Job ID = 9732057 sra ファイルのダウンロード中... Completed: 290734K bytes transferred in 9 seconds (247445K 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 13249160 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675857/SRR5380634.sra Written 13249160 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: 00:06:25 13249160 reads; of these: 13249160 (100.00%) were paired; of these: 2883453 (21.76%) aligned concordantly 0 times 9534226 (71.96%) aligned concordantly exactly 1 time 831481 (6.28%) aligned concordantly >1 times ---- 2883453 pairs aligned concordantly 0 times; of these: 985685 (34.18%) aligned discordantly 1 time ---- 1897768 pairs aligned 0 times concordantly or discordantly; of these: 3795536 mates make up the pairs; of these: 3170521 (83.53%) aligned 0 times 401578 (10.58%) aligned exactly 1 time 223437 (5.89%) aligned >1 times 88.04% overall alignment rate Time searching: 00:06:25 Overall time: 00:06:25 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] 1362782 / 11256641 = 0.1211 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 19:27:55: # Command line: callpeak -t SRX2675857.bam -f BAM -g 12100000 -n SRX2675857.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675857.10 # format = BAM # ChIP-seq file = ['SRX2675857.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 19:27:55: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:27:55: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:27:55: # Command line: callpeak -t SRX2675857.bam -f BAM -g 12100000 -n SRX2675857.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675857.05 # format = BAM # ChIP-seq file = ['SRX2675857.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 19:27:55: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:27:55: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:27:55: # Command line: callpeak -t SRX2675857.bam -f BAM -g 12100000 -n SRX2675857.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675857.20 # format = BAM # ChIP-seq file = ['SRX2675857.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 19:27:55: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:27:55: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:27:59: 1000000 INFO @ Sun, 03 Sep 2017 19:27:59: 1000000 INFO @ Sun, 03 Sep 2017 19:27:59: 1000000 INFO @ Sun, 03 Sep 2017 19:28:04: 2000000 INFO @ Sun, 03 Sep 2017 19:28:04: 2000000 INFO @ Sun, 03 Sep 2017 19:28:04: 2000000 INFO @ Sun, 03 Sep 2017 19:28:08: 3000000 INFO @ Sun, 03 Sep 2017 19:28:08: 3000000 INFO @ Sun, 03 Sep 2017 19:28:09: 3000000 INFO @ Sun, 03 Sep 2017 19:28:13: 4000000 INFO @ Sun, 03 Sep 2017 19:28:13: 4000000 INFO @ Sun, 03 Sep 2017 19:28:13: 4000000 INFO @ Sun, 03 Sep 2017 19:28:17: 5000000 INFO @ Sun, 03 Sep 2017 19:28:18: 5000000 INFO @ Sun, 03 Sep 2017 19:28:18: 5000000 INFO @ Sun, 03 Sep 2017 19:28:22: 6000000 INFO @ Sun, 03 Sep 2017 19:28:22: 6000000 INFO @ Sun, 03 Sep 2017 19:28:23: 6000000 INFO @ Sun, 03 Sep 2017 19:28:26: 7000000 INFO @ Sun, 03 Sep 2017 19:28:27: 7000000 INFO @ Sun, 03 Sep 2017 19:28:27: 7000000 INFO @ Sun, 03 Sep 2017 19:28:31: 8000000 INFO @ Sun, 03 Sep 2017 19:28:32: 8000000 INFO @ Sun, 03 Sep 2017 19:28:32: 8000000 INFO @ Sun, 03 Sep 2017 19:28:36: 9000000 INFO @ Sun, 03 Sep 2017 19:28:36: 9000000 INFO @ Sun, 03 Sep 2017 19:28:37: 9000000 INFO @ Sun, 03 Sep 2017 19:28:41: 10000000 INFO @ Sun, 03 Sep 2017 19:28:41: 10000000 INFO @ Sun, 03 Sep 2017 19:28:42: 10000000 INFO @ Sun, 03 Sep 2017 19:28:45: 11000000 INFO @ Sun, 03 Sep 2017 19:28:45: 11000000 INFO @ Sun, 03 Sep 2017 19:28:47: 11000000 INFO @ Sun, 03 Sep 2017 19:28:50: 12000000 INFO @ Sun, 03 Sep 2017 19:28:50: 12000000 INFO @ Sun, 03 Sep 2017 19:28:52: 12000000 INFO @ Sun, 03 Sep 2017 19:28:55: 13000000 INFO @ Sun, 03 Sep 2017 19:28:55: 13000000 INFO @ Sun, 03 Sep 2017 19:28:57: 13000000 INFO @ Sun, 03 Sep 2017 19:28:59: 14000000 INFO @ Sun, 03 Sep 2017 19:29:00: 14000000 INFO @ Sun, 03 Sep 2017 19:29:02: 14000000 INFO @ Sun, 03 Sep 2017 19:29:04: 15000000 INFO @ Sun, 03 Sep 2017 19:29:05: 15000000 INFO @ Sun, 03 Sep 2017 19:29:07: 15000000 INFO @ Sun, 03 Sep 2017 19:29:09: 16000000 INFO @ Sun, 03 Sep 2017 19:29:10: 16000000 INFO @ Sun, 03 Sep 2017 19:29:12: 16000000 INFO @ Sun, 03 Sep 2017 19:29:13: 17000000 INFO @ Sun, 03 Sep 2017 19:29:14: 17000000 INFO @ Sun, 03 Sep 2017 19:29:17: 17000000 INFO @ Sun, 03 Sep 2017 19:29:18: 18000000 INFO @ Sun, 03 Sep 2017 19:29:19: 18000000 INFO @ Sun, 03 Sep 2017 19:29:22: 18000000 INFO @ Sun, 03 Sep 2017 19:29:22: 19000000 INFO @ Sun, 03 Sep 2017 19:29:24: 19000000 INFO @ Sun, 03 Sep 2017 19:29:27: 19000000 INFO @ Sun, 03 Sep 2017 19:29:27: 20000000 INFO @ Sun, 03 Sep 2017 19:29:29: 20000000 INFO @ Sun, 03 Sep 2017 19:29:30: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:29:30: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:29:30: #1 total tags in treatment: 9024019 INFO @ Sun, 03 Sep 2017 19:29:30: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:29:30: #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 19:29:30: #1 tags after filtering in treatment: 4207962 INFO @ Sun, 03 Sep 2017 19:29:30: #1 Redundant rate of treatment: 0.53 INFO @ Sun, 03 Sep 2017 19:29:30: #1 finished! INFO @ Sun, 03 Sep 2017 19:29:30: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:29:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:29:30: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:29:30: 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 19:29:30: Process for pairing-model is terminated! cat: SRX2675857.20_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): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675857.20_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 `SRX2675857.20_*.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 `SRX2675857.20_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 @ Sun, 03 Sep 2017 19:29:32: 20000000 INFO @ Sun, 03 Sep 2017 19:29:32: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:29:32: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:29:32: #1 total tags in treatment: 9024019 INFO @ Sun, 03 Sep 2017 19:29:32: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:29:32: #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 19:29:32: #1 tags after filtering in treatment: 4207962 INFO @ Sun, 03 Sep 2017 19:29:32: #1 Redundant rate of treatment: 0.53 INFO @ Sun, 03 Sep 2017 19:29:32: #1 finished! INFO @ Sun, 03 Sep 2017 19:29:32: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:29:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:29:32: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:29:32: 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 19:29:32: Process for pairing-model is terminated! cat: SRX2675857.10_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): 8 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675857.10_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 `SRX2675857.10_*.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 `SRX2675857.10_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 19:29:35: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:29:35: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:29:35: #1 total tags in treatment: 9024019 INFO @ Sun, 03 Sep 2017 19:29:35: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:29:35: #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 19:29:35: #1 tags after filtering in treatment: 4207962 INFO @ Sun, 03 Sep 2017 19:29:35: #1 Redundant rate of treatment: 0.53 INFO @ Sun, 03 Sep 2017 19:29:35: #1 finished! INFO @ Sun, 03 Sep 2017 19:29:35: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:29:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:29:35: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:29:35: 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 19:29:35: Process for pairing-model is terminated! cat: SRX2675857.05_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): 12 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675857.05_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 `SRX2675857.05_*.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 `SRX2675857.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。