Job ID = 9732060 sra ファイルのダウンロード中... Completed: 284115K bytes transferred in 9 seconds (232778K bits/sec), in 1 file, 2 directories. 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 12859396 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675860/SRR5380637.sra Written 12859396 spots total 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: 00:06:01 12859396 reads; of these: 12859396 (100.00%) were paired; of these: 2521954 (19.61%) aligned concordantly 0 times 9464735 (73.60%) aligned concordantly exactly 1 time 872707 (6.79%) aligned concordantly >1 times ---- 2521954 pairs aligned concordantly 0 times; of these: 870847 (34.53%) aligned discordantly 1 time ---- 1651107 pairs aligned 0 times concordantly or discordantly; of these: 3302214 mates make up the pairs; of these: 2745892 (83.15%) aligned 0 times 354024 (10.72%) aligned exactly 1 time 202298 (6.13%) aligned >1 times 89.32% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 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] 1489110 / 11094737 = 0.1342 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 @ Sun, 03 Sep 2017 19:30:08: # Command line: callpeak -t SRX2675860.bam -f BAM -g 12100000 -n SRX2675860.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675860.20 # format = BAM # ChIP-seq file = ['SRX2675860.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 @ Sun, 03 Sep 2017 19:30:08: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:30:08: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:30:08: # Command line: callpeak -t SRX2675860.bam -f BAM -g 12100000 -n SRX2675860.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675860.10 # format = BAM # ChIP-seq file = ['SRX2675860.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 @ Sun, 03 Sep 2017 19:30:08: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:30:08: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:30:08: # Command line: callpeak -t SRX2675860.bam -f BAM -g 12100000 -n SRX2675860.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675860.05 # format = BAM # ChIP-seq file = ['SRX2675860.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 @ Sun, 03 Sep 2017 19:30:08: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:30:08: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:30:13: 1000000 INFO @ Sun, 03 Sep 2017 19:30:14: 1000000 INFO @ Sun, 03 Sep 2017 19:30:14: 1000000 INFO @ Sun, 03 Sep 2017 19:30:18: 2000000 INFO @ Sun, 03 Sep 2017 19:30:19: 2000000 INFO @ Sun, 03 Sep 2017 19:30:19: 2000000 INFO @ Sun, 03 Sep 2017 19:30:23: 3000000 INFO @ Sun, 03 Sep 2017 19:30:25: 3000000 INFO @ Sun, 03 Sep 2017 19:30:25: 3000000 INFO @ Sun, 03 Sep 2017 19:30:28: 4000000 INFO @ Sun, 03 Sep 2017 19:30:30: 4000000 INFO @ Sun, 03 Sep 2017 19:30:30: 4000000 INFO @ Sun, 03 Sep 2017 19:30:33: 5000000 INFO @ Sun, 03 Sep 2017 19:30:36: 5000000 INFO @ Sun, 03 Sep 2017 19:30:36: 5000000 INFO @ Sun, 03 Sep 2017 19:30:38: 6000000 INFO @ Sun, 03 Sep 2017 19:30:41: 6000000 INFO @ Sun, 03 Sep 2017 19:30:41: 6000000 INFO @ Sun, 03 Sep 2017 19:30:43: 7000000 INFO @ Sun, 03 Sep 2017 19:30:46: 7000000 INFO @ Sun, 03 Sep 2017 19:30:47: 7000000 INFO @ Sun, 03 Sep 2017 19:30:48: 8000000 INFO @ Sun, 03 Sep 2017 19:30:52: 8000000 INFO @ Sun, 03 Sep 2017 19:30:52: 8000000 INFO @ Sun, 03 Sep 2017 19:30:53: 9000000 INFO @ Sun, 03 Sep 2017 19:30:57: 9000000 INFO @ Sun, 03 Sep 2017 19:30:58: 9000000 INFO @ Sun, 03 Sep 2017 19:30:58: 10000000 INFO @ Sun, 03 Sep 2017 19:31:02: 10000000 INFO @ Sun, 03 Sep 2017 19:31:03: 10000000 INFO @ Sun, 03 Sep 2017 19:31:03: 11000000 INFO @ Sun, 03 Sep 2017 19:31:08: 11000000 INFO @ Sun, 03 Sep 2017 19:31:08: 12000000 INFO @ Sun, 03 Sep 2017 19:31:08: 11000000 INFO @ Sun, 03 Sep 2017 19:31:13: 13000000 INFO @ Sun, 03 Sep 2017 19:31:13: 12000000 INFO @ Sun, 03 Sep 2017 19:31:14: 12000000 INFO @ Sun, 03 Sep 2017 19:31:18: 14000000 INFO @ Sun, 03 Sep 2017 19:31:19: 13000000 INFO @ Sun, 03 Sep 2017 19:31:19: 13000000 INFO @ Sun, 03 Sep 2017 19:31:23: 15000000 INFO @ Sun, 03 Sep 2017 19:31:24: 14000000 INFO @ Sun, 03 Sep 2017 19:31:24: 14000000 INFO @ Sun, 03 Sep 2017 19:31:28: 16000000 INFO @ Sun, 03 Sep 2017 19:31:29: 15000000 INFO @ Sun, 03 Sep 2017 19:31:30: 15000000 INFO @ Sun, 03 Sep 2017 19:31:33: 17000000 INFO @ Sun, 03 Sep 2017 19:31:35: 16000000 INFO @ Sun, 03 Sep 2017 19:31:35: 16000000 INFO @ Sun, 03 Sep 2017 19:31:38: 18000000 INFO @ Sun, 03 Sep 2017 19:31:40: 17000000 INFO @ Sun, 03 Sep 2017 19:31:40: 17000000 INFO @ Sun, 03 Sep 2017 19:31:43: 19000000 INFO @ Sun, 03 Sep 2017 19:31:45: 18000000 INFO @ Sun, 03 Sep 2017 19:31:46: 18000000 INFO @ Sun, 03 Sep 2017 19:31:47: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:31:47: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:31:47: #1 total tags in treatment: 8865204 INFO @ Sun, 03 Sep 2017 19:31:47: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:31:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:31:48: #1 tags after filtering in treatment: 4127137 INFO @ Sun, 03 Sep 2017 19:31:48: #1 Redundant rate of treatment: 0.53 INFO @ Sun, 03 Sep 2017 19:31:48: #1 finished! INFO @ Sun, 03 Sep 2017 19:31:48: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:31:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:31:48: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:31:48: 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 @ Sun, 03 Sep 2017 19:31:48: Process for pairing-model is terminated! cat: SRX2675860.20_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675860.20_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 `SRX2675860.20_*.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 `SRX2675860.20_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 @ Sun, 03 Sep 2017 19:31:51: 19000000 INFO @ Sun, 03 Sep 2017 19:31:51: 19000000 INFO @ Sun, 03 Sep 2017 19:31:56: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:31:56: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:31:56: #1 total tags in treatment: 8865204 INFO @ Sun, 03 Sep 2017 19:31:56: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:31:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:31:56: #1 tags after filtering in treatment: 4127137 INFO @ Sun, 03 Sep 2017 19:31:56: #1 Redundant rate of treatment: 0.53 INFO @ Sun, 03 Sep 2017 19:31:56: #1 finished! INFO @ Sun, 03 Sep 2017 19:31:56: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:31:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:31:56: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:31:56: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:31:56: #1 total tags in treatment: 8865204 INFO @ Sun, 03 Sep 2017 19:31:56: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:31:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:31:56: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:31:56: 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 @ Sun, 03 Sep 2017 19:31:56: Process for pairing-model is terminated! INFO @ Sun, 03 Sep 2017 19:31:56: #1 tags after filtering in treatment: 4127137 INFO @ Sun, 03 Sep 2017 19:31:56: #1 Redundant rate of treatment: 0.53 INFO @ Sun, 03 Sep 2017 19:31:56: #1 finished! INFO @ Sun, 03 Sep 2017 19:31:56: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:31:56: #2 looking for paired plus/minus strand peaks... cat: SRX2675860.05_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675860.05_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 `SRX2675860.05_*.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 `SRX2675860.05_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 @ Sun, 03 Sep 2017 19:31:56: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:31:56: 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 @ Sun, 03 Sep 2017 19:31:56: Process for pairing-model is terminated! cat: SRX2675860.10_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): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675860.10_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 `SRX2675860.10_*.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 `SRX2675860.10_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。