Job ID = 9161977 sra ファイルのダウンロード中... Completed: 1879313K bytes transferred in 18 seconds (812302K 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 31174598 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423709/SRR2930998.sra Written 31174598 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: 00:16:11 31174598 reads; of these: 31174598 (100.00%) were paired; of these: 13831329 (44.37%) aligned concordantly 0 times 15956910 (51.19%) aligned concordantly exactly 1 time 1386359 (4.45%) aligned concordantly >1 times ---- 13831329 pairs aligned concordantly 0 times; of these: 251764 (1.82%) aligned discordantly 1 time ---- 13579565 pairs aligned 0 times concordantly or discordantly; of these: 27159130 mates make up the pairs; of these: 26612181 (97.99%) aligned 0 times 444990 (1.64%) aligned exactly 1 time 101959 (0.38%) aligned >1 times 57.32% overall alignment rate Time searching: 00:16:11 Overall time: 00:16:11 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 16 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] 6361483 / 17565297 = 0.3622 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 05:37:16: # Command line: callpeak -t SRX1423709.bam -f BAM -g 12100000 -n SRX1423709.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423709.05 # format = BAM # ChIP-seq file = ['SRX1423709.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 05:37:16: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:37:16: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:37:16: # Command line: callpeak -t SRX1423709.bam -f BAM -g 12100000 -n SRX1423709.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423709.10 # format = BAM # ChIP-seq file = ['SRX1423709.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 05:37:16: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:37:16: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:37:16: # Command line: callpeak -t SRX1423709.bam -f BAM -g 12100000 -n SRX1423709.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423709.20 # format = BAM # ChIP-seq file = ['SRX1423709.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 05:37:16: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:37:16: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:37:23: 1000000 INFO @ Wed, 28 Jun 2017 05:37:23: 1000000 INFO @ Wed, 28 Jun 2017 05:37:23: 1000000 INFO @ Wed, 28 Jun 2017 05:37:30: 2000000 INFO @ Wed, 28 Jun 2017 05:37:30: 2000000 INFO @ Wed, 28 Jun 2017 05:37:30: 2000000 INFO @ Wed, 28 Jun 2017 05:37:37: 3000000 INFO @ Wed, 28 Jun 2017 05:37:37: 3000000 INFO @ Wed, 28 Jun 2017 05:37:37: 3000000 INFO @ Wed, 28 Jun 2017 05:37:44: 4000000 INFO @ Wed, 28 Jun 2017 05:37:44: 4000000 INFO @ Wed, 28 Jun 2017 05:37:44: 4000000 INFO @ Wed, 28 Jun 2017 05:37:51: 5000000 INFO @ Wed, 28 Jun 2017 05:37:51: 5000000 INFO @ Wed, 28 Jun 2017 05:37:52: 5000000 INFO @ Wed, 28 Jun 2017 05:37:58: 6000000 INFO @ Wed, 28 Jun 2017 05:37:58: 6000000 INFO @ Wed, 28 Jun 2017 05:37:59: 6000000 INFO @ Wed, 28 Jun 2017 05:38:05: 7000000 INFO @ Wed, 28 Jun 2017 05:38:05: 7000000 INFO @ Wed, 28 Jun 2017 05:38:05: 7000000 INFO @ Wed, 28 Jun 2017 05:38:12: 8000000 INFO @ Wed, 28 Jun 2017 05:38:12: 8000000 INFO @ Wed, 28 Jun 2017 05:38:12: 8000000 INFO @ Wed, 28 Jun 2017 05:38:19: 9000000 INFO @ Wed, 28 Jun 2017 05:38:19: 9000000 INFO @ Wed, 28 Jun 2017 05:38:19: 9000000 INFO @ Wed, 28 Jun 2017 05:38:26: 10000000 INFO @ Wed, 28 Jun 2017 05:38:26: 10000000 INFO @ Wed, 28 Jun 2017 05:38:26: 10000000 INFO @ Wed, 28 Jun 2017 05:38:33: 11000000 INFO @ Wed, 28 Jun 2017 05:38:33: 11000000 INFO @ Wed, 28 Jun 2017 05:38:33: 11000000 INFO @ Wed, 28 Jun 2017 05:38:40: 12000000 INFO @ Wed, 28 Jun 2017 05:38:40: 12000000 INFO @ Wed, 28 Jun 2017 05:38:40: 12000000 INFO @ Wed, 28 Jun 2017 05:38:47: 13000000 INFO @ Wed, 28 Jun 2017 05:38:47: 13000000 INFO @ Wed, 28 Jun 2017 05:38:47: 13000000 INFO @ Wed, 28 Jun 2017 05:38:54: 14000000 INFO @ Wed, 28 Jun 2017 05:38:54: 14000000 INFO @ Wed, 28 Jun 2017 05:38:54: 14000000 INFO @ Wed, 28 Jun 2017 05:39:01: 15000000 INFO @ Wed, 28 Jun 2017 05:39:01: 15000000 INFO @ Wed, 28 Jun 2017 05:39:02: 15000000 INFO @ Wed, 28 Jun 2017 05:39:08: 16000000 INFO @ Wed, 28 Jun 2017 05:39:09: 16000000 INFO @ Wed, 28 Jun 2017 05:39:09: 16000000 INFO @ Wed, 28 Jun 2017 05:39:16: 17000000 INFO @ Wed, 28 Jun 2017 05:39:16: 17000000 INFO @ Wed, 28 Jun 2017 05:39:17: 17000000 INFO @ Wed, 28 Jun 2017 05:39:23: 18000000 INFO @ Wed, 28 Jun 2017 05:39:23: 18000000 INFO @ Wed, 28 Jun 2017 05:39:24: 18000000 INFO @ Wed, 28 Jun 2017 05:39:31: 19000000 INFO @ Wed, 28 Jun 2017 05:39:31: 19000000 INFO @ Wed, 28 Jun 2017 05:39:32: 19000000 INFO @ Wed, 28 Jun 2017 05:39:38: 20000000 INFO @ Wed, 28 Jun 2017 05:39:38: 20000000 INFO @ Wed, 28 Jun 2017 05:39:40: 20000000 INFO @ Wed, 28 Jun 2017 05:39:45: 21000000 INFO @ Wed, 28 Jun 2017 05:39:45: 21000000 INFO @ Wed, 28 Jun 2017 05:39:47: 21000000 INFO @ Wed, 28 Jun 2017 05:39:53: 22000000 INFO @ Wed, 28 Jun 2017 05:39:53: 22000000 INFO @ Wed, 28 Jun 2017 05:39:55: 22000000 INFO @ Wed, 28 Jun 2017 05:40:00: 23000000 INFO @ Wed, 28 Jun 2017 05:40:00: 23000000 INFO @ Wed, 28 Jun 2017 05:40:00: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:40:00: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:40:00: #1 total tags in treatment: 11010896 INFO @ Wed, 28 Jun 2017 05:40:00: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:40:00: #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 05:40:00: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:40:00: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:40:00: #1 total tags in treatment: 11010896 INFO @ Wed, 28 Jun 2017 05:40:00: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:40:00: #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 05:40:01: #1 tags after filtering in treatment: 7364667 INFO @ Wed, 28 Jun 2017 05:40:01: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 28 Jun 2017 05:40:01: #1 finished! INFO @ Wed, 28 Jun 2017 05:40:01: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:40:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:40:01: #1 tags after filtering in treatment: 7364667 INFO @ Wed, 28 Jun 2017 05:40:01: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 28 Jun 2017 05:40:01: #1 finished! INFO @ Wed, 28 Jun 2017 05:40:01: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:40:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:40:01: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:40:01: 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 05:40:01: Process for pairing-model is terminated! INFO @ Wed, 28 Jun 2017 05:40:01: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:40:01: 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 05:40:01: Process for pairing-model is terminated! cat: SRX1423709.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX1423709.05_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1423709.20_model.r'rm: cannot remove `SRX1423709.05_model.r': そのようなファイルやディレクトリはありません : 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 `SRX1423709.20_*.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 `SRX1423709.05_*.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 `SRX1423709.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません rm: cannot remove `SRX1423709.05_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 CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 05:40:02: 23000000 INFO @ Wed, 28 Jun 2017 05:40:02: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:40:02: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:40:02: #1 total tags in treatment: 11010896 INFO @ Wed, 28 Jun 2017 05:40:02: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:40:02: #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 05:40:02: #1 tags after filtering in treatment: 7364667 INFO @ Wed, 28 Jun 2017 05:40:02: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 28 Jun 2017 05:40:02: #1 finished! INFO @ Wed, 28 Jun 2017 05:40:02: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:40:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:40:03: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:40:03: 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 05:40:03: Process for pairing-model is terminated! cat: SRX1423709.10_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 `SRX1423709.10_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 `SRX1423709.10_*.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 `SRX1423709.10_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。