Job ID = 9161954 sra ファイルのダウンロード中... Completed: 1851352K bytes transferred in 19 seconds (777842K 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 30728286 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423688/SRR2930977.sra Written 30728286 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: 00:16:38 30728286 reads; of these: 30728286 (100.00%) were paired; of these: 13008116 (42.33%) aligned concordantly 0 times 15623298 (50.84%) aligned concordantly exactly 1 time 2096872 (6.82%) aligned concordantly >1 times ---- 13008116 pairs aligned concordantly 0 times; of these: 418931 (3.22%) aligned discordantly 1 time ---- 12589185 pairs aligned 0 times concordantly or discordantly; of these: 25178370 mates make up the pairs; of these: 24900330 (98.90%) aligned 0 times 130945 (0.52%) aligned exactly 1 time 147095 (0.58%) aligned >1 times 59.48% overall alignment rate Time searching: 00:16:38 Overall time: 00:16:38 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 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] 4262076 / 18117659 = 0.2352 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 05:33:44: # Command line: callpeak -t SRX1423688.bam -f BAM -g 12100000 -n SRX1423688.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423688.20 # format = BAM # ChIP-seq file = ['SRX1423688.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 05:33:44: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:33:44: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:33:44: # Command line: callpeak -t SRX1423688.bam -f BAM -g 12100000 -n SRX1423688.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423688.05 # format = BAM # ChIP-seq file = ['SRX1423688.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 05:33:44: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:33:44: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:33:44: # Command line: callpeak -t SRX1423688.bam -f BAM -g 12100000 -n SRX1423688.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423688.10 # format = BAM # ChIP-seq file = ['SRX1423688.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 05:33:44: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:33:44: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:33:53: 1000000 INFO @ Wed, 28 Jun 2017 05:33:53: 1000000 INFO @ Wed, 28 Jun 2017 05:33:53: 1000000 INFO @ Wed, 28 Jun 2017 05:34:01: 2000000 INFO @ Wed, 28 Jun 2017 05:34:02: 2000000 INFO @ Wed, 28 Jun 2017 05:34:02: 2000000 INFO @ Wed, 28 Jun 2017 05:34:09: 3000000 INFO @ Wed, 28 Jun 2017 05:34:11: 3000000 INFO @ Wed, 28 Jun 2017 05:34:11: 3000000 INFO @ Wed, 28 Jun 2017 05:34:18: 4000000 INFO @ Wed, 28 Jun 2017 05:34:21: 4000000 INFO @ Wed, 28 Jun 2017 05:34:21: 4000000 INFO @ Wed, 28 Jun 2017 05:34:26: 5000000 INFO @ Wed, 28 Jun 2017 05:34:30: 5000000 INFO @ Wed, 28 Jun 2017 05:34:30: 5000000 INFO @ Wed, 28 Jun 2017 05:34:32: 6000000 INFO @ Wed, 28 Jun 2017 05:34:39: 6000000 INFO @ Wed, 28 Jun 2017 05:34:39: 6000000 INFO @ Wed, 28 Jun 2017 05:34:39: 7000000 INFO @ Wed, 28 Jun 2017 05:34:46: 8000000 INFO @ Wed, 28 Jun 2017 05:34:47: 7000000 INFO @ Wed, 28 Jun 2017 05:34:47: 7000000 INFO @ Wed, 28 Jun 2017 05:34:52: 9000000 INFO @ Wed, 28 Jun 2017 05:34:55: 8000000 INFO @ Wed, 28 Jun 2017 05:34:55: 8000000 INFO @ Wed, 28 Jun 2017 05:34:59: 10000000 INFO @ Wed, 28 Jun 2017 05:35:03: 9000000 INFO @ Wed, 28 Jun 2017 05:35:03: 9000000 INFO @ Wed, 28 Jun 2017 05:35:05: 11000000 INFO @ Wed, 28 Jun 2017 05:35:11: 10000000 INFO @ Wed, 28 Jun 2017 05:35:11: 10000000 INFO @ Wed, 28 Jun 2017 05:35:12: 12000000 INFO @ Wed, 28 Jun 2017 05:35:19: 13000000 INFO @ Wed, 28 Jun 2017 05:35:19: 11000000 INFO @ Wed, 28 Jun 2017 05:35:19: 11000000 INFO @ Wed, 28 Jun 2017 05:35:26: 14000000 INFO @ Wed, 28 Jun 2017 05:35:28: 12000000 INFO @ Wed, 28 Jun 2017 05:35:28: 12000000 INFO @ Wed, 28 Jun 2017 05:35:32: 15000000 INFO @ Wed, 28 Jun 2017 05:35:36: 13000000 INFO @ Wed, 28 Jun 2017 05:35:36: 13000000 INFO @ Wed, 28 Jun 2017 05:35:39: 16000000 INFO @ Wed, 28 Jun 2017 05:35:44: 14000000 INFO @ Wed, 28 Jun 2017 05:35:44: 14000000 INFO @ Wed, 28 Jun 2017 05:35:45: 17000000 INFO @ Wed, 28 Jun 2017 05:35:52: 18000000 INFO @ Wed, 28 Jun 2017 05:35:53: 15000000 INFO @ Wed, 28 Jun 2017 05:35:53: 15000000 INFO @ Wed, 28 Jun 2017 05:35:58: 19000000 INFO @ Wed, 28 Jun 2017 05:36:01: 16000000 INFO @ Wed, 28 Jun 2017 05:36:01: 16000000 INFO @ Wed, 28 Jun 2017 05:36:05: 20000000 INFO @ Wed, 28 Jun 2017 05:36:10: 17000000 INFO @ Wed, 28 Jun 2017 05:36:10: 17000000 INFO @ Wed, 28 Jun 2017 05:36:11: 21000000 INFO @ Wed, 28 Jun 2017 05:36:18: 22000000 INFO @ Wed, 28 Jun 2017 05:36:18: 18000000 INFO @ Wed, 28 Jun 2017 05:36:18: 18000000 INFO @ Wed, 28 Jun 2017 05:36:24: 23000000 INFO @ Wed, 28 Jun 2017 05:36:26: 19000000 INFO @ Wed, 28 Jun 2017 05:36:26: 19000000 INFO @ Wed, 28 Jun 2017 05:36:31: 24000000 INFO @ Wed, 28 Jun 2017 05:36:35: 20000000 INFO @ Wed, 28 Jun 2017 05:36:35: 20000000 INFO @ Wed, 28 Jun 2017 05:36:37: 25000000 INFO @ Wed, 28 Jun 2017 05:36:43: 21000000 INFO @ Wed, 28 Jun 2017 05:36:43: 21000000 INFO @ Wed, 28 Jun 2017 05:36:44: 26000000 INFO @ Wed, 28 Jun 2017 05:36:50: 27000000 INFO @ Wed, 28 Jun 2017 05:36:52: 22000000 INFO @ Wed, 28 Jun 2017 05:36:52: 22000000 INFO @ Wed, 28 Jun 2017 05:36:56: 28000000 INFO @ Wed, 28 Jun 2017 05:36:57: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:36:57: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:36:57: #1 total tags in treatment: 13494510 INFO @ Wed, 28 Jun 2017 05:36:57: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:36:57: #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 05:36:57: #1 tags after filtering in treatment: 9519126 INFO @ Wed, 28 Jun 2017 05:36:57: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 28 Jun 2017 05:36:57: #1 finished! INFO @ Wed, 28 Jun 2017 05:36:57: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:36:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:36:58: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:36:58: 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 05:36:58: Process for pairing-model is terminated! cat: SRX1423688.10_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 `SRX1423688.10_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 `SRX1423688.10_*.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 `SRX1423688.10_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 05:37:00: 23000000 INFO @ Wed, 28 Jun 2017 05:37:00: 23000000 INFO @ Wed, 28 Jun 2017 05:37:09: 24000000 INFO @ Wed, 28 Jun 2017 05:37:09: 24000000 INFO @ Wed, 28 Jun 2017 05:37:17: 25000000 INFO @ Wed, 28 Jun 2017 05:37:17: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 28 Jun 2017 05:37:26: 26000000 INFO @ Wed, 28 Jun 2017 05:37:26: 26000000 INFO @ Wed, 28 Jun 2017 05:37:34: 27000000 INFO @ Wed, 28 Jun 2017 05:37:34: 27000000 BigWig に変換しました。 INFO @ Wed, 28 Jun 2017 05:37:43: 28000000 INFO @ Wed, 28 Jun 2017 05:37:43: 28000000 INFO @ Wed, 28 Jun 2017 05:37:43: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:37:43: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:37:43: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:37:43: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:37:43: #1 total tags in treatment: 13494510 INFO @ Wed, 28 Jun 2017 05:37:43: #1 total tags in treatment: 13494510 INFO @ Wed, 28 Jun 2017 05:37:43: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:37:43: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:37:43: #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 05:37:43: #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 05:37:43: #1 tags after filtering in treatment: 9519126 INFO @ Wed, 28 Jun 2017 05:37:43: #1 tags after filtering in treatment: 9519126 INFO @ Wed, 28 Jun 2017 05:37:43: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 28 Jun 2017 05:37:43: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 28 Jun 2017 05:37:43: #1 finished! INFO @ Wed, 28 Jun 2017 05:37:43: #1 finished! INFO @ Wed, 28 Jun 2017 05:37:43: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:37:43: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:37:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:37:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:37:44: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:37:44: 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 05:37:44: Process for pairing-model is terminated! INFO @ Wed, 28 Jun 2017 05:37:44: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:37:44: 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 05:37:44: Process for pairing-model is terminated! cat: SRX1423688.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX1423688.20_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 `SRX1423688.05_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 `SRX1423688.05_*.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 `SRX1423688.05_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1423688.20_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 `SRX1423688.20_*.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 `SRX1423688.20_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