Job ID = 9160023 sra ファイルのダウンロード中... Completed: 1025896K bytes transferred in 11 seconds (701393K 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 9846045 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2402748/SRR5085193.sra Written 9846045 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: 00:10:23 9846045 reads; of these: 9846045 (100.00%) were paired; of these: 305208 (3.10%) aligned concordantly 0 times 7113196 (72.24%) aligned concordantly exactly 1 time 2427641 (24.66%) aligned concordantly >1 times ---- 305208 pairs aligned concordantly 0 times; of these: 33887 (11.10%) aligned discordantly 1 time ---- 271321 pairs aligned 0 times concordantly or discordantly; of these: 542642 mates make up the pairs; of these: 459228 (84.63%) aligned 0 times 41959 (7.73%) aligned exactly 1 time 41455 (7.64%) aligned >1 times 97.67% overall alignment rate Time searching: 00:10:23 Overall time: 00:10:23 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] 824826 / 9568537 = 0.0862 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 01:58:45: # Command line: callpeak -t SRX2402748.bam -f BAM -g 12100000 -n SRX2402748.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2402748.05 # format = BAM # ChIP-seq file = ['SRX2402748.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 01:58:45: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:58:45: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:58:45: # Command line: callpeak -t SRX2402748.bam -f BAM -g 12100000 -n SRX2402748.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2402748.10 # format = BAM # ChIP-seq file = ['SRX2402748.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 01:58:45: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:58:45: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:58:45: # Command line: callpeak -t SRX2402748.bam -f BAM -g 12100000 -n SRX2402748.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2402748.20 # format = BAM # ChIP-seq file = ['SRX2402748.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 01:58:45: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:58:45: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:58:52: 1000000 INFO @ Wed, 28 Jun 2017 01:58:52: 1000000 INFO @ Wed, 28 Jun 2017 01:58:52: 1000000 INFO @ Wed, 28 Jun 2017 01:58:58: 2000000 INFO @ Wed, 28 Jun 2017 01:58:58: 2000000 INFO @ Wed, 28 Jun 2017 01:58:59: 2000000 INFO @ Wed, 28 Jun 2017 01:59:05: 3000000 INFO @ Wed, 28 Jun 2017 01:59:05: 3000000 INFO @ Wed, 28 Jun 2017 01:59:07: 3000000 INFO @ Wed, 28 Jun 2017 01:59:12: 4000000 INFO @ Wed, 28 Jun 2017 01:59:12: 4000000 INFO @ Wed, 28 Jun 2017 01:59:15: 4000000 INFO @ Wed, 28 Jun 2017 01:59:19: 5000000 INFO @ Wed, 28 Jun 2017 01:59:19: 5000000 INFO @ Wed, 28 Jun 2017 01:59:23: 5000000 INFO @ Wed, 28 Jun 2017 01:59:26: 6000000 INFO @ Wed, 28 Jun 2017 01:59:26: 6000000 INFO @ Wed, 28 Jun 2017 01:59:31: 6000000 INFO @ Wed, 28 Jun 2017 01:59:33: 7000000 INFO @ Wed, 28 Jun 2017 01:59:34: 7000000 INFO @ Wed, 28 Jun 2017 01:59:39: 7000000 INFO @ Wed, 28 Jun 2017 01:59:40: 8000000 INFO @ Wed, 28 Jun 2017 01:59:41: 8000000 INFO @ Wed, 28 Jun 2017 01:59:47: 8000000 INFO @ Wed, 28 Jun 2017 01:59:47: 9000000 INFO @ Wed, 28 Jun 2017 01:59:48: 9000000 INFO @ Wed, 28 Jun 2017 01:59:54: 10000000 INFO @ Wed, 28 Jun 2017 01:59:54: 9000000 INFO @ Wed, 28 Jun 2017 01:59:55: 10000000 INFO @ Wed, 28 Jun 2017 02:00:01: 11000000 INFO @ Wed, 28 Jun 2017 02:00:02: 11000000 INFO @ Wed, 28 Jun 2017 02:00:02: 10000000 INFO @ Wed, 28 Jun 2017 02:00:08: 12000000 INFO @ Wed, 28 Jun 2017 02:00:09: 12000000 INFO @ Wed, 28 Jun 2017 02:00:10: 11000000 INFO @ Wed, 28 Jun 2017 02:00:15: 13000000 INFO @ Wed, 28 Jun 2017 02:00:16: 13000000 INFO @ Wed, 28 Jun 2017 02:00:17: 12000000 INFO @ Wed, 28 Jun 2017 02:00:22: 14000000 INFO @ Wed, 28 Jun 2017 02:00:24: 14000000 INFO @ Wed, 28 Jun 2017 02:00:26: 13000000 INFO @ Wed, 28 Jun 2017 02:00:31: 15000000 INFO @ Wed, 28 Jun 2017 02:00:32: 15000000 INFO @ Wed, 28 Jun 2017 02:00:35: 14000000 INFO @ Wed, 28 Jun 2017 02:00:38: 16000000 INFO @ Wed, 28 Jun 2017 02:00:40: 16000000 INFO @ Wed, 28 Jun 2017 02:00:44: 15000000 INFO @ Wed, 28 Jun 2017 02:00:46: 17000000 INFO @ Wed, 28 Jun 2017 02:00:48: 17000000 INFO @ Wed, 28 Jun 2017 02:00:51: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 02:00:51: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 02:00:51: #1 total tags in treatment: 8716384 INFO @ Wed, 28 Jun 2017 02:00:51: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 02:00:51: #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 02:00:51: #1 tags after filtering in treatment: 6195940 INFO @ Wed, 28 Jun 2017 02:00:51: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 28 Jun 2017 02:00:51: #1 finished! INFO @ Wed, 28 Jun 2017 02:00:51: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 02:00:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 02:00:51: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 02:00:51: 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 02:00:51: Process for pairing-model is terminated! cat: SRX2402748.20_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2402748.20_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 `SRX2402748.20_*.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 `SRX2402748.20_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 02:00:52: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 02:00:52: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 02:00:52: #1 total tags in treatment: 8716384 INFO @ Wed, 28 Jun 2017 02:00:52: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 02:00:52: #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 02:00:52: #1 tags after filtering in treatment: 6195940 INFO @ Wed, 28 Jun 2017 02:00:52: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 28 Jun 2017 02:00:52: #1 finished! INFO @ Wed, 28 Jun 2017 02:00:52: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 02:00:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 02:00:52: 16000000 INFO @ Wed, 28 Jun 2017 02:00:53: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 02:00:53: 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 02:00:53: Process for pairing-model is terminated! cat: SRX2402748.10_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 `SRX2402748.10_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 `SRX2402748.10_*.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 `SRX2402748.10_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 02:00:59: 17000000 INFO @ Wed, 28 Jun 2017 02:01:02: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 02:01:02: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 02:01:02: #1 total tags in treatment: 8716384 INFO @ Wed, 28 Jun 2017 02:01:02: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 02:01:02: #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 02:01:03: #1 tags after filtering in treatment: 6195940 INFO @ Wed, 28 Jun 2017 02:01:03: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 28 Jun 2017 02:01:03: #1 finished! INFO @ Wed, 28 Jun 2017 02:01:03: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 02:01:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 02:01:03: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 02:01:03: 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 02:01:03: Process for pairing-model is terminated! cat: SRX2402748.05_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 `SRX2402748.05_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 `SRX2402748.05_*.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 `SRX2402748.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。