Job ID = 9732088 sra ファイルのダウンロード中... Completed: 415402K bytes transferred in 10 seconds (318156K 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 17956878 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675878/SRR5380655.sra Written 17956878 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: 00:00:01 Multiseed full-index search: 00:07:37 17956878 reads; of these: 17956878 (100.00%) were paired; of these: 5735141 (31.94%) aligned concordantly 0 times 10645310 (59.28%) aligned concordantly exactly 1 time 1576427 (8.78%) aligned concordantly >1 times ---- 5735141 pairs aligned concordantly 0 times; of these: 588333 (10.26%) aligned discordantly 1 time ---- 5146808 pairs aligned 0 times concordantly or discordantly; of these: 10293616 mates make up the pairs; of these: 9435152 (91.66%) aligned 0 times 579155 (5.63%) aligned exactly 1 time 279309 (2.71%) aligned >1 times 73.73% overall alignment rate Time searching: 00:07:38 Overall time: 00:07:38 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] 1758139 / 12569086 = 0.1399 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 19:40:06: # Command line: callpeak -t SRX2675878.bam -f BAM -g 12100000 -n SRX2675878.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675878.05 # format = BAM # ChIP-seq file = ['SRX2675878.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 19:40:06: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:40:06: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:40:06: # Command line: callpeak -t SRX2675878.bam -f BAM -g 12100000 -n SRX2675878.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675878.10 # format = BAM # ChIP-seq file = ['SRX2675878.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 19:40:06: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:40:06: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:40:06: # Command line: callpeak -t SRX2675878.bam -f BAM -g 12100000 -n SRX2675878.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675878.20 # format = BAM # ChIP-seq file = ['SRX2675878.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 19:40:06: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:40:06: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:40:11: 1000000 INFO @ Sun, 03 Sep 2017 19:40:11: 1000000 INFO @ Sun, 03 Sep 2017 19:40:11: 1000000 INFO @ Sun, 03 Sep 2017 19:40:16: 2000000 INFO @ Sun, 03 Sep 2017 19:40:16: 2000000 INFO @ Sun, 03 Sep 2017 19:40:16: 2000000 INFO @ Sun, 03 Sep 2017 19:40:21: 3000000 INFO @ Sun, 03 Sep 2017 19:40:21: 3000000 INFO @ Sun, 03 Sep 2017 19:40:21: 3000000 INFO @ Sun, 03 Sep 2017 19:40:26: 4000000 INFO @ Sun, 03 Sep 2017 19:40:26: 4000000 INFO @ Sun, 03 Sep 2017 19:40:26: 4000000 INFO @ Sun, 03 Sep 2017 19:40:31: 5000000 INFO @ Sun, 03 Sep 2017 19:40:31: 5000000 INFO @ Sun, 03 Sep 2017 19:40:31: 5000000 INFO @ Sun, 03 Sep 2017 19:40:36: 6000000 INFO @ Sun, 03 Sep 2017 19:40:37: 6000000 INFO @ Sun, 03 Sep 2017 19:40:37: 6000000 INFO @ Sun, 03 Sep 2017 19:40:41: 7000000 INFO @ Sun, 03 Sep 2017 19:40:42: 7000000 INFO @ Sun, 03 Sep 2017 19:40:42: 7000000 INFO @ Sun, 03 Sep 2017 19:40:46: 8000000 INFO @ Sun, 03 Sep 2017 19:40:47: 8000000 INFO @ Sun, 03 Sep 2017 19:40:47: 8000000 INFO @ Sun, 03 Sep 2017 19:40:51: 9000000 INFO @ Sun, 03 Sep 2017 19:40:52: 9000000 INFO @ Sun, 03 Sep 2017 19:40:52: 9000000 INFO @ Sun, 03 Sep 2017 19:40:56: 10000000 INFO @ Sun, 03 Sep 2017 19:40:56: 10000000 INFO @ Sun, 03 Sep 2017 19:40:58: 10000000 INFO @ Sun, 03 Sep 2017 19:41:00: 11000000 INFO @ Sun, 03 Sep 2017 19:41:01: 11000000 INFO @ Sun, 03 Sep 2017 19:41:03: 11000000 INFO @ Sun, 03 Sep 2017 19:41:05: 12000000 INFO @ Sun, 03 Sep 2017 19:41:06: 12000000 INFO @ Sun, 03 Sep 2017 19:41:08: 12000000 INFO @ Sun, 03 Sep 2017 19:41:10: 13000000 INFO @ Sun, 03 Sep 2017 19:41:11: 13000000 INFO @ Sun, 03 Sep 2017 19:41:13: 13000000 INFO @ Sun, 03 Sep 2017 19:41:15: 14000000 INFO @ Sun, 03 Sep 2017 19:41:16: 14000000 INFO @ Sun, 03 Sep 2017 19:41:18: 14000000 INFO @ Sun, 03 Sep 2017 19:41:20: 15000000 INFO @ Sun, 03 Sep 2017 19:41:21: 15000000 INFO @ Sun, 03 Sep 2017 19:41:24: 15000000 INFO @ Sun, 03 Sep 2017 19:41:25: 16000000 INFO @ Sun, 03 Sep 2017 19:41:26: 16000000 INFO @ Sun, 03 Sep 2017 19:41:29: 16000000 INFO @ Sun, 03 Sep 2017 19:41:30: 17000000 INFO @ Sun, 03 Sep 2017 19:41:30: 17000000 INFO @ Sun, 03 Sep 2017 19:41:34: 17000000 INFO @ Sun, 03 Sep 2017 19:41:35: 18000000 INFO @ Sun, 03 Sep 2017 19:41:35: 18000000 INFO @ Sun, 03 Sep 2017 19:41:39: 18000000 INFO @ Sun, 03 Sep 2017 19:41:39: 19000000 INFO @ Sun, 03 Sep 2017 19:41:40: 19000000 INFO @ Sun, 03 Sep 2017 19:41:44: 19000000 INFO @ Sun, 03 Sep 2017 19:41:44: 20000000 INFO @ Sun, 03 Sep 2017 19:41:45: 20000000 INFO @ Sun, 03 Sep 2017 19:41:49: 21000000 INFO @ Sun, 03 Sep 2017 19:41:49: 20000000 INFO @ Sun, 03 Sep 2017 19:41:50: 21000000 INFO @ Sun, 03 Sep 2017 19:41:54: 22000000 INFO @ Sun, 03 Sep 2017 19:41:55: 21000000 INFO @ Sun, 03 Sep 2017 19:41:55: 22000000 INFO @ Sun, 03 Sep 2017 19:41:59: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:41:59: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:41:59: #1 total tags in treatment: 10470476 INFO @ Sun, 03 Sep 2017 19:41:59: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:41:59: #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 19:41:59: #1 tags after filtering in treatment: 5041404 INFO @ Sun, 03 Sep 2017 19:41:59: #1 Redundant rate of treatment: 0.52 INFO @ Sun, 03 Sep 2017 19:41:59: #1 finished! INFO @ Sun, 03 Sep 2017 19:41:59: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:41:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:42:00: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:42:00: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:42:00: #1 total tags in treatment: 10470476 INFO @ Sun, 03 Sep 2017 19:42:00: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:42:00: #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 19:42:00: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:42:00: 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 19:42:00: Process for pairing-model is terminated! cat: SRX2675878.05_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675878.05_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 `SRX2675878.05_*.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 `SRX2675878.05_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 19:42:00: 22000000 INFO @ Sun, 03 Sep 2017 19:42:00: #1 tags after filtering in treatment: 5041404 INFO @ Sun, 03 Sep 2017 19:42:00: #1 Redundant rate of treatment: 0.52 INFO @ Sun, 03 Sep 2017 19:42:00: #1 finished! INFO @ Sun, 03 Sep 2017 19:42:00: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:42:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:42:00: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:42:00: 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 19:42:00: Process for pairing-model is terminated! cat: SRX2675878.10_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675878.10_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 `SRX2675878.10_*.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 `SRX2675878.10_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 @ Sun, 03 Sep 2017 19:42:04: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:42:04: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:42:04: #1 total tags in treatment: 10470476 INFO @ Sun, 03 Sep 2017 19:42:04: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:42:04: #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 19:42:05: #1 tags after filtering in treatment: 5041404 INFO @ Sun, 03 Sep 2017 19:42:05: #1 Redundant rate of treatment: 0.52 INFO @ Sun, 03 Sep 2017 19:42:05: #1 finished! INFO @ Sun, 03 Sep 2017 19:42:05: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:42:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:42:05: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:42:05: 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 19:42:05: Process for pairing-model is terminated! cat: SRX2675878.20_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 `SRX2675878.20_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 `SRX2675878.20_*.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 `SRX2675878.20_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。