05 Apr 2018 09:31:17: 10000000 INFO @ Thu, 05 Apr 2018 09:31:21: 11000000 INFO @ Thu, 05 Apr 2018 09:31:22: 11000000 INFO @ Thu, 05 Apr 2018 09:31:22: 11000000 INFO @ Thu, 05 Apr 2018 09:31:26: 12000000 INFO @ Thu, 05 Apr 2018 09:31:27: 12000000 INFO @ Thu, 05 Apr 2018 09:31:27: 12000000 INFO @ Thu, 05 Apr 2018 09:31:31: 13000000 INFO @ Thu, 05 Apr 2018 09:31:31: 13000000 INFO @ Thu, 05 Apr 2018 09:31:32: 13000000 INFO @ Thu, 05 Apr 2018 09:31:36: 14000000 INFO @ Thu, 05 Apr 2018 09:31:36: 14000000 INFO @ Thu, 05 Apr 2018 09:31:37: 14000000 INFO @ Thu, 05 Apr 2018 09:31:40: 15000000 INFO @ Thu, 05 Apr 2018 09:31:41: 15000000 INFO @ Thu, 05 Apr 2018 09:31:42: 15000000 INFO @ Thu, 05 Apr 2018 09:31:45: 16000000 INFO @ Thu, 05 Apr 2018 09:31:46: 16000000 INFO @ Thu, 05 Apr 2018 09:31:47: 16000000 INFO @ Thu, 05 Apr 2018 09:31:50: 17000000 INFO @ Thu, 05 Apr 2018 09:31:51: 17000000 INFO @ Thu, 05 Apr 2018 09:31:52: 17000000 INFO @ Thu, 05 Apr 2018 09:31:55: 18000000 INFO @ Thu, 05 Apr 2018 09:31:56: 18000000 INFO @ Thu, 05 Apr 2018 09:31:58: 18000000 INFO @ Thu, 05 Apr 2018 09:32:00: 19000000 INFO @ Thu, 05 Apr 2018 09:32:01: 19000000 INFO @ Thu, 05 Apr 2018 09:32:03: 19000000 INFO @ Thu, 05 Apr 2018 09:32:05: 20000000 INFO @ Thu, 05 Apr 2018 09:32:06: 20000000 INFO @ Thu, 05 Apr 2018 09:32:08: 20000000 INFO @ Thu, 05 Apr 2018 09:32:09: 21000000 INFO @ Thu, 05 Apr 2018 09:32:11: 21000000 INFO @ Thu, 05 Apr 2018 09:32:13: 21000000 INFO @ Thu, 05 Apr 2018 09:32:14: 22000000 INFO @ Thu, 05 Apr 2018 09:32:16: 22000000 INFO @ Thu, 05 Apr 2018 09:32:18: 22000000 INFO @ Thu, 05 Apr 2018 09:32:19: 23000000 INFO @ Thu, 05 Apr 2018 09:32:21: 23000000 INFO @ Thu, 05 Apr 2018 09:32:23: 23000000 INFO @ Thu, 05 Apr 2018 09:32:24: 24000000 INFO @ Thu, 05 Apr 2018 09:32:26: 24000000 INFO @ Thu, 05 Apr 2018 09:32:28: 24000000 INFO @ Thu, 05 Apr 2018 09:32:29: 25000000 INFO @ Thu, 05 Apr 2018 09:32:31: 25000000 INFO @ Thu, 05 Apr 2018 09:32:33: 25000000 INFO @ Thu, 05 Apr 2018 09:32:34: 26000000 INFO @ Thu, 05 Apr 2018 09:32:36: 26000000 INFO @ Thu, 05 Apr 2018 09:32:38: 26000000 INFO @ Thu, 05 Apr 2018 09:32:38: 27000000 INFO @ Thu, 05 Apr 2018 09:32:41: 27000000 INFO @ Thu, 05 Apr 2018 09:32:43: 27000000 INFO @ Thu, 05 Apr 2018 09:32:43: 28000000 INFO @ Thu, 05 Apr 2018 09:32:46: 28000000 INFO @ Thu, 05 Apr 2018 09:32:48: 29000000 INFO @ Thu, 05 Apr 2018 09:32:48: 28000000 INFO @ Thu, 05 Apr 2018 09:32:51: 29000000 INFO @ Thu, 05 Apr 2018 09:32:53: 30000000 INFO @ Thu, 05 Apr 2018 09:32:53: 29000000 INFO @ Thu, 05 Apr 2018 09:32:56: 30000000 INFO @ Thu, 05 Apr 2018 09:32:58: 31000000 INFO @ Thu, 05 Apr 2018 09:32:58: 30000000 INFO @ Thu, 05 Apr 2018 09:33:01: 31000000 INFO @ Thu, 05 Apr 2018 09:33:03: 32000000 INFO @ Thu, 05 Apr 2018 09:33:03: 31000000 INFO @ Thu, 05 Apr 2018 09:33:06: 32000000 INFO @ Thu, 05 Apr 2018 09:33:07: 33000000 INFO @ Thu, 05 Apr 2018 09:33:08: 32000000 INFO @ Thu, 05 Apr 2018 09:33:11: 33000000 INFO @ Thu, 05 Apr 2018 09:33:12: 34000000 INFO @ Thu, 05 Apr 2018 09:33:14: 33000000 INFO @ Thu, 05 Apr 2018 09:33:16: 34000000 INFO @ Thu, 05 Apr 2018 09:33:17: 35000000 INFO @ Thu, 05 Apr 2018 09:33:19: 34000000 INFO @ Thu, 05 Apr 2018 09:33:21: 35000000 INFO @ Thu, 05 Apr 2018 09:33:22: 36000000 INFO @ Thu, 05 Apr 2018 09:33:24: 35000000 INFO @ Thu, 05 Apr 2018 09:33:26: 36000000 INFO @ Thu, 05 Apr 2018 09:33:27: 37000000 INFO @ Thu, 05 Apr 2018 09:33:29: 36000000 INFO @ Thu, 05 Apr 2018 09:33:31: 37000000 INFO @ Thu, 05 Apr 2018 09:33:32: 38000000 INFO @ Thu, 05 Apr 2018 09:33:34: 37000000 INFO @ Thu, 05 Apr 2018 09:33:34: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:33:34: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:33:34: #1 total tags in treatment: 17122392 INFO @ Thu, 05 Apr 2018 09:33:34: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:33:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:33:35: #1 tags after filtering in treatment: 10212182 INFO @ Thu, 05 Apr 2018 09:33:35: #1 Redundant rate of treatment: 0.40 INFO @ Thu, 05 Apr 2018 09:33:35: #1 finished! INFO @ Thu, 05 Apr 2018 09:33:35: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:33:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:33:35: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:33:35: 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 @ Thu, 05 Apr 2018 09:33:35: Process for pairing-model is terminated! cat: SRX3433230.20_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): 14 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3433230.20_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 `SRX3433230.20_*.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 `SRX3433230.20_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 @ Thu, 05 Apr 2018 09:33:36: 38000000 INFO @ Thu, 05 Apr 2018 09:33:39: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:33:39: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:33:39: #1 total tags in treatment: 17122392 INFO @ Thu, 05 Apr 2018 09:33:39: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:33:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:33:39: 38000000 INFO @ Thu, 05 Apr 2018 09:33:39: #1 tags after filtering in treatment: 10212182 INFO @ Thu, 05 Apr 2018 09:33:39: #1 Redundant rate of treatment: 0.40 INFO @ Thu, 05 Apr 2018 09:33:39: #1 finished! INFO @ Thu, 05 Apr 2018 09:33:39: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:33:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:33:40: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:33:40: 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 @ Thu, 05 Apr 2018 09:33:40: Process for pairing-model is terminated! cat: SRX3433230.05_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 `SRX3433230.05_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 `SRX3433230.05_*.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 `SRX3433230.05_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 @ Thu, 05 Apr 2018 09:33:42: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:33:42: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:33:42: #1 total tags in treatment: 17122392 INFO @ Thu, 05 Apr 2018 09:33:42: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:33:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:33:42: #1 tags after filtering in treatment: 10212182 INFO @ Thu, 05 Apr 2018 09:33:42: #1 Redundant rate of treatment: 0.40 INFO @ Thu, 05 Apr 2018 09:33:42: #1 finished! INFO @ Thu, 05 Apr 2018 09:33:42: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:33:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:33:43: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:33:43: 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 @ Thu, 05 Apr 2018 09:33:43: Process for pairing-model is terminated! cat: SRX3433230.10_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 `SRX3433230.10_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 `SRX3433230.10_*.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 `SRX3433230.10_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。