Job ID = 10536408 sra ファイルのダウンロード中... Completed: 1411081K bytes transferred in 55 seconds (206482K 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 36453764 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671153/SRR6696905.sra Written 36453764 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: 00:19:37 36453764 reads; of these: 36453764 (100.00%) were paired; of these: 14035345 (38.50%) aligned concordantly 0 times 19453461 (53.36%) aligned concordantly exactly 1 time 2964958 (8.13%) aligned concordantly >1 times ---- 14035345 pairs aligned concordantly 0 times; of these: 68013 (0.48%) aligned discordantly 1 time ---- 13967332 pairs aligned 0 times concordantly or discordantly; of these: 27934664 mates make up the pairs; of these: 27576016 (98.72%) aligned 0 times 287711 (1.03%) aligned exactly 1 time 70937 (0.25%) aligned >1 times 62.18% overall alignment rate Time searching: 00:19:37 Overall time: 00:19:37 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] 11016912 / 22429086 = 0.4912 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 09:50:22: # Command line: callpeak -t SRX3671153.bam -f BAM -g 12100000 -n SRX3671153.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671153.05 # format = BAM # ChIP-seq file = ['SRX3671153.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 09:50:22: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:50:22: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:50:22: # Command line: callpeak -t SRX3671153.bam -f BAM -g 12100000 -n SRX3671153.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671153.20 # format = BAM # ChIP-seq file = ['SRX3671153.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 09:50:22: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:50:22: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:50:22: # Command line: callpeak -t SRX3671153.bam -f BAM -g 12100000 -n SRX3671153.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671153.10 # format = BAM # ChIP-seq file = ['SRX3671153.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 09:50:22: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:50:22: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:50:27: 1000000 INFO @ Thu, 05 Apr 2018 09:50:27: 1000000 INFO @ Thu, 05 Apr 2018 09:50:27: 1000000 INFO @ Thu, 05 Apr 2018 09:50:32: 2000000 INFO @ Thu, 05 Apr 2018 09:50:32: 2000000 INFO @ Thu, 05 Apr 2018 09:50:33: 2000000 INFO @ Thu, 05 Apr 2018 09:50:37: 3000000 INFO @ Thu, 05 Apr 2018 09:50:37: 3000000 INFO @ Thu, 05 Apr 2018 09:50:38: 3000000 INFO @ Thu, 05 Apr 2018 09:50:42: 4000000 INFO @ Thu, 05 Apr 2018 09:50:42: 4000000 INFO @ Thu, 05 Apr 2018 09:50:43: 4000000 INFO @ Thu, 05 Apr 2018 09:50:47: 5000000 INFO @ Thu, 05 Apr 2018 09:50:48: 5000000 INFO @ Thu, 05 Apr 2018 09:50:48: 5000000 INFO @ Thu, 05 Apr 2018 09:50:52: 6000000 INFO @ Thu, 05 Apr 2018 09:50:53: 6000000 INFO @ Thu, 05 Apr 2018 09:50:53: 6000000 INFO @ Thu, 05 Apr 2018 09:50:57: 7000000 INFO @ Thu, 05 Apr 2018 09:50:58: 7000000 INFO @ Thu, 05 Apr 2018 09:50:58: 7000000 INFO @ Thu, 05 Apr 2018 09:51:03: 8000000 INFO @ Thu, 05 Apr 2018 09:51:03: 8000000 INFO @ Thu, 05 Apr 2018 09:51:03: 8000000 INFO @ Thu, 05 Apr 2018 09:51:08: 9000000 INFO @ Thu, 05 Apr 2018 09:51:08: 9000000 INFO @ Thu, 05 Apr 2018 09:51:09: 9000000 INFO @ Thu, 05 Apr 2018 09:51:13: 10000000 INFO @ Thu, 05 Apr 2018 09:51:13: 10000000 INFO @ Thu, 05 Apr 2018 09:51:14: 10000000 INFO @ Thu, 05 Apr 2018 09:51:18: 11000000 INFO @ Thu, 05 Apr 2018 09:51:18: 11000000 INFO @ Thu, 05 Apr 2018 09:51:19: 11000000 INFO @ Thu, 05 Apr 2018 09:51:23: 12000000 INFO @ Thu, 05 Apr 2018 09:51:23: 12000000 INFO @ Thu, 05 Apr 2018 09:51:25: 12000000 INFO @ Thu, 05 Apr 2018 09:51:29: 13000000 INFO @ Thu, 05 Apr 2018 09:51:29: 13000000 INFO @ Thu, 05 Apr 2018 09:51:30: 13000000 INFO @ Thu, 05 Apr 2018 09:51:34: 14000000 INFO @ Thu, 05 Apr 2018 09:51:34: 14000000 INFO @ Thu, 05 Apr 2018 09:51:35: 14000000 INFO @ Thu, 05 Apr 2018 09:51:39: 15000000 INFO @ Thu, 05 Apr 2018 09:51:39: 15000000 INFO @ Thu, 05 Apr 2018 09:51:41: 15000000 INFO @ Thu, 05 Apr 2018 09:51:44: 16000000 INFO @ Thu, 05 Apr 2018 09:51:45: 16000000 INFO @ Thu, 05 Apr 2018 09:51:46: 16000000 INFO @ Thu, 05 Apr 2018 09:51:49: 17000000 INFO @ Thu, 05 Apr 2018 09:51:50: 17000000 INFO @ Thu, 05 Apr 2018 09:51:52: 17000000 INFO @ Thu, 05 Apr 2018 09:51:54: 18000000 INFO @ Thu, 05 Apr 2018 09:51:55: 18000000 INFO @ Thu, 05 Apr 2018 09:51:57: 18000000 INFO @ Thu, 05 Apr 2018 09:51:59: 19000000 INFO @ Thu, 05 Apr 2018 09:52:01: 19000000 INFO @ Thu, 05 Apr 2018 09:52:03: 19000000 INFO @ Thu, 05 Apr 2018 09:52:04: 20000000 INFO @ Thu, 05 Apr 2018 09:52:06: 20000000 INFO @ Thu, 05 Apr 2018 09:52:08: 20000000 INFO @ Thu, 05 Apr 2018 09:52:09: 21000000 INFO @ Thu, 05 Apr 2018 09:52:11: 21000000 INFO @ Thu, 05 Apr 2018 09:52:13: 21000000 INFO @ Thu, 05 Apr 2018 09:52:14: 22000000 INFO @ Thu, 05 Apr 2018 09:52:16: 22000000 INFO @ Thu, 05 Apr 2018 09:52:19: 23000000 INFO @ Thu, 05 Apr 2018 09:52:19: 22000000 INFO @ Thu, 05 Apr 2018 09:52:20: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:52:20: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:52:20: #1 total tags in treatment: 11406455 INFO @ Thu, 05 Apr 2018 09:52:20: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:52:20: #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 09:52:20: #1 tags after filtering in treatment: 8281573 INFO @ Thu, 05 Apr 2018 09:52:20: #1 Redundant rate of treatment: 0.27 INFO @ Thu, 05 Apr 2018 09:52:20: #1 finished! INFO @ Thu, 05 Apr 2018 09:52:20: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:52:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:52:21: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:52:21: 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 09:52:21: Process for pairing-model is terminated! cat: SRX3671153.05_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 `SRX3671153.05_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 `SRX3671153.05_*.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 `SRX3671153.05_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 09:52:22: 23000000 INFO @ Thu, 05 Apr 2018 09:52:23: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:52:23: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:52:23: #1 total tags in treatment: 11406455 INFO @ Thu, 05 Apr 2018 09:52:23: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:52:23: #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 09:52:24: #1 tags after filtering in treatment: 8281573 INFO @ Thu, 05 Apr 2018 09:52:24: #1 Redundant rate of treatment: 0.27 INFO @ Thu, 05 Apr 2018 09:52:24: #1 finished! INFO @ Thu, 05 Apr 2018 09:52:24: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:52:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:52:24: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:52:24: 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 09:52:24: Process for pairing-model is terminated! cat: SRX3671153.10_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 `SRX3671153.10_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 `SRX3671153.10_*.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 `SRX3671153.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません INFO @ Thu, 05 Apr 2018 09:52:24: 23000000 CompletedMACS2peakCalling INFO @ Thu, 05 Apr 2018 09:52:26: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:52:26: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:52:26: #1 total tags in treatment: 11406455 INFO @ Thu, 05 Apr 2018 09:52:26: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:52:26: #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 09:52:26: #1 tags after filtering in treatment: 8281573 INFO @ Thu, 05 Apr 2018 09:52:26: #1 Redundant rate of treatment: 0.27 INFO @ Thu, 05 Apr 2018 09:52:26: #1 finished! INFO @ Thu, 05 Apr 2018 09:52:26: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:52:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:52:27: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:52:27: 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 @ Thu, 05 Apr 2018 09:52:27: Process for pairing-model is terminated! cat: SRX3671153.20_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 `SRX3671153.20_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 `SRX3671153.20_*.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 `SRX3671153.20_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。