Job ID = 9161918 sra ファイルのダウンロード中... Completed: 2747910K bytes transferred in 24 seconds (910277K 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 20679563 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1406640/SRR2889263.sra Written 20679563 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: 00:24:24 20679563 reads; of these: 20679563 (100.00%) were paired; of these: 4640947 (22.44%) aligned concordantly 0 times 13028112 (63.00%) aligned concordantly exactly 1 time 3010504 (14.56%) aligned concordantly >1 times ---- 4640947 pairs aligned concordantly 0 times; of these: 613296 (13.21%) aligned discordantly 1 time ---- 4027651 pairs aligned 0 times concordantly or discordantly; of these: 8055302 mates make up the pairs; of these: 7476548 (92.82%) aligned 0 times 195638 (2.43%) aligned exactly 1 time 383116 (4.76%) aligned >1 times 81.92% overall alignment rate Time searching: 00:24:24 Overall time: 00:24:24 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] 1567211 / 16569843 = 0.0946 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 05:40:06: # Command line: callpeak -t SRX1406640.bam -f BAM -g 12100000 -n SRX1406640.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1406640.10 # format = BAM # ChIP-seq file = ['SRX1406640.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 05:40:06: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:40:06: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:40:06: # Command line: callpeak -t SRX1406640.bam -f BAM -g 12100000 -n SRX1406640.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1406640.05 # format = BAM # ChIP-seq file = ['SRX1406640.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 05:40:06: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:40:06: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:40:06: # Command line: callpeak -t SRX1406640.bam -f BAM -g 12100000 -n SRX1406640.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1406640.20 # format = BAM # ChIP-seq file = ['SRX1406640.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 05:40:06: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:40:06: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:40:18: 1000000 INFO @ Wed, 28 Jun 2017 05:40:18: 1000000 INFO @ Wed, 28 Jun 2017 05:40:18: 1000000 INFO @ Wed, 28 Jun 2017 05:40:29: 2000000 INFO @ Wed, 28 Jun 2017 05:40:30: 2000000 INFO @ Wed, 28 Jun 2017 05:40:32: 2000000 INFO @ Wed, 28 Jun 2017 05:40:40: 3000000 INFO @ Wed, 28 Jun 2017 05:40:41: 3000000 INFO @ Wed, 28 Jun 2017 05:40:44: 3000000 INFO @ Wed, 28 Jun 2017 05:40:50: 4000000 INFO @ Wed, 28 Jun 2017 05:40:51: 4000000 INFO @ Wed, 28 Jun 2017 05:40:54: 4000000 INFO @ Wed, 28 Jun 2017 05:41:00: 5000000 INFO @ Wed, 28 Jun 2017 05:41:01: 5000000 INFO @ Wed, 28 Jun 2017 05:41:05: 5000000 INFO @ Wed, 28 Jun 2017 05:41:09: 6000000 INFO @ Wed, 28 Jun 2017 05:41:11: 6000000 INFO @ Wed, 28 Jun 2017 05:41:17: 6000000 INFO @ Wed, 28 Jun 2017 05:41:19: 7000000 INFO @ Wed, 28 Jun 2017 05:41:21: 7000000 INFO @ Wed, 28 Jun 2017 05:41:28: 7000000 INFO @ Wed, 28 Jun 2017 05:41:31: 8000000 INFO @ Wed, 28 Jun 2017 05:41:32: 8000000 INFO @ Wed, 28 Jun 2017 05:41:39: 8000000 INFO @ Wed, 28 Jun 2017 05:41:43: 9000000 INFO @ Wed, 28 Jun 2017 05:41:43: 9000000 INFO @ Wed, 28 Jun 2017 05:41:53: 9000000 INFO @ Wed, 28 Jun 2017 05:41:54: 10000000 INFO @ Wed, 28 Jun 2017 05:41:55: 10000000 INFO @ Wed, 28 Jun 2017 05:42:06: 10000000 INFO @ Wed, 28 Jun 2017 05:42:06: 11000000 INFO @ Wed, 28 Jun 2017 05:42:09: 11000000 INFO @ Wed, 28 Jun 2017 05:42:17: 12000000 INFO @ Wed, 28 Jun 2017 05:42:19: 11000000 INFO @ Wed, 28 Jun 2017 05:42:22: 12000000 INFO @ Wed, 28 Jun 2017 05:42:29: 13000000 INFO @ Wed, 28 Jun 2017 05:42:31: 12000000 INFO @ Wed, 28 Jun 2017 05:42:34: 13000000 INFO @ Wed, 28 Jun 2017 05:42:39: 14000000 INFO @ Wed, 28 Jun 2017 05:42:44: 13000000 INFO @ Wed, 28 Jun 2017 05:42:45: 14000000 INFO @ Wed, 28 Jun 2017 05:42:48: 15000000 INFO @ Wed, 28 Jun 2017 05:42:55: 15000000 INFO @ Wed, 28 Jun 2017 05:42:56: 14000000 INFO @ Wed, 28 Jun 2017 05:42:58: 16000000 INFO @ Wed, 28 Jun 2017 05:43:05: 16000000 INFO @ Wed, 28 Jun 2017 05:43:07: 15000000 INFO @ Wed, 28 Jun 2017 05:43:07: 17000000 INFO @ Wed, 28 Jun 2017 05:43:14: 17000000 INFO @ Wed, 28 Jun 2017 05:43:16: 18000000 INFO @ Wed, 28 Jun 2017 05:43:16: 16000000 INFO @ Wed, 28 Jun 2017 05:43:22: 18000000 INFO @ Wed, 28 Jun 2017 05:43:24: 19000000 INFO @ Wed, 28 Jun 2017 05:43:25: 17000000 INFO @ Wed, 28 Jun 2017 05:43:31: 19000000 INFO @ Wed, 28 Jun 2017 05:43:32: 20000000 INFO @ Wed, 28 Jun 2017 05:43:35: 18000000 INFO @ Wed, 28 Jun 2017 05:43:40: 20000000 INFO @ Wed, 28 Jun 2017 05:43:41: 21000000 INFO @ Wed, 28 Jun 2017 05:43:45: 19000000 INFO @ Wed, 28 Jun 2017 05:43:49: 21000000 INFO @ Wed, 28 Jun 2017 05:43:49: 22000000 INFO @ Wed, 28 Jun 2017 05:43:54: 20000000 INFO @ Wed, 28 Jun 2017 05:43:58: 22000000 INFO @ Wed, 28 Jun 2017 05:43:58: 23000000 INFO @ Wed, 28 Jun 2017 05:44:05: 21000000 INFO @ Wed, 28 Jun 2017 05:44:07: 24000000 INFO @ Wed, 28 Jun 2017 05:44:07: 23000000 INFO @ Wed, 28 Jun 2017 05:44:15: 25000000 INFO @ Wed, 28 Jun 2017 05:44:15: 22000000 INFO @ Wed, 28 Jun 2017 05:44:17: 24000000 INFO @ Wed, 28 Jun 2017 05:44:24: 26000000 INFO @ Wed, 28 Jun 2017 05:44:26: 23000000 INFO @ Wed, 28 Jun 2017 05:44:26: 25000000 INFO @ Wed, 28 Jun 2017 05:44:32: 27000000 INFO @ Wed, 28 Jun 2017 05:44:35: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 28 Jun 2017 05:44:36: 24000000 INFO @ Wed, 28 Jun 2017 05:44:41: 28000000 INFO @ Wed, 28 Jun 2017 05:44:44: 27000000 INFO @ Wed, 28 Jun 2017 05:44:46: 25000000 INFO @ Wed, 28 Jun 2017 05:44:50: 29000000 INFO @ Wed, 28 Jun 2017 05:44:53: 28000000 INFO @ Wed, 28 Jun 2017 05:44:55: 26000000 BigWig に変換しました。 INFO @ Wed, 28 Jun 2017 05:44:59: 30000000 INFO @ Wed, 28 Jun 2017 05:45:02: 29000000 INFO @ Wed, 28 Jun 2017 05:45:05: #1 tag size is determined as 100 bps INFO @ Wed, 28 Jun 2017 05:45:05: #1 tag size = 100 INFO @ Wed, 28 Jun 2017 05:45:05: #1 total tags in treatment: 14504531 INFO @ Wed, 28 Jun 2017 05:45:05: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:45:05: #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 05:45:06: #1 tags after filtering in treatment: 9858422 INFO @ Wed, 28 Jun 2017 05:45:06: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 28 Jun 2017 05:45:06: #1 finished! INFO @ Wed, 28 Jun 2017 05:45:06: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:45:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:45:06: 27000000 INFO @ Wed, 28 Jun 2017 05:45:06: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:45:06: 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 05:45:06: Process for pairing-model is terminated! cat: SRX1406640.05_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 `SRX1406640.05_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 `SRX1406640.05_*.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 `SRX1406640.05_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 @ Wed, 28 Jun 2017 05:45:11: 30000000 INFO @ Wed, 28 Jun 2017 05:45:16: 28000000 INFO @ Wed, 28 Jun 2017 05:45:18: #1 tag size is determined as 100 bps INFO @ Wed, 28 Jun 2017 05:45:18: #1 tag size = 100 INFO @ Wed, 28 Jun 2017 05:45:18: #1 total tags in treatment: 14504531 INFO @ Wed, 28 Jun 2017 05:45:18: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:45:18: #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 05:45:18: #1 tags after filtering in treatment: 9858422 INFO @ Wed, 28 Jun 2017 05:45:18: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 28 Jun 2017 05:45:18: #1 finished! INFO @ Wed, 28 Jun 2017 05:45:18: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:45:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:45:19: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:45:19: 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 05:45:19: Process for pairing-model is terminated! cat: SRX1406640.20_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): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1406640.20_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 `SRX1406640.20_*.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 `SRX1406640.20_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 05:45:25: 29000000 INFO @ Wed, 28 Jun 2017 05:45:33: 30000000 INFO @ Wed, 28 Jun 2017 05:45:40: #1 tag size is determined as 100 bps INFO @ Wed, 28 Jun 2017 05:45:40: #1 tag size = 100 INFO @ Wed, 28 Jun 2017 05:45:40: #1 total tags in treatment: 14504531 INFO @ Wed, 28 Jun 2017 05:45:40: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:45:40: #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 05:45:40: #1 tags after filtering in treatment: 9858422 INFO @ Wed, 28 Jun 2017 05:45:40: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 28 Jun 2017 05:45:40: #1 finished! INFO @ Wed, 28 Jun 2017 05:45:40: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:45:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:45:40: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:45:40: 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 05:45:40: Process for pairing-model is terminated! cat: SRX1406640.10_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 `SRX1406640.10_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 `SRX1406640.10_*.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 `SRX1406640.10_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