Job ID = 10536380 sra ファイルのダウンロード中... Completed: 1238995K bytes transferred in 33 seconds (301650K 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 31145152 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671139/SRR6696891.sra Written 31145152 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: 00:20:52 31145152 reads; of these: 31145152 (100.00%) were paired; of these: 5771125 (18.53%) aligned concordantly 0 times 22368464 (71.82%) aligned concordantly exactly 1 time 3005563 (9.65%) aligned concordantly >1 times ---- 5771125 pairs aligned concordantly 0 times; of these: 62725 (1.09%) aligned discordantly 1 time ---- 5708400 pairs aligned 0 times concordantly or discordantly; of these: 11416800 mates make up the pairs; of these: 11035262 (96.66%) aligned 0 times 315501 (2.76%) aligned exactly 1 time 66037 (0.58%) aligned >1 times 82.28% overall alignment rate Time searching: 00:20:52 Overall time: 00:20:52 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 24 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] 9429276 / 25390533 = 0.3714 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 09:39:56: # Command line: callpeak -t SRX3671139.bam -f BAM -g 12100000 -n SRX3671139.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671139.20 # format = BAM # ChIP-seq file = ['SRX3671139.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 09:39:56: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:39:56: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:39:56: # Command line: callpeak -t SRX3671139.bam -f BAM -g 12100000 -n SRX3671139.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671139.05 # format = BAM # ChIP-seq file = ['SRX3671139.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 09:39:56: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:39:56: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:39:56: # Command line: callpeak -t SRX3671139.bam -f BAM -g 12100000 -n SRX3671139.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671139.10 # format = BAM # ChIP-seq file = ['SRX3671139.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 09:39:56: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:39:56: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:40:02: 1000000 INFO @ Thu, 05 Apr 2018 09:40:02: 1000000 INFO @ Thu, 05 Apr 2018 09:40:02: 1000000 INFO @ Thu, 05 Apr 2018 09:40:08: 2000000 INFO @ Thu, 05 Apr 2018 09:40:08: 2000000 INFO @ Thu, 05 Apr 2018 09:40:08: 2000000 INFO @ Thu, 05 Apr 2018 09:40:13: 3000000 INFO @ Thu, 05 Apr 2018 09:40:13: 3000000 INFO @ Thu, 05 Apr 2018 09:40:13: 3000000 INFO @ Thu, 05 Apr 2018 09:40:19: 4000000 INFO @ Thu, 05 Apr 2018 09:40:19: 4000000 INFO @ Thu, 05 Apr 2018 09:40:19: 4000000 INFO @ Thu, 05 Apr 2018 09:40:24: 5000000 INFO @ Thu, 05 Apr 2018 09:40:25: 5000000 INFO @ Thu, 05 Apr 2018 09:40:25: 5000000 INFO @ Thu, 05 Apr 2018 09:40:29: 6000000 INFO @ Thu, 05 Apr 2018 09:40:30: 6000000 INFO @ Thu, 05 Apr 2018 09:40:31: 6000000 INFO @ Thu, 05 Apr 2018 09:40:35: 7000000 INFO @ Thu, 05 Apr 2018 09:40:36: 7000000 INFO @ Thu, 05 Apr 2018 09:40:36: 7000000 INFO @ Thu, 05 Apr 2018 09:40:40: 8000000 INFO @ Thu, 05 Apr 2018 09:40:42: 8000000 INFO @ Thu, 05 Apr 2018 09:40:42: 8000000 INFO @ Thu, 05 Apr 2018 09:40:46: 9000000 INFO @ Thu, 05 Apr 2018 09:40:47: 9000000 INFO @ Thu, 05 Apr 2018 09:40:48: 9000000 INFO @ Thu, 05 Apr 2018 09:40:51: 10000000 INFO @ Thu, 05 Apr 2018 09:40:53: 10000000 INFO @ Thu, 05 Apr 2018 09:40:54: 10000000 INFO @ Thu, 05 Apr 2018 09:40:57: 11000000 INFO @ Thu, 05 Apr 2018 09:40:59: 11000000 INFO @ Thu, 05 Apr 2018 09:41:00: 11000000 INFO @ Thu, 05 Apr 2018 09:41:02: 12000000 INFO @ Thu, 05 Apr 2018 09:41:05: 12000000 INFO @ Thu, 05 Apr 2018 09:41:06: 12000000 INFO @ Thu, 05 Apr 2018 09:41:08: 13000000 INFO @ Thu, 05 Apr 2018 09:41:11: 13000000 INFO @ Thu, 05 Apr 2018 09:41:12: 13000000 INFO @ Thu, 05 Apr 2018 09:41:14: 14000000 INFO @ Thu, 05 Apr 2018 09:41:17: 14000000 INFO @ Thu, 05 Apr 2018 09:41:18: 14000000 INFO @ Thu, 05 Apr 2018 09:41:19: 15000000 INFO @ Thu, 05 Apr 2018 09:41:23: 15000000 INFO @ Thu, 05 Apr 2018 09:41:25: 15000000 INFO @ Thu, 05 Apr 2018 09:41:25: 16000000 INFO @ Thu, 05 Apr 2018 09:41:29: 16000000 INFO @ Thu, 05 Apr 2018 09:41:31: 16000000 INFO @ Thu, 05 Apr 2018 09:41:31: 17000000 INFO @ Thu, 05 Apr 2018 09:41:35: 17000000 INFO @ Thu, 05 Apr 2018 09:41:36: 18000000 INFO @ Thu, 05 Apr 2018 09:41:37: 17000000 INFO @ Thu, 05 Apr 2018 09:41:41: 18000000 INFO @ Thu, 05 Apr 2018 09:41:42: 19000000 INFO @ Thu, 05 Apr 2018 09:41:43: 18000000 INFO @ Thu, 05 Apr 2018 09:41:47: 19000000 INFO @ Thu, 05 Apr 2018 09:41:48: 20000000 INFO @ Thu, 05 Apr 2018 09:41:49: 19000000 INFO @ Thu, 05 Apr 2018 09:41:53: 20000000 INFO @ Thu, 05 Apr 2018 09:41:53: 21000000 INFO @ Thu, 05 Apr 2018 09:41:55: 20000000 INFO @ Thu, 05 Apr 2018 09:41:59: 22000000 INFO @ Thu, 05 Apr 2018 09:42:00: 21000000 INFO @ Thu, 05 Apr 2018 09:42:02: 21000000 INFO @ Thu, 05 Apr 2018 09:42:05: 23000000 INFO @ Thu, 05 Apr 2018 09:42:06: 22000000 INFO @ Thu, 05 Apr 2018 09:42:08: 22000000 INFO @ Thu, 05 Apr 2018 09:42:11: 24000000 INFO @ Thu, 05 Apr 2018 09:42:11: 23000000 INFO @ Thu, 05 Apr 2018 09:42:14: 23000000 INFO @ Thu, 05 Apr 2018 09:42:17: 25000000 INFO @ Thu, 05 Apr 2018 09:42:18: 24000000 INFO @ Thu, 05 Apr 2018 09:42:20: 24000000 INFO @ Thu, 05 Apr 2018 09:42:22: 26000000 INFO @ Thu, 05 Apr 2018 09:42:24: 25000000 INFO @ Thu, 05 Apr 2018 09:42:26: 25000000 INFO @ Thu, 05 Apr 2018 09:42:28: 27000000 INFO @ Thu, 05 Apr 2018 09:42:30: 26000000 INFO @ Thu, 05 Apr 2018 09:42:33: 26000000 INFO @ Thu, 05 Apr 2018 09:42:34: 28000000 INFO @ Thu, 05 Apr 2018 09:42:36: 27000000 INFO @ Thu, 05 Apr 2018 09:42:39: 27000000 INFO @ Thu, 05 Apr 2018 09:42:39: 29000000 INFO @ Thu, 05 Apr 2018 09:42:42: 28000000 INFO @ Thu, 05 Apr 2018 09:42:45: 30000000 INFO @ Thu, 05 Apr 2018 09:42:45: 28000000 INFO @ Thu, 05 Apr 2018 09:42:48: 29000000 INFO @ Thu, 05 Apr 2018 09:42:50: 31000000 INFO @ Thu, 05 Apr 2018 09:42:51: 29000000 INFO @ Thu, 05 Apr 2018 09:42:53: 30000000 INFO @ Thu, 05 Apr 2018 09:42:56: 32000000 INFO @ Thu, 05 Apr 2018 09:42:57: 30000000 INFO @ Thu, 05 Apr 2018 09:42:58: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:42:58: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:42:58: #1 total tags in treatment: 15947767 INFO @ Thu, 05 Apr 2018 09:42:58: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:42:58: #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 09:42:58: #1 tags after filtering in treatment: 10695779 INFO @ Thu, 05 Apr 2018 09:42:58: #1 Redundant rate of treatment: 0.33 INFO @ Thu, 05 Apr 2018 09:42:58: #1 finished! INFO @ Thu, 05 Apr 2018 09:42:58: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:42:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:42:59: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:42:59: 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 09:42:59: Process for pairing-model is terminated! cat: SRX3671139.10_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 `SRX3671139.10_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 `SRX3671139.10_*.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 `SRX3671139.10_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 @ Thu, 05 Apr 2018 09:42:59: 31000000 INFO @ Thu, 05 Apr 2018 09:43:03: 31000000 INFO @ Thu, 05 Apr 2018 09:43:05: 32000000 INFO @ Thu, 05 Apr 2018 09:43:07: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:43:07: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:43:07: #1 total tags in treatment: 15947767 INFO @ Thu, 05 Apr 2018 09:43:07: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:43:07: #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 09:43:08: #1 tags after filtering in treatment: 10695779 INFO @ Thu, 05 Apr 2018 09:43:08: #1 Redundant rate of treatment: 0.33 INFO @ Thu, 05 Apr 2018 09:43:08: #1 finished! INFO @ Thu, 05 Apr 2018 09:43:08: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:43:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:43:08: 32000000 INFO @ Thu, 05 Apr 2018 09:43:08: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:43:08: 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 09:43:08: Process for pairing-model is terminated! cat: SRX3671139.05_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 `SRX3671139.05_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 `SRX3671139.05_*.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 `SRX3671139.05_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 09:43:11: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:43:11: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:43:11: #1 total tags in treatment: 15947767 INFO @ Thu, 05 Apr 2018 09:43:11: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:43:11: #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 09:43:11: #1 tags after filtering in treatment: 10695779 INFO @ Thu, 05 Apr 2018 09:43:11: #1 Redundant rate of treatment: 0.33 INFO @ Thu, 05 Apr 2018 09:43:11: #1 finished! INFO @ Thu, 05 Apr 2018 09:43:11: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:43:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:43:12: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:43:12: 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 09:43:12: Process for pairing-model is terminated! cat: SRX3671139.20_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 `SRX3671139.20_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 `SRX3671139.20_*.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 `SRX3671139.20_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。