Job ID = 10937435 sra ファイルのダウンロード中... Completed: 542425K bytes transferred in 7 seconds (591218K 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... Read 9911344 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198729/SRR4304459.sra Written 9911344 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198729/SRR4304459.sra 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: 00:08:07 9911344 reads; of these: 9911344 (100.00%) were paired; of these: 1262113 (12.73%) aligned concordantly 0 times 6890980 (69.53%) aligned concordantly exactly 1 time 1758251 (17.74%) aligned concordantly >1 times ---- 1262113 pairs aligned concordantly 0 times; of these: 148233 (11.74%) aligned discordantly 1 time ---- 1113880 pairs aligned 0 times concordantly or discordantly; of these: 2227760 mates make up the pairs; of these: 1975044 (88.66%) aligned 0 times 102989 (4.62%) aligned exactly 1 time 149727 (6.72%) aligned >1 times 90.04% overall alignment rate Time searching: 00:08:07 Overall time: 00:08:07 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 8 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] 449458 / 8775677 = 0.0512 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 @ Fri, 10 Aug 2018 02:19:18: # Command line: callpeak -t SRX2198729.bam -f BAM -g 12100000 -n SRX2198729.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2198729.20 # format = BAM # ChIP-seq file = ['SRX2198729.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 @ Fri, 10 Aug 2018 02:19:18: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:19:18: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:19:18: # Command line: callpeak -t SRX2198729.bam -f BAM -g 12100000 -n SRX2198729.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2198729.05 # format = BAM # ChIP-seq file = ['SRX2198729.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 @ Fri, 10 Aug 2018 02:19:18: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:19:18: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:19:18: # Command line: callpeak -t SRX2198729.bam -f BAM -g 12100000 -n SRX2198729.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2198729.10 # format = BAM # ChIP-seq file = ['SRX2198729.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 @ Fri, 10 Aug 2018 02:19:18: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:19:18: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:19:23: 1000000 INFO @ Fri, 10 Aug 2018 02:19:23: 1000000 INFO @ Fri, 10 Aug 2018 02:19:24: 1000000 INFO @ Fri, 10 Aug 2018 02:19:28: 2000000 INFO @ Fri, 10 Aug 2018 02:19:28: 2000000 INFO @ Fri, 10 Aug 2018 02:19:29: 2000000 INFO @ Fri, 10 Aug 2018 02:19:32: 3000000 INFO @ Fri, 10 Aug 2018 02:19:33: 3000000 INFO @ Fri, 10 Aug 2018 02:19:34: 3000000 INFO @ Fri, 10 Aug 2018 02:19:37: 4000000 INFO @ Fri, 10 Aug 2018 02:19:37: 4000000 INFO @ Fri, 10 Aug 2018 02:19:39: 4000000 INFO @ Fri, 10 Aug 2018 02:19:42: 5000000 INFO @ Fri, 10 Aug 2018 02:19:42: 5000000 INFO @ Fri, 10 Aug 2018 02:19:44: 5000000 INFO @ Fri, 10 Aug 2018 02:19:47: 6000000 INFO @ Fri, 10 Aug 2018 02:19:47: 6000000 INFO @ Fri, 10 Aug 2018 02:19:49: 6000000 INFO @ Fri, 10 Aug 2018 02:19:51: 7000000 INFO @ Fri, 10 Aug 2018 02:19:52: 7000000 INFO @ Fri, 10 Aug 2018 02:19:54: 7000000 INFO @ Fri, 10 Aug 2018 02:19:56: 8000000 INFO @ Fri, 10 Aug 2018 02:19:57: 8000000 INFO @ Fri, 10 Aug 2018 02:19:59: 8000000 INFO @ Fri, 10 Aug 2018 02:20:01: 9000000 INFO @ Fri, 10 Aug 2018 02:20:02: 9000000 INFO @ Fri, 10 Aug 2018 02:20:04: 9000000 INFO @ Fri, 10 Aug 2018 02:20:06: 10000000 INFO @ Fri, 10 Aug 2018 02:20:07: 10000000 INFO @ Fri, 10 Aug 2018 02:20:09: 10000000 INFO @ Fri, 10 Aug 2018 02:20:11: 11000000 INFO @ Fri, 10 Aug 2018 02:20:12: 11000000 INFO @ Fri, 10 Aug 2018 02:20:14: 11000000 INFO @ Fri, 10 Aug 2018 02:20:16: 12000000 INFO @ Fri, 10 Aug 2018 02:20:17: 12000000 INFO @ Fri, 10 Aug 2018 02:20:19: 12000000 INFO @ Fri, 10 Aug 2018 02:20:21: 13000000 INFO @ Fri, 10 Aug 2018 02:20:22: 13000000 INFO @ Fri, 10 Aug 2018 02:20:24: 13000000 INFO @ Fri, 10 Aug 2018 02:20:27: 14000000 INFO @ Fri, 10 Aug 2018 02:20:28: 14000000 INFO @ Fri, 10 Aug 2018 02:20:29: 14000000 INFO @ Fri, 10 Aug 2018 02:20:32: 15000000 INFO @ Fri, 10 Aug 2018 02:20:33: 15000000 INFO @ Fri, 10 Aug 2018 02:20:34: 15000000 INFO @ Fri, 10 Aug 2018 02:20:37: 16000000 INFO @ Fri, 10 Aug 2018 02:20:38: 16000000 INFO @ Fri, 10 Aug 2018 02:20:38: 16000000 INFO @ Fri, 10 Aug 2018 02:20:43: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:20:43: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:20:43: #1 total tags in treatment: 8201318 INFO @ Fri, 10 Aug 2018 02:20:43: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:20:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:20:43: #1 tags after filtering in treatment: 3748060 INFO @ Fri, 10 Aug 2018 02:20:43: #1 Redundant rate of treatment: 0.54 INFO @ Fri, 10 Aug 2018 02:20:43: #1 finished! INFO @ Fri, 10 Aug 2018 02:20:43: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:20:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:20:43: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:20:43: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:20:43: #1 total tags in treatment: 8201318 INFO @ Fri, 10 Aug 2018 02:20:43: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:20:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:20:43: #1 tags after filtering in treatment: 3748060 INFO @ Fri, 10 Aug 2018 02:20:43: #1 Redundant rate of treatment: 0.54 INFO @ Fri, 10 Aug 2018 02:20:43: #1 finished! INFO @ Fri, 10 Aug 2018 02:20:43: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:20:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:20:43: #2 number of paired peaks: 6 WARNING @ Fri, 10 Aug 2018 02:20:43: Too few paired peaks (6) 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 @ Fri, 10 Aug 2018 02:20:43: Process for pairing-model is terminated! cat: SRX2198729.05_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 `SRX2198729.05_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 `SRX2198729.05_*.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 `SRX2198729.05_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 @ Fri, 10 Aug 2018 02:20:43: #2 number of paired peaks: 6 WARNING @ Fri, 10 Aug 2018 02:20:43: Too few paired peaks (6) 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 @ Fri, 10 Aug 2018 02:20:43: Process for pairing-model is terminated! cat: SRX2198729.20_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2198729.20_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 `SRX2198729.20_*.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 `SRX2198729.20_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 @ Fri, 10 Aug 2018 02:20:44: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:20:44: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:20:44: #1 total tags in treatment: 8201318 INFO @ Fri, 10 Aug 2018 02:20:44: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:20:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:20:44: #1 tags after filtering in treatment: 3748060 INFO @ Fri, 10 Aug 2018 02:20:44: #1 Redundant rate of treatment: 0.54 INFO @ Fri, 10 Aug 2018 02:20:44: #1 finished! INFO @ Fri, 10 Aug 2018 02:20:44: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:20:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:20:44: #2 number of paired peaks: 6 WARNING @ Fri, 10 Aug 2018 02:20:44: Too few paired peaks (6) 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 @ Fri, 10 Aug 2018 02:20:44: Process for pairing-model is terminated! cat: SRX2198729.10_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 `SRX2198729.10_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 `SRX2198729.10_*.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 `SRX2198729.10_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。