Job ID = 10536474 sra ファイルのダウンロード中... Completed: 394283K bytes transferred in 15 seconds (213627K 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 12792473 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671173/SRR6696925.sra Written 12792473 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: 00:09:31 12792473 reads; of these: 12792473 (100.00%) were paired; of these: 794177 (6.21%) aligned concordantly 0 times 10581927 (82.72%) aligned concordantly exactly 1 time 1416369 (11.07%) aligned concordantly >1 times ---- 794177 pairs aligned concordantly 0 times; of these: 37969 (4.78%) aligned discordantly 1 time ---- 756208 pairs aligned 0 times concordantly or discordantly; of these: 1512416 mates make up the pairs; of these: 1456649 (96.31%) aligned 0 times 35341 (2.34%) aligned exactly 1 time 20426 (1.35%) aligned >1 times 94.31% overall alignment rate Time searching: 00:09:31 Overall time: 00:09:31 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] 3434330 / 12005541 = 0.2861 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 09:58:54: # Command line: callpeak -t SRX3671173.bam -f BAM -g 12100000 -n SRX3671173.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671173.20 # format = BAM # ChIP-seq file = ['SRX3671173.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 09:58:54: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:58:54: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:58:54: # Command line: callpeak -t SRX3671173.bam -f BAM -g 12100000 -n SRX3671173.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671173.10 # format = BAM # ChIP-seq file = ['SRX3671173.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 09:58:54: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:58:54: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:58:54: # Command line: callpeak -t SRX3671173.bam -f BAM -g 12100000 -n SRX3671173.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671173.05 # format = BAM # ChIP-seq file = ['SRX3671173.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 09:58:54: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:58:54: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:59:00: 1000000 INFO @ Thu, 05 Apr 2018 09:59:00: 1000000 INFO @ Thu, 05 Apr 2018 09:59:01: 1000000 INFO @ Thu, 05 Apr 2018 09:59:06: 2000000 INFO @ Thu, 05 Apr 2018 09:59:07: 2000000 INFO @ Thu, 05 Apr 2018 09:59:08: 2000000 INFO @ Thu, 05 Apr 2018 09:59:11: 3000000 INFO @ Thu, 05 Apr 2018 09:59:13: 3000000 INFO @ Thu, 05 Apr 2018 09:59:15: 3000000 INFO @ Thu, 05 Apr 2018 09:59:17: 4000000 INFO @ Thu, 05 Apr 2018 09:59:20: 4000000 INFO @ Thu, 05 Apr 2018 09:59:23: 4000000 INFO @ Thu, 05 Apr 2018 09:59:23: 5000000 INFO @ Thu, 05 Apr 2018 09:59:26: 5000000 INFO @ Thu, 05 Apr 2018 09:59:28: 6000000 INFO @ Thu, 05 Apr 2018 09:59:30: 5000000 INFO @ Thu, 05 Apr 2018 09:59:33: 6000000 INFO @ Thu, 05 Apr 2018 09:59:34: 7000000 INFO @ Thu, 05 Apr 2018 09:59:37: 6000000 INFO @ Thu, 05 Apr 2018 09:59:40: 7000000 INFO @ Thu, 05 Apr 2018 09:59:40: 8000000 INFO @ Thu, 05 Apr 2018 09:59:45: 7000000 INFO @ Thu, 05 Apr 2018 09:59:45: 9000000 INFO @ Thu, 05 Apr 2018 09:59:46: 8000000 INFO @ Thu, 05 Apr 2018 09:59:51: 10000000 INFO @ Thu, 05 Apr 2018 09:59:52: 8000000 INFO @ Thu, 05 Apr 2018 09:59:53: 9000000 INFO @ Thu, 05 Apr 2018 09:59:57: 11000000 INFO @ Thu, 05 Apr 2018 09:59:59: 10000000 INFO @ Thu, 05 Apr 2018 09:59:59: 9000000 INFO @ Thu, 05 Apr 2018 10:00:02: 12000000 INFO @ Thu, 05 Apr 2018 10:00:06: 11000000 INFO @ Thu, 05 Apr 2018 10:00:07: 10000000 INFO @ Thu, 05 Apr 2018 10:00:08: 13000000 INFO @ Thu, 05 Apr 2018 10:00:12: 12000000 INFO @ Thu, 05 Apr 2018 10:00:14: 14000000 INFO @ Thu, 05 Apr 2018 10:00:14: 11000000 INFO @ Thu, 05 Apr 2018 10:00:18: 13000000 INFO @ Thu, 05 Apr 2018 10:00:19: 15000000 INFO @ Thu, 05 Apr 2018 10:00:21: 12000000 INFO @ Thu, 05 Apr 2018 10:00:25: 14000000 INFO @ Thu, 05 Apr 2018 10:00:25: 16000000 INFO @ Thu, 05 Apr 2018 10:00:28: 13000000 INFO @ Thu, 05 Apr 2018 10:00:31: 17000000 INFO @ Thu, 05 Apr 2018 10:00:31: 15000000 INFO @ Thu, 05 Apr 2018 10:00:32: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:00:32: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:00:32: #1 total tags in treatment: 8565021 INFO @ Thu, 05 Apr 2018 10:00:32: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:00:32: #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 10:00:32: #1 tags after filtering in treatment: 6761219 INFO @ Thu, 05 Apr 2018 10:00:32: #1 Redundant rate of treatment: 0.21 INFO @ Thu, 05 Apr 2018 10:00:32: #1 finished! INFO @ Thu, 05 Apr 2018 10:00:32: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:00:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:00:33: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:00:33: 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 10:00:33: Process for pairing-model is terminated! cat: SRX3671173.20_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 `SRX3671173.20_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 `SRX3671173.20_*.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 `SRX3671173.20_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 10:00:35: 14000000 INFO @ Thu, 05 Apr 2018 10:00:37: 16000000 INFO @ Thu, 05 Apr 2018 10:00:41: 15000000 INFO @ Thu, 05 Apr 2018 10:00:43: 17000000 INFO @ Thu, 05 Apr 2018 10:00:44: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:00:44: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:00:44: #1 total tags in treatment: 8565021 INFO @ Thu, 05 Apr 2018 10:00:44: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:00:44: #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 10:00:45: #1 tags after filtering in treatment: 6761219 INFO @ Thu, 05 Apr 2018 10:00:45: #1 Redundant rate of treatment: 0.21 INFO @ Thu, 05 Apr 2018 10:00:45: #1 finished! INFO @ Thu, 05 Apr 2018 10:00:45: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:00:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:00:45: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:00:45: 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 10:00:45: Process for pairing-model is terminated! cat: SRX3671173.05_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 `SRX3671173.05_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 `SRX3671173.05_*.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 `SRX3671173.05_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 10:00:47: 16000000 INFO @ Thu, 05 Apr 2018 10:00:52: 17000000 INFO @ Thu, 05 Apr 2018 10:00:54: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:00:54: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:00:54: #1 total tags in treatment: 8565021 INFO @ Thu, 05 Apr 2018 10:00:54: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:00:54: #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 10:00:54: #1 tags after filtering in treatment: 6761219 INFO @ Thu, 05 Apr 2018 10:00:54: #1 Redundant rate of treatment: 0.21 INFO @ Thu, 05 Apr 2018 10:00:54: #1 finished! INFO @ Thu, 05 Apr 2018 10:00:54: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:00:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:00:54: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:00:54: 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 10:00:54: Process for pairing-model is terminated! cat: SRX3671173.10_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 `SRX3671173.10_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 `SRX3671173.10_*.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 `SRX3671173.10_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。