Job ID = 9732081 sra ファイルのダウンロード中... Completed: 272622K bytes transferred in 14 seconds (157228K 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 11772338 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675871/SRR5380647.sra Written 11772338 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: 00:05:14 11772338 reads; of these: 11772338 (100.00%) were paired; of these: 2901754 (24.65%) aligned concordantly 0 times 7994954 (67.91%) aligned concordantly exactly 1 time 875630 (7.44%) aligned concordantly >1 times ---- 2901754 pairs aligned concordantly 0 times; of these: 537211 (18.51%) aligned discordantly 1 time ---- 2364543 pairs aligned 0 times concordantly or discordantly; of these: 4729086 mates make up the pairs; of these: 4139595 (87.53%) aligned 0 times 408742 (8.64%) aligned exactly 1 time 180749 (3.82%) aligned >1 times 82.42% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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] 1224538 / 9149845 = 0.1338 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 19:33:24: # Command line: callpeak -t SRX2675871.bam -f BAM -g 12100000 -n SRX2675871.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675871.10 # format = BAM # ChIP-seq file = ['SRX2675871.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 19:33:24: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:33:24: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:33:25: # Command line: callpeak -t SRX2675871.bam -f BAM -g 12100000 -n SRX2675871.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675871.05 # format = BAM # ChIP-seq file = ['SRX2675871.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 19:33:25: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:33:25: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:33:25: # Command line: callpeak -t SRX2675871.bam -f BAM -g 12100000 -n SRX2675871.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675871.20 # format = BAM # ChIP-seq file = ['SRX2675871.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 19:33:25: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:33:25: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:33:31: 1000000 INFO @ Sun, 03 Sep 2017 19:33:32: 1000000 INFO @ Sun, 03 Sep 2017 19:33:32: 1000000 INFO @ Sun, 03 Sep 2017 19:33:37: 2000000 INFO @ Sun, 03 Sep 2017 19:33:40: 2000000 INFO @ Sun, 03 Sep 2017 19:33:40: 2000000 INFO @ Sun, 03 Sep 2017 19:33:43: 3000000 INFO @ Sun, 03 Sep 2017 19:33:47: 3000000 INFO @ Sun, 03 Sep 2017 19:33:48: 3000000 INFO @ Sun, 03 Sep 2017 19:33:49: 4000000 INFO @ Sun, 03 Sep 2017 19:33:55: 4000000 INFO @ Sun, 03 Sep 2017 19:33:55: 5000000 INFO @ Sun, 03 Sep 2017 19:33:56: 4000000 INFO @ Sun, 03 Sep 2017 19:34:01: 6000000 INFO @ Sun, 03 Sep 2017 19:34:03: 5000000 INFO @ Sun, 03 Sep 2017 19:34:04: 5000000 INFO @ Sun, 03 Sep 2017 19:34:07: 7000000 INFO @ Sun, 03 Sep 2017 19:34:10: 6000000 INFO @ Sun, 03 Sep 2017 19:34:13: 6000000 INFO @ Sun, 03 Sep 2017 19:34:13: 8000000 INFO @ Sun, 03 Sep 2017 19:34:18: 7000000 INFO @ Sun, 03 Sep 2017 19:34:20: 9000000 INFO @ Sun, 03 Sep 2017 19:34:21: 7000000 INFO @ Sun, 03 Sep 2017 19:34:26: 10000000 INFO @ Sun, 03 Sep 2017 19:34:26: 8000000 INFO @ Sun, 03 Sep 2017 19:34:29: 8000000 INFO @ Sun, 03 Sep 2017 19:34:32: 11000000 INFO @ Sun, 03 Sep 2017 19:34:33: 9000000 INFO @ Sun, 03 Sep 2017 19:34:37: 9000000 INFO @ Sun, 03 Sep 2017 19:34:38: 12000000 INFO @ Sun, 03 Sep 2017 19:34:41: 10000000 INFO @ Sun, 03 Sep 2017 19:34:44: 13000000 INFO @ Sun, 03 Sep 2017 19:34:45: 10000000 INFO @ Sun, 03 Sep 2017 19:34:49: 11000000 INFO @ Sun, 03 Sep 2017 19:34:50: 14000000 INFO @ Sun, 03 Sep 2017 19:34:53: 11000000 INFO @ Sun, 03 Sep 2017 19:34:56: 15000000 INFO @ Sun, 03 Sep 2017 19:34:56: 12000000 INFO @ Sun, 03 Sep 2017 19:35:01: 12000000 INFO @ Sun, 03 Sep 2017 19:35:03: 16000000 INFO @ Sun, 03 Sep 2017 19:35:03: 13000000 INFO @ Sun, 03 Sep 2017 19:35:08: 13000000 INFO @ Sun, 03 Sep 2017 19:35:09: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:35:09: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:35:09: #1 total tags in treatment: 7649378 INFO @ Sun, 03 Sep 2017 19:35:09: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:35:09: #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 19:35:09: #1 tags after filtering in treatment: 3925847 INFO @ Sun, 03 Sep 2017 19:35:09: #1 Redundant rate of treatment: 0.49 INFO @ Sun, 03 Sep 2017 19:35:09: #1 finished! INFO @ Sun, 03 Sep 2017 19:35:09: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:35:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:35:09: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:35:09: 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 19:35:09: Process for pairing-model is terminated! cat: SRX2675871.10_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): 12 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675871.10_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 `SRX2675871.10_*.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 `SRX2675871.10_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 19:35:11: 14000000 INFO @ Sun, 03 Sep 2017 19:35:15: 14000000 INFO @ Sun, 03 Sep 2017 19:35:18: 15000000 INFO @ Sun, 03 Sep 2017 19:35:21: 15000000 INFO @ Sun, 03 Sep 2017 19:35:25: 16000000 INFO @ Sun, 03 Sep 2017 19:35:27: 16000000 INFO @ Sun, 03 Sep 2017 19:35:32: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:35:32: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:35:32: #1 total tags in treatment: 7649378 INFO @ Sun, 03 Sep 2017 19:35:32: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:35:32: #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 19:35:32: #1 tags after filtering in treatment: 3925847 INFO @ Sun, 03 Sep 2017 19:35:32: #1 Redundant rate of treatment: 0.49 INFO @ Sun, 03 Sep 2017 19:35:32: #1 finished! INFO @ Sun, 03 Sep 2017 19:35:32: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:35:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:35:32: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:35:32: 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 19:35:32: Process for pairing-model is terminated! cat: SRX2675871.05_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): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675871.05_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 `SRX2675871.05_*.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 `SRX2675871.05_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 @ Sun, 03 Sep 2017 19:35:33: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:35:33: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:35:33: #1 total tags in treatment: 7649378 INFO @ Sun, 03 Sep 2017 19:35:33: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:35:33: #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 19:35:33: #1 tags after filtering in treatment: 3925847 INFO @ Sun, 03 Sep 2017 19:35:33: #1 Redundant rate of treatment: 0.49 INFO @ Sun, 03 Sep 2017 19:35:33: #1 finished! INFO @ Sun, 03 Sep 2017 19:35:33: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:35:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:35:33: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:35:33: 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 19:35:33: Process for pairing-model is terminated! cat: SRX2675871.20_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): 10 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675871.20_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 `SRX2675871.20_*.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 `SRX2675871.20_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。