Job ID = 9162416 sra ファイルのダウンロード中... Completed: 831295K bytes transferred in 13 seconds (518562K 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 9619580 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2457696/SRR5138811.sra Written 9619580 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: 00:12:36 9619580 reads; of these: 9619580 (100.00%) were paired; of these: 788558 (8.20%) aligned concordantly 0 times 8192127 (85.16%) aligned concordantly exactly 1 time 638895 (6.64%) aligned concordantly >1 times ---- 788558 pairs aligned concordantly 0 times; of these: 475590 (60.31%) aligned discordantly 1 time ---- 312968 pairs aligned 0 times concordantly or discordantly; of these: 625936 mates make up the pairs; of these: 467482 (74.69%) aligned 0 times 83676 (13.37%) aligned exactly 1 time 74778 (11.95%) aligned >1 times 97.57% overall alignment rate Time searching: 00:12:36 Overall time: 00:12:36 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] 1091808 / 9230783 = 0.1183 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 @ Wed, 28 Jun 2017 08:02:59: # Command line: callpeak -t SRX2457696.bam -f BAM -g 12100000 -n SRX2457696.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2457696.10 # format = BAM # ChIP-seq file = ['SRX2457696.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 @ Wed, 28 Jun 2017 08:02:59: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:02:59: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:02:59: # Command line: callpeak -t SRX2457696.bam -f BAM -g 12100000 -n SRX2457696.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2457696.05 # format = BAM # ChIP-seq file = ['SRX2457696.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 @ Wed, 28 Jun 2017 08:02:59: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:02:59: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:02:59: # Command line: callpeak -t SRX2457696.bam -f BAM -g 12100000 -n SRX2457696.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2457696.20 # format = BAM # ChIP-seq file = ['SRX2457696.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 @ Wed, 28 Jun 2017 08:02:59: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:02:59: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:03:08: 1000000 INFO @ Wed, 28 Jun 2017 08:03:11: 1000000 INFO @ Wed, 28 Jun 2017 08:03:11: 1000000 INFO @ Wed, 28 Jun 2017 08:03:17: 2000000 INFO @ Wed, 28 Jun 2017 08:03:23: 2000000 INFO @ Wed, 28 Jun 2017 08:03:23: 2000000 INFO @ Wed, 28 Jun 2017 08:03:26: 3000000 INFO @ Wed, 28 Jun 2017 08:03:34: 3000000 INFO @ Wed, 28 Jun 2017 08:03:35: 3000000 INFO @ Wed, 28 Jun 2017 08:03:35: 4000000 INFO @ Wed, 28 Jun 2017 08:03:44: 5000000 INFO @ Wed, 28 Jun 2017 08:03:46: 4000000 INFO @ Wed, 28 Jun 2017 08:03:46: 4000000 INFO @ Wed, 28 Jun 2017 08:03:53: 6000000 INFO @ Wed, 28 Jun 2017 08:03:58: 5000000 INFO @ Wed, 28 Jun 2017 08:03:58: 5000000 INFO @ Wed, 28 Jun 2017 08:04:01: 7000000 INFO @ Wed, 28 Jun 2017 08:04:09: 6000000 INFO @ Wed, 28 Jun 2017 08:04:10: 6000000 INFO @ Wed, 28 Jun 2017 08:04:10: 8000000 INFO @ Wed, 28 Jun 2017 08:04:19: 9000000 INFO @ Wed, 28 Jun 2017 08:04:21: 7000000 INFO @ Wed, 28 Jun 2017 08:04:22: 7000000 INFO @ Wed, 28 Jun 2017 08:04:27: 10000000 INFO @ Wed, 28 Jun 2017 08:04:33: 8000000 INFO @ Wed, 28 Jun 2017 08:04:33: 8000000 INFO @ Wed, 28 Jun 2017 08:04:36: 11000000 INFO @ Wed, 28 Jun 2017 08:04:45: 9000000 INFO @ Wed, 28 Jun 2017 08:04:45: 12000000 INFO @ Wed, 28 Jun 2017 08:04:45: 9000000 INFO @ Wed, 28 Jun 2017 08:04:53: 13000000 INFO @ Wed, 28 Jun 2017 08:04:56: 10000000 INFO @ Wed, 28 Jun 2017 08:04:57: 10000000 INFO @ Wed, 28 Jun 2017 08:05:02: 14000000 INFO @ Wed, 28 Jun 2017 08:05:08: 11000000 INFO @ Wed, 28 Jun 2017 08:05:08: 11000000 INFO @ Wed, 28 Jun 2017 08:05:11: 15000000 INFO @ Wed, 28 Jun 2017 08:05:20: 12000000 INFO @ Wed, 28 Jun 2017 08:05:20: 16000000 INFO @ Wed, 28 Jun 2017 08:05:20: 12000000 INFO @ Wed, 28 Jun 2017 08:05:25: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 08:05:25: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 08:05:25: #1 total tags in treatment: 7763694 INFO @ Wed, 28 Jun 2017 08:05:25: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:05:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 08:05:25: #1 tags after filtering in treatment: 4421005 INFO @ Wed, 28 Jun 2017 08:05:25: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 28 Jun 2017 08:05:25: #1 finished! INFO @ Wed, 28 Jun 2017 08:05:25: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:05:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:05:25: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 08:05:25: 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 @ Wed, 28 Jun 2017 08:05:25: Process for pairing-model is terminated! cat: SRX2457696.10_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 `SRX2457696.10_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 `SRX2457696.10_*.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 `SRX2457696.10_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 @ Wed, 28 Jun 2017 08:05:31: 13000000 INFO @ Wed, 28 Jun 2017 08:05:31: 13000000 INFO @ Wed, 28 Jun 2017 08:05:40: 14000000 INFO @ Wed, 28 Jun 2017 08:05:41: 14000000 INFO @ Wed, 28 Jun 2017 08:05:49: 15000000 INFO @ Wed, 28 Jun 2017 08:05:50: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 28 Jun 2017 08:05:58: 16000000 INFO @ Wed, 28 Jun 2017 08:05:59: 16000000 INFO @ Wed, 28 Jun 2017 08:06:04: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 08:06:04: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 08:06:04: #1 total tags in treatment: 7763694 INFO @ Wed, 28 Jun 2017 08:06:04: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:06:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 08:06:04: #1 tags after filtering in treatment: 4421005 INFO @ Wed, 28 Jun 2017 08:06:04: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 28 Jun 2017 08:06:04: #1 finished! INFO @ Wed, 28 Jun 2017 08:06:04: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:06:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:06:04: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 08:06:04: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 08:06:04: #1 total tags in treatment: 7763694 INFO @ Wed, 28 Jun 2017 08:06:04: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:06:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 08:06:04: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 08:06:04: 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 @ Wed, 28 Jun 2017 08:06:04: Process for pairing-model is terminated! cat: SRX2457696.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Wed, 28 Jun 2017 08:06:04: #1 tags after filtering in treatment: 4421005 INFO @ Wed, 28 Jun 2017 08:06:04: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 28 Jun 2017 08:06:04: #1 finished! INFO @ Wed, 28 Jun 2017 08:06:04: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:06:04: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2457696.20_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 `SRX2457696.20_*.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 `SRX2457696.20_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 @ Wed, 28 Jun 2017 08:06:04: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 08:06:04: 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 @ Wed, 28 Jun 2017 08:06:04: Process for pairing-model is terminated! cat: SRX2457696.05_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 `SRX2457696.05_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 `SRX2457696.05_*.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 `SRX2457696.05_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。