Job ID = 9161955 sra ファイルのダウンロード中... Completed: 1145175K bytes transferred in 13 seconds (691605K 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 27312607 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423689/SRR2930978.sra Written 27312607 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: 00:21:53 27312607 reads; of these: 27312607 (100.00%) were paired; of these: 1414667 (5.18%) aligned concordantly 0 times 23141200 (84.73%) aligned concordantly exactly 1 time 2756740 (10.09%) aligned concordantly >1 times ---- 1414667 pairs aligned concordantly 0 times; of these: 50607 (3.58%) aligned discordantly 1 time ---- 1364060 pairs aligned 0 times concordantly or discordantly; of these: 2728120 mates make up the pairs; of these: 2505984 (91.86%) aligned 0 times 174749 (6.41%) aligned exactly 1 time 47387 (1.74%) aligned >1 times 95.41% overall alignment rate Time searching: 00:21:53 Overall time: 00:21:53 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 24 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] 13837899 / 25909273 = 0.5341 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 05:38:16: # Command line: callpeak -t SRX1423689.bam -f BAM -g 12100000 -n SRX1423689.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423689.05 # format = BAM # ChIP-seq file = ['SRX1423689.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 05:38:16: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:38:16: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:38:16: # Command line: callpeak -t SRX1423689.bam -f BAM -g 12100000 -n SRX1423689.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423689.20 # format = BAM # ChIP-seq file = ['SRX1423689.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 05:38:16: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:38:16: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:38:16: # Command line: callpeak -t SRX1423689.bam -f BAM -g 12100000 -n SRX1423689.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423689.10 # format = BAM # ChIP-seq file = ['SRX1423689.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 05:38:16: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:38:16: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:38:21: 1000000 INFO @ Wed, 28 Jun 2017 05:38:21: 1000000 INFO @ Wed, 28 Jun 2017 05:38:21: 1000000 INFO @ Wed, 28 Jun 2017 05:38:26: 2000000 INFO @ Wed, 28 Jun 2017 05:38:27: 2000000 INFO @ Wed, 28 Jun 2017 05:38:27: 2000000 INFO @ Wed, 28 Jun 2017 05:38:31: 3000000 INFO @ Wed, 28 Jun 2017 05:38:33: 3000000 INFO @ Wed, 28 Jun 2017 05:38:33: 3000000 INFO @ Wed, 28 Jun 2017 05:38:37: 4000000 INFO @ Wed, 28 Jun 2017 05:38:39: 4000000 INFO @ Wed, 28 Jun 2017 05:38:39: 4000000 INFO @ Wed, 28 Jun 2017 05:38:42: 5000000 INFO @ Wed, 28 Jun 2017 05:38:45: 5000000 INFO @ Wed, 28 Jun 2017 05:38:45: 5000000 INFO @ Wed, 28 Jun 2017 05:38:48: 6000000 INFO @ Wed, 28 Jun 2017 05:38:51: 6000000 INFO @ Wed, 28 Jun 2017 05:38:51: 6000000 INFO @ Wed, 28 Jun 2017 05:38:54: 7000000 INFO @ Wed, 28 Jun 2017 05:38:59: 7000000 INFO @ Wed, 28 Jun 2017 05:38:59: 7000000 INFO @ Wed, 28 Jun 2017 05:39:02: 8000000 INFO @ Wed, 28 Jun 2017 05:39:06: 8000000 INFO @ Wed, 28 Jun 2017 05:39:06: 8000000 INFO @ Wed, 28 Jun 2017 05:39:09: 9000000 INFO @ Wed, 28 Jun 2017 05:39:12: 9000000 INFO @ Wed, 28 Jun 2017 05:39:14: 9000000 INFO @ Wed, 28 Jun 2017 05:39:16: 10000000 INFO @ Wed, 28 Jun 2017 05:39:18: 10000000 INFO @ Wed, 28 Jun 2017 05:39:21: 10000000 INFO @ Wed, 28 Jun 2017 05:39:24: 11000000 INFO @ Wed, 28 Jun 2017 05:39:25: 11000000 INFO @ Wed, 28 Jun 2017 05:39:26: 11000000 INFO @ Wed, 28 Jun 2017 05:39:30: 12000000 INFO @ Wed, 28 Jun 2017 05:39:31: 12000000 INFO @ Wed, 28 Jun 2017 05:39:32: 12000000 INFO @ Wed, 28 Jun 2017 05:39:37: 13000000 INFO @ Wed, 28 Jun 2017 05:39:37: 13000000 INFO @ Wed, 28 Jun 2017 05:39:39: 13000000 INFO @ Wed, 28 Jun 2017 05:39:43: 14000000 INFO @ Wed, 28 Jun 2017 05:39:43: 14000000 INFO @ Wed, 28 Jun 2017 05:39:45: 14000000 INFO @ Wed, 28 Jun 2017 05:39:48: 15000000 INFO @ Wed, 28 Jun 2017 05:39:50: 15000000 INFO @ Wed, 28 Jun 2017 05:39:52: 15000000 INFO @ Wed, 28 Jun 2017 05:39:54: 16000000 INFO @ Wed, 28 Jun 2017 05:39:57: 16000000 INFO @ Wed, 28 Jun 2017 05:39:59: 16000000 INFO @ Wed, 28 Jun 2017 05:39:59: 17000000 INFO @ Wed, 28 Jun 2017 05:40:03: 17000000 INFO @ Wed, 28 Jun 2017 05:40:05: 18000000 INFO @ Wed, 28 Jun 2017 05:40:05: 17000000 INFO @ Wed, 28 Jun 2017 05:40:10: 19000000 INFO @ Wed, 28 Jun 2017 05:40:10: 18000000 INFO @ Wed, 28 Jun 2017 05:40:12: 18000000 INFO @ Wed, 28 Jun 2017 05:40:15: 20000000 INFO @ Wed, 28 Jun 2017 05:40:17: 19000000 INFO @ Wed, 28 Jun 2017 05:40:19: 19000000 INFO @ Wed, 28 Jun 2017 05:40:22: 21000000 INFO @ Wed, 28 Jun 2017 05:40:25: 20000000 INFO @ Wed, 28 Jun 2017 05:40:28: 20000000 INFO @ Wed, 28 Jun 2017 05:40:28: 22000000 INFO @ Wed, 28 Jun 2017 05:40:34: 21000000 INFO @ Wed, 28 Jun 2017 05:40:35: 23000000 INFO @ Wed, 28 Jun 2017 05:40:36: 21000000 INFO @ Wed, 28 Jun 2017 05:40:40: 24000000 INFO @ Wed, 28 Jun 2017 05:40:41: 22000000 INFO @ Wed, 28 Jun 2017 05:40:42: 22000000 INFO @ Wed, 28 Jun 2017 05:40:43: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:40:43: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:40:43: #1 total tags in treatment: 12063980 INFO @ Wed, 28 Jun 2017 05:40:43: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:40:43: #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 05:40:43: #1 tags after filtering in treatment: 8813490 INFO @ Wed, 28 Jun 2017 05:40:43: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 28 Jun 2017 05:40:43: #1 finished! INFO @ Wed, 28 Jun 2017 05:40:43: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:40:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:40:44: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:40:44: 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 05:40:44: Process for pairing-model is terminated! cat: SRX1423689.05_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 `SRX1423689.05_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 `SRX1423689.05_*.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 `SRX1423689.05_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 05:40:47: 23000000 INFO @ Wed, 28 Jun 2017 05:40:49: 23000000 INFO @ Wed, 28 Jun 2017 05:40:53: 24000000 INFO @ Wed, 28 Jun 2017 05:40:54: 24000000 INFO @ Wed, 28 Jun 2017 05:40:55: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:40:55: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:40:55: #1 total tags in treatment: 12063980 INFO @ Wed, 28 Jun 2017 05:40:55: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:40:55: #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 05:40:56: #1 tags after filtering in treatment: 8813490 INFO @ Wed, 28 Jun 2017 05:40:56: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 28 Jun 2017 05:40:56: #1 finished! INFO @ Wed, 28 Jun 2017 05:40:56: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:40:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:40:56: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:40:56: 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 05:40:56: Process for pairing-model is terminated! cat: SRX1423689.10_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 `SRX1423689.10_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 `SRX1423689.10_*.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 `SRX1423689.10_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 05:40:57: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:40:57: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:40:57: #1 total tags in treatment: 12063980 INFO @ Wed, 28 Jun 2017 05:40:57: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:40:57: #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 05:40:57: #1 tags after filtering in treatment: 8813490 INFO @ Wed, 28 Jun 2017 05:40:57: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 28 Jun 2017 05:40:57: #1 finished! INFO @ Wed, 28 Jun 2017 05:40:57: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:40:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:40:58: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:40:58: 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 05:40:58: Process for pairing-model is terminated! cat: SRX1423689.20_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 `SRX1423689.20_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 `SRX1423689.20_*.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 `SRX1423689.20_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。