Job ID = 9302979 sra ファイルのダウンロード中... Completed: 654882K bytes transferred in 16 seconds (331443K 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 11975806 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2961332/SRR5761581.sra Written 11975806 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: 00:09:22 11975806 reads; of these: 11975806 (100.00%) were paired; of these: 1162084 (9.70%) aligned concordantly 0 times 9147882 (76.39%) aligned concordantly exactly 1 time 1665840 (13.91%) aligned concordantly >1 times ---- 1162084 pairs aligned concordantly 0 times; of these: 60610 (5.22%) aligned discordantly 1 time ---- 1101474 pairs aligned 0 times concordantly or discordantly; of these: 2202948 mates make up the pairs; of these: 1872727 (85.01%) aligned 0 times 176854 (8.03%) aligned exactly 1 time 153367 (6.96%) aligned >1 times 92.18% overall alignment rate Time searching: 00:09:22 Overall time: 00:09:22 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 12 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] 1506652 / 10830867 = 0.1391 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 @ Fri, 28 Jul 2017 11:55:55: # Command line: callpeak -t SRX2961332.bam -f BAM -g 12100000 -n SRX2961332.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2961332.10 # format = BAM # ChIP-seq file = ['SRX2961332.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 @ Fri, 28 Jul 2017 11:55:55: #1 read tag files... INFO @ Fri, 28 Jul 2017 11:55:55: #1 read treatment tags... INFO @ Fri, 28 Jul 2017 11:55:55: # Command line: callpeak -t SRX2961332.bam -f BAM -g 12100000 -n SRX2961332.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2961332.20 # format = BAM # ChIP-seq file = ['SRX2961332.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 @ Fri, 28 Jul 2017 11:55:55: #1 read tag files... INFO @ Fri, 28 Jul 2017 11:55:55: #1 read treatment tags... INFO @ Fri, 28 Jul 2017 11:55:55: # Command line: callpeak -t SRX2961332.bam -f BAM -g 12100000 -n SRX2961332.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2961332.05 # format = BAM # ChIP-seq file = ['SRX2961332.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 @ Fri, 28 Jul 2017 11:55:55: #1 read tag files... INFO @ Fri, 28 Jul 2017 11:55:55: #1 read treatment tags... INFO @ Fri, 28 Jul 2017 11:56:00: 1000000 INFO @ Fri, 28 Jul 2017 11:56:00: 1000000 INFO @ Fri, 28 Jul 2017 11:56:01: 1000000 INFO @ Fri, 28 Jul 2017 11:56:06: 2000000 INFO @ Fri, 28 Jul 2017 11:56:06: 2000000 INFO @ Fri, 28 Jul 2017 11:56:06: 2000000 INFO @ Fri, 28 Jul 2017 11:56:11: 3000000 INFO @ Fri, 28 Jul 2017 11:56:11: 3000000 INFO @ Fri, 28 Jul 2017 11:56:12: 3000000 INFO @ Fri, 28 Jul 2017 11:56:16: 4000000 INFO @ Fri, 28 Jul 2017 11:56:16: 4000000 INFO @ Fri, 28 Jul 2017 11:56:17: 4000000 INFO @ Fri, 28 Jul 2017 11:56:22: 5000000 INFO @ Fri, 28 Jul 2017 11:56:22: 5000000 INFO @ Fri, 28 Jul 2017 11:56:22: 5000000 INFO @ Fri, 28 Jul 2017 11:56:27: 6000000 INFO @ Fri, 28 Jul 2017 11:56:27: 6000000 INFO @ Fri, 28 Jul 2017 11:56:28: 6000000 INFO @ Fri, 28 Jul 2017 11:56:32: 7000000 INFO @ Fri, 28 Jul 2017 11:56:33: 7000000 INFO @ Fri, 28 Jul 2017 11:56:33: 7000000 INFO @ Fri, 28 Jul 2017 11:56:38: 8000000 INFO @ Fri, 28 Jul 2017 11:56:38: 8000000 INFO @ Fri, 28 Jul 2017 11:56:39: 8000000 INFO @ Fri, 28 Jul 2017 11:56:43: 9000000 INFO @ Fri, 28 Jul 2017 11:56:43: 9000000 INFO @ Fri, 28 Jul 2017 11:56:44: 9000000 INFO @ Fri, 28 Jul 2017 11:56:49: 10000000 INFO @ Fri, 28 Jul 2017 11:56:49: 10000000 INFO @ Fri, 28 Jul 2017 11:56:49: 10000000 INFO @ Fri, 28 Jul 2017 11:56:54: 11000000 INFO @ Fri, 28 Jul 2017 11:56:54: 11000000 INFO @ Fri, 28 Jul 2017 11:56:55: 11000000 INFO @ Fri, 28 Jul 2017 11:56:59: 12000000 INFO @ Fri, 28 Jul 2017 11:57:00: 12000000 INFO @ Fri, 28 Jul 2017 11:57:00: 12000000 INFO @ Fri, 28 Jul 2017 11:57:05: 13000000 INFO @ Fri, 28 Jul 2017 11:57:05: 13000000 INFO @ Fri, 28 Jul 2017 11:57:06: 13000000 INFO @ Fri, 28 Jul 2017 11:57:10: 14000000 INFO @ Fri, 28 Jul 2017 11:57:10: 14000000 INFO @ Fri, 28 Jul 2017 11:57:11: 14000000 INFO @ Fri, 28 Jul 2017 11:57:16: 15000000 INFO @ Fri, 28 Jul 2017 11:57:16: 15000000 INFO @ Fri, 28 Jul 2017 11:57:17: 15000000 INFO @ Fri, 28 Jul 2017 11:57:21: 16000000 INFO @ Fri, 28 Jul 2017 11:57:21: 16000000 INFO @ Fri, 28 Jul 2017 11:57:23: 16000000 INFO @ Fri, 28 Jul 2017 11:57:26: 17000000 INFO @ Fri, 28 Jul 2017 11:57:27: 17000000 INFO @ Fri, 28 Jul 2017 11:57:29: 17000000 INFO @ Fri, 28 Jul 2017 11:57:32: 18000000 INFO @ Fri, 28 Jul 2017 11:57:33: 18000000 INFO @ Fri, 28 Jul 2017 11:57:36: 18000000 INFO @ Fri, 28 Jul 2017 11:57:38: 19000000 INFO @ Fri, 28 Jul 2017 11:57:38: #1 tag size is determined as 50 bps INFO @ Fri, 28 Jul 2017 11:57:38: #1 tag size = 50 INFO @ Fri, 28 Jul 2017 11:57:38: #1 total tags in treatment: 9308244 INFO @ Fri, 28 Jul 2017 11:57:38: #1 user defined the maximum tags... INFO @ Fri, 28 Jul 2017 11:57:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 28 Jul 2017 11:57:38: #1 tags after filtering in treatment: 5088380 INFO @ Fri, 28 Jul 2017 11:57:38: #1 Redundant rate of treatment: 0.45 INFO @ Fri, 28 Jul 2017 11:57:38: #1 finished! INFO @ Fri, 28 Jul 2017 11:57:38: #2 Build Peak Model... INFO @ Fri, 28 Jul 2017 11:57:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 28 Jul 2017 11:57:39: #2 number of paired peaks: 0 WARNING @ Fri, 28 Jul 2017 11:57:39: 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 @ Fri, 28 Jul 2017 11:57:39: Process for pairing-model is terminated! cat: SRX2961332.05_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 `SRX2961332.05_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 `SRX2961332.05_*.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 `SRX2961332.05_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 @ Fri, 28 Jul 2017 11:57:40: 19000000 INFO @ Fri, 28 Jul 2017 11:57:41: #1 tag size is determined as 50 bps INFO @ Fri, 28 Jul 2017 11:57:41: #1 tag size = 50 INFO @ Fri, 28 Jul 2017 11:57:41: #1 total tags in treatment: 9308244 INFO @ Fri, 28 Jul 2017 11:57:41: #1 user defined the maximum tags... INFO @ Fri, 28 Jul 2017 11:57:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 28 Jul 2017 11:57:41: #1 tags after filtering in treatment: 5088380 INFO @ Fri, 28 Jul 2017 11:57:41: #1 Redundant rate of treatment: 0.45 INFO @ Fri, 28 Jul 2017 11:57:41: #1 finished! INFO @ Fri, 28 Jul 2017 11:57:41: #2 Build Peak Model... INFO @ Fri, 28 Jul 2017 11:57:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 28 Jul 2017 11:57:42: #2 number of paired peaks: 0 WARNING @ Fri, 28 Jul 2017 11:57:42: 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 @ Fri, 28 Jul 2017 11:57:42: Process for pairing-model is terminated! cat: SRX2961332.10_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 `SRX2961332.10_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 `SRX2961332.10_*.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 `SRX2961332.10_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 @ Fri, 28 Jul 2017 11:57:44: 19000000 INFO @ Fri, 28 Jul 2017 11:57:45: #1 tag size is determined as 50 bps INFO @ Fri, 28 Jul 2017 11:57:45: #1 tag size = 50 INFO @ Fri, 28 Jul 2017 11:57:45: #1 total tags in treatment: 9308244 INFO @ Fri, 28 Jul 2017 11:57:45: #1 user defined the maximum tags... INFO @ Fri, 28 Jul 2017 11:57:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 28 Jul 2017 11:57:45: #1 tags after filtering in treatment: 5088380 INFO @ Fri, 28 Jul 2017 11:57:45: #1 Redundant rate of treatment: 0.45 INFO @ Fri, 28 Jul 2017 11:57:45: #1 finished! INFO @ Fri, 28 Jul 2017 11:57:45: #2 Build Peak Model... INFO @ Fri, 28 Jul 2017 11:57:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 28 Jul 2017 11:57:45: #2 number of paired peaks: 0 WARNING @ Fri, 28 Jul 2017 11:57:45: 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 @ Fri, 28 Jul 2017 11:57:45: Process for pairing-model is terminated! cat: SRX2961332.20_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2961332.20_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 `SRX2961332.20_*.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 `SRX2961332.20_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。