Job ID = 9161958 sra ファイルのダウンロード中... Completed: 1114679K bytes transferred in 12 seconds (746771K 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 26846307 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423692/SRR2930981.sra Written 26846307 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: 00:23:12 26846307 reads; of these: 26846307 (100.00%) were paired; of these: 1913786 (7.13%) aligned concordantly 0 times 22155419 (82.53%) aligned concordantly exactly 1 time 2777102 (10.34%) aligned concordantly >1 times ---- 1913786 pairs aligned concordantly 0 times; of these: 28492 (1.49%) aligned discordantly 1 time ---- 1885294 pairs aligned 0 times concordantly or discordantly; of these: 3770588 mates make up the pairs; of these: 3517524 (93.29%) aligned 0 times 209125 (5.55%) aligned exactly 1 time 43939 (1.17%) aligned >1 times 93.45% overall alignment rate Time searching: 00:23:12 Overall time: 00:23:12 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] 15562349 / 24937367 = 0.6241 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 05:39:09: # Command line: callpeak -t SRX1423692.bam -f BAM -g 12100000 -n SRX1423692.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423692.05 # format = BAM # ChIP-seq file = ['SRX1423692.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 05:39:09: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:39:09: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:39:09: # Command line: callpeak -t SRX1423692.bam -f BAM -g 12100000 -n SRX1423692.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423692.10 # format = BAM # ChIP-seq file = ['SRX1423692.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 05:39:09: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:39:09: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:39:09: # Command line: callpeak -t SRX1423692.bam -f BAM -g 12100000 -n SRX1423692.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423692.20 # format = BAM # ChIP-seq file = ['SRX1423692.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 05:39:09: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:39:09: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:39:14: 1000000 INFO @ Wed, 28 Jun 2017 05:39:14: 1000000 INFO @ Wed, 28 Jun 2017 05:39:15: 1000000 INFO @ Wed, 28 Jun 2017 05:39:20: 2000000 INFO @ Wed, 28 Jun 2017 05:39:20: 2000000 INFO @ Wed, 28 Jun 2017 05:39:21: 2000000 INFO @ Wed, 28 Jun 2017 05:39:26: 3000000 INFO @ Wed, 28 Jun 2017 05:39:26: 3000000 INFO @ Wed, 28 Jun 2017 05:39:27: 3000000 INFO @ Wed, 28 Jun 2017 05:39:32: 4000000 INFO @ Wed, 28 Jun 2017 05:39:33: 4000000 INFO @ Wed, 28 Jun 2017 05:39:34: 4000000 INFO @ Wed, 28 Jun 2017 05:39:40: 5000000 INFO @ Wed, 28 Jun 2017 05:39:40: 5000000 INFO @ Wed, 28 Jun 2017 05:39:43: 5000000 INFO @ Wed, 28 Jun 2017 05:39:46: 6000000 INFO @ Wed, 28 Jun 2017 05:39:48: 6000000 INFO @ Wed, 28 Jun 2017 05:39:51: 6000000 INFO @ Wed, 28 Jun 2017 05:39:53: 7000000 INFO @ Wed, 28 Jun 2017 05:39:55: 7000000 INFO @ Wed, 28 Jun 2017 05:39:58: 7000000 INFO @ Wed, 28 Jun 2017 05:40:00: 8000000 INFO @ Wed, 28 Jun 2017 05:40:03: 8000000 INFO @ Wed, 28 Jun 2017 05:40:06: 8000000 INFO @ Wed, 28 Jun 2017 05:40:07: 9000000 INFO @ Wed, 28 Jun 2017 05:40:11: 9000000 INFO @ Wed, 28 Jun 2017 05:40:13: 10000000 INFO @ Wed, 28 Jun 2017 05:40:14: 9000000 INFO @ Wed, 28 Jun 2017 05:40:18: 10000000 INFO @ Wed, 28 Jun 2017 05:40:20: 11000000 INFO @ Wed, 28 Jun 2017 05:40:22: 10000000 INFO @ Wed, 28 Jun 2017 05:40:26: 11000000 INFO @ Wed, 28 Jun 2017 05:40:26: 12000000 INFO @ Wed, 28 Jun 2017 05:40:30: 11000000 INFO @ Wed, 28 Jun 2017 05:40:32: 13000000 INFO @ Wed, 28 Jun 2017 05:40:33: 12000000 INFO @ Wed, 28 Jun 2017 05:40:38: 12000000 INFO @ Wed, 28 Jun 2017 05:40:39: 14000000 INFO @ Wed, 28 Jun 2017 05:40:41: 13000000 INFO @ Wed, 28 Jun 2017 05:40:45: 13000000 INFO @ Wed, 28 Jun 2017 05:40:46: 15000000 INFO @ Wed, 28 Jun 2017 05:40:48: 14000000 INFO @ Wed, 28 Jun 2017 05:40:53: 14000000 INFO @ Wed, 28 Jun 2017 05:40:53: 16000000 INFO @ Wed, 28 Jun 2017 05:40:55: 15000000 INFO @ Wed, 28 Jun 2017 05:41:00: 15000000 INFO @ Wed, 28 Jun 2017 05:41:00: 17000000 INFO @ Wed, 28 Jun 2017 05:41:02: 16000000 INFO @ Wed, 28 Jun 2017 05:41:07: 18000000 INFO @ Wed, 28 Jun 2017 05:41:07: 16000000 INFO @ Wed, 28 Jun 2017 05:41:09: 17000000 INFO @ Wed, 28 Jun 2017 05:41:15: 19000000 INFO @ Wed, 28 Jun 2017 05:41:15: 17000000 INFO @ Wed, 28 Jun 2017 05:41:15: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:41:15: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:41:15: #1 total tags in treatment: 9372169 INFO @ Wed, 28 Jun 2017 05:41:15: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:41:15: #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 05:41:16: #1 tags after filtering in treatment: 7184367 INFO @ Wed, 28 Jun 2017 05:41:16: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 28 Jun 2017 05:41:16: #1 finished! INFO @ Wed, 28 Jun 2017 05:41:16: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:41:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:41:16: 18000000 INFO @ Wed, 28 Jun 2017 05:41:16: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:41:16: 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 05:41:16: Process for pairing-model is terminated! cat: SRX1423692.20_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 `SRX1423692.20_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 `SRX1423692.20_*.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 `SRX1423692.20_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 05:41:22: 18000000 INFO @ Wed, 28 Jun 2017 05:41:22: 19000000 INFO @ Wed, 28 Jun 2017 05:41:22: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:41:22: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:41:22: #1 total tags in treatment: 9372169 INFO @ Wed, 28 Jun 2017 05:41:22: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:41:22: #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 05:41:23: #1 tags after filtering in treatment: 7184367 INFO @ Wed, 28 Jun 2017 05:41:23: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 28 Jun 2017 05:41:23: #1 finished! INFO @ Wed, 28 Jun 2017 05:41:23: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:41:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:41:23: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:41:23: 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 05:41:23: Process for pairing-model is terminated! cat: SRX1423692.05_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 `SRX1423692.05_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 `SRX1423692.05_*.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 `SRX1423692.05_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 05:41:28: 19000000 INFO @ Wed, 28 Jun 2017 05:41:28: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:41:28: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:41:28: #1 total tags in treatment: 9372169 INFO @ Wed, 28 Jun 2017 05:41:28: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:41:28: #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 05:41:28: #1 tags after filtering in treatment: 7184367 INFO @ Wed, 28 Jun 2017 05:41:28: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 28 Jun 2017 05:41:28: #1 finished! INFO @ Wed, 28 Jun 2017 05:41:28: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:41:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:41:29: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:41:29: 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 05:41:29: Process for pairing-model is terminated! cat: SRX1423692.10_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 `SRX1423692.10_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 `SRX1423692.10_*.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 `SRX1423692.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。