Job ID = 10536516 sra ファイルのダウンロード中... Completed: 1097135K bytes transferred in 26 seconds (335171K 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 30544163 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671209/SRR6696961.sra Written 30544163 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: 00:22:17 30544163 reads; of these: 30544163 (100.00%) were paired; of these: 3360020 (11.00%) aligned concordantly 0 times 22828875 (74.74%) aligned concordantly exactly 1 time 4355268 (14.26%) aligned concordantly >1 times ---- 3360020 pairs aligned concordantly 0 times; of these: 77150 (2.30%) aligned discordantly 1 time ---- 3282870 pairs aligned 0 times concordantly or discordantly; of these: 6565740 mates make up the pairs; of these: 6371401 (97.04%) aligned 0 times 125406 (1.91%) aligned exactly 1 time 68933 (1.05%) aligned >1 times 89.57% overall alignment rate Time searching: 00:22:17 Overall time: 00:22:17 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] 9705608 / 27232750 = 0.3564 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 10:32:36: # Command line: callpeak -t SRX3671209.bam -f BAM -g 12100000 -n SRX3671209.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671209.05 # format = BAM # ChIP-seq file = ['SRX3671209.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 10:32:36: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:32:36: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:32:36: # Command line: callpeak -t SRX3671209.bam -f BAM -g 12100000 -n SRX3671209.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671209.20 # format = BAM # ChIP-seq file = ['SRX3671209.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 10:32:36: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:32:36: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:32:36: # Command line: callpeak -t SRX3671209.bam -f BAM -g 12100000 -n SRX3671209.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671209.10 # format = BAM # ChIP-seq file = ['SRX3671209.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 10:32:36: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:32:36: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:32:42: 1000000 INFO @ Thu, 05 Apr 2018 10:32:43: 1000000 INFO @ Thu, 05 Apr 2018 10:32:43: 1000000 INFO @ Thu, 05 Apr 2018 10:32:48: 2000000 INFO @ Thu, 05 Apr 2018 10:32:51: 2000000 INFO @ Thu, 05 Apr 2018 10:32:51: 2000000 INFO @ Thu, 05 Apr 2018 10:32:54: 3000000 INFO @ Thu, 05 Apr 2018 10:32:58: 3000000 INFO @ Thu, 05 Apr 2018 10:32:58: 3000000 INFO @ Thu, 05 Apr 2018 10:32:59: 4000000 INFO @ Thu, 05 Apr 2018 10:33:05: 5000000 INFO @ Thu, 05 Apr 2018 10:33:05: 4000000 INFO @ Thu, 05 Apr 2018 10:33:05: 4000000 INFO @ Thu, 05 Apr 2018 10:33:11: 6000000 INFO @ Thu, 05 Apr 2018 10:33:13: 5000000 INFO @ Thu, 05 Apr 2018 10:33:13: 5000000 INFO @ Thu, 05 Apr 2018 10:33:17: 7000000 INFO @ Thu, 05 Apr 2018 10:33:20: 6000000 INFO @ Thu, 05 Apr 2018 10:33:20: 6000000 INFO @ Thu, 05 Apr 2018 10:33:24: 8000000 INFO @ Thu, 05 Apr 2018 10:33:28: 7000000 INFO @ Thu, 05 Apr 2018 10:33:28: 7000000 INFO @ Thu, 05 Apr 2018 10:33:31: 9000000 INFO @ Thu, 05 Apr 2018 10:33:36: 8000000 INFO @ Thu, 05 Apr 2018 10:33:36: 8000000 INFO @ Thu, 05 Apr 2018 10:33:38: 10000000 INFO @ Thu, 05 Apr 2018 10:33:44: 9000000 INFO @ Thu, 05 Apr 2018 10:33:44: 9000000 INFO @ Thu, 05 Apr 2018 10:33:46: 11000000 INFO @ Thu, 05 Apr 2018 10:33:52: 10000000 INFO @ Thu, 05 Apr 2018 10:33:52: 10000000 INFO @ Thu, 05 Apr 2018 10:33:53: 12000000 INFO @ Thu, 05 Apr 2018 10:34:00: 11000000 INFO @ Thu, 05 Apr 2018 10:34:00: 11000000 INFO @ Thu, 05 Apr 2018 10:34:00: 13000000 INFO @ Thu, 05 Apr 2018 10:34:08: 12000000 INFO @ Thu, 05 Apr 2018 10:34:08: 12000000 INFO @ Thu, 05 Apr 2018 10:34:08: 14000000 INFO @ Thu, 05 Apr 2018 10:34:15: 15000000 INFO @ Thu, 05 Apr 2018 10:34:16: 13000000 INFO @ Thu, 05 Apr 2018 10:34:16: 13000000 INFO @ Thu, 05 Apr 2018 10:34:23: 16000000 INFO @ Thu, 05 Apr 2018 10:34:24: 14000000 INFO @ Thu, 05 Apr 2018 10:34:24: 14000000 INFO @ Thu, 05 Apr 2018 10:34:30: 17000000 INFO @ Thu, 05 Apr 2018 10:34:32: 15000000 INFO @ Thu, 05 Apr 2018 10:34:32: 15000000 INFO @ Thu, 05 Apr 2018 10:34:38: 18000000 INFO @ Thu, 05 Apr 2018 10:34:40: 16000000 INFO @ Thu, 05 Apr 2018 10:34:40: 16000000 INFO @ Thu, 05 Apr 2018 10:34:45: 19000000 INFO @ Thu, 05 Apr 2018 10:34:49: 17000000 INFO @ Thu, 05 Apr 2018 10:34:49: 17000000 INFO @ Thu, 05 Apr 2018 10:34:53: 20000000 INFO @ Thu, 05 Apr 2018 10:34:57: 18000000 INFO @ Thu, 05 Apr 2018 10:34:57: 18000000 INFO @ Thu, 05 Apr 2018 10:35:00: 21000000 INFO @ Thu, 05 Apr 2018 10:35:05: 19000000 INFO @ Thu, 05 Apr 2018 10:35:05: 19000000 INFO @ Thu, 05 Apr 2018 10:35:07: 22000000 INFO @ Thu, 05 Apr 2018 10:35:13: 20000000 INFO @ Thu, 05 Apr 2018 10:35:13: 20000000 INFO @ Thu, 05 Apr 2018 10:35:15: 23000000 INFO @ Thu, 05 Apr 2018 10:35:21: 21000000 INFO @ Thu, 05 Apr 2018 10:35:21: 21000000 INFO @ Thu, 05 Apr 2018 10:35:22: 24000000 INFO @ Thu, 05 Apr 2018 10:35:29: 22000000 INFO @ Thu, 05 Apr 2018 10:35:29: 22000000 INFO @ Thu, 05 Apr 2018 10:35:30: 25000000 INFO @ Thu, 05 Apr 2018 10:35:37: 26000000 INFO @ Thu, 05 Apr 2018 10:35:38: 23000000 INFO @ Thu, 05 Apr 2018 10:35:38: 23000000 INFO @ Thu, 05 Apr 2018 10:35:45: 27000000 INFO @ Thu, 05 Apr 2018 10:35:46: 24000000 INFO @ Thu, 05 Apr 2018 10:35:46: 24000000 INFO @ Thu, 05 Apr 2018 10:35:52: 28000000 INFO @ Thu, 05 Apr 2018 10:35:54: 25000000 INFO @ Thu, 05 Apr 2018 10:35:54: 25000000 INFO @ Thu, 05 Apr 2018 10:36:00: 29000000 INFO @ Thu, 05 Apr 2018 10:36:02: 26000000 INFO @ Thu, 05 Apr 2018 10:36:02: 26000000 INFO @ Thu, 05 Apr 2018 10:36:07: 30000000 INFO @ Thu, 05 Apr 2018 10:36:10: 27000000 INFO @ Thu, 05 Apr 2018 10:36:10: 27000000 INFO @ Thu, 05 Apr 2018 10:36:15: 31000000 INFO @ Thu, 05 Apr 2018 10:36:19: 28000000 INFO @ Thu, 05 Apr 2018 10:36:19: 28000000 INFO @ Thu, 05 Apr 2018 10:36:22: 32000000 INFO @ Thu, 05 Apr 2018 10:36:27: 29000000 INFO @ Thu, 05 Apr 2018 10:36:27: 29000000 INFO @ Thu, 05 Apr 2018 10:36:30: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Apr 2018 10:36:35: 30000000 INFO @ Thu, 05 Apr 2018 10:36:35: 30000000 INFO @ Thu, 05 Apr 2018 10:36:37: 34000000 INFO @ Thu, 05 Apr 2018 10:36:43: 31000000 INFO @ Thu, 05 Apr 2018 10:36:43: 31000000 INFO @ Thu, 05 Apr 2018 10:36:44: 35000000 INFO @ Thu, 05 Apr 2018 10:36:47: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:36:47: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:36:47: #1 total tags in treatment: 17495407 INFO @ Thu, 05 Apr 2018 10:36:47: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:36:47: #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 10:36:47: #1 tags after filtering in treatment: 6740032 INFO @ Thu, 05 Apr 2018 10:36:47: #1 Redundant rate of treatment: 0.61 INFO @ Thu, 05 Apr 2018 10:36:47: #1 finished! INFO @ Thu, 05 Apr 2018 10:36:47: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:36:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:36:48: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:36:48: 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 10:36:48: Process for pairing-model is terminated! cat: SRX3671209.05_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 `SRX3671209.05_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 `SRX3671209.05_*.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 `SRX3671209.05_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 BigWig に変換しました。 INFO @ Thu, 05 Apr 2018 10:36:51: 32000000 INFO @ Thu, 05 Apr 2018 10:36:51: 32000000 INFO @ Thu, 05 Apr 2018 10:37:00: 33000000 INFO @ Thu, 05 Apr 2018 10:37:00: 33000000 INFO @ Thu, 05 Apr 2018 10:37:08: 34000000 INFO @ Thu, 05 Apr 2018 10:37:08: 34000000 INFO @ Thu, 05 Apr 2018 10:37:16: 35000000 INFO @ Thu, 05 Apr 2018 10:37:16: 35000000 INFO @ Thu, 05 Apr 2018 10:37:19: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:37:19: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:37:19: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:37:19: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:37:19: #1 total tags in treatment: 17495407 INFO @ Thu, 05 Apr 2018 10:37:19: #1 total tags in treatment: 17495407 INFO @ Thu, 05 Apr 2018 10:37:19: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:37:19: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:37:19: #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 10:37:19: #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 10:37:19: #1 tags after filtering in treatment: 6740032 INFO @ Thu, 05 Apr 2018 10:37:19: #1 tags after filtering in treatment: 6740032 INFO @ Thu, 05 Apr 2018 10:37:19: #1 Redundant rate of treatment: 0.61 INFO @ Thu, 05 Apr 2018 10:37:19: #1 Redundant rate of treatment: 0.61 INFO @ Thu, 05 Apr 2018 10:37:19: #1 finished! INFO @ Thu, 05 Apr 2018 10:37:19: #1 finished! INFO @ Thu, 05 Apr 2018 10:37:19: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:37:19: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:37:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:37:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:37:20: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:37:20: 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 10:37:20: Process for pairing-model is terminated! cat: SRX3671209.10_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 `SRX3671209.10_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 `SRX3671209.10_*.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 `SRX3671209.10_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 10:37:20: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:37:20: 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 10:37:20: Process for pairing-model is terminated! cat: SRX3671209.20_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 `SRX3671209.20_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 `SRX3671209.20_*.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 `SRX3671209.20_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