Job ID = 9732041 sra ファイルのダウンロード中... Completed: 337426K bytes transferred in 13 seconds (205977K 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 15341603 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675844/SRR5380621.sra Written 15341603 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: 00:07:13 15341603 reads; of these: 15341603 (100.00%) were paired; of these: 3068524 (20.00%) aligned concordantly 0 times 11268686 (73.45%) aligned concordantly exactly 1 time 1004393 (6.55%) aligned concordantly >1 times ---- 3068524 pairs aligned concordantly 0 times; of these: 1061952 (34.61%) aligned discordantly 1 time ---- 2006572 pairs aligned 0 times concordantly or discordantly; of these: 4013144 mates make up the pairs; of these: 3302267 (82.29%) aligned 0 times 461411 (11.50%) aligned exactly 1 time 249466 (6.22%) aligned >1 times 89.24% overall alignment rate Time searching: 00:07:13 Overall time: 00:07:13 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] 1735303 / 13185545 = 0.1316 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 19:17:33: # Command line: callpeak -t SRX2675844.bam -f BAM -g 12100000 -n SRX2675844.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675844.10 # format = BAM # ChIP-seq file = ['SRX2675844.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 19:17:33: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:17:33: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:17:33: # Command line: callpeak -t SRX2675844.bam -f BAM -g 12100000 -n SRX2675844.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675844.20 # format = BAM # ChIP-seq file = ['SRX2675844.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 19:17:33: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:17:33: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:17:33: # Command line: callpeak -t SRX2675844.bam -f BAM -g 12100000 -n SRX2675844.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675844.05 # format = BAM # ChIP-seq file = ['SRX2675844.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 19:17:33: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:17:33: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:17:38: 1000000 INFO @ Sun, 03 Sep 2017 19:17:39: 1000000 INFO @ Sun, 03 Sep 2017 19:17:39: 1000000 INFO @ Sun, 03 Sep 2017 19:17:43: 2000000 INFO @ Sun, 03 Sep 2017 19:17:44: 2000000 INFO @ Sun, 03 Sep 2017 19:17:44: 2000000 INFO @ Sun, 03 Sep 2017 19:17:48: 3000000 INFO @ Sun, 03 Sep 2017 19:17:49: 3000000 INFO @ Sun, 03 Sep 2017 19:17:49: 3000000 INFO @ Sun, 03 Sep 2017 19:17:53: 4000000 INFO @ Sun, 03 Sep 2017 19:17:54: 4000000 INFO @ Sun, 03 Sep 2017 19:17:54: 4000000 INFO @ Sun, 03 Sep 2017 19:17:58: 5000000 INFO @ Sun, 03 Sep 2017 19:17:59: 5000000 INFO @ Sun, 03 Sep 2017 19:17:59: 5000000 INFO @ Sun, 03 Sep 2017 19:18:03: 6000000 INFO @ Sun, 03 Sep 2017 19:18:04: 6000000 INFO @ Sun, 03 Sep 2017 19:18:04: 6000000 INFO @ Sun, 03 Sep 2017 19:18:07: 7000000 INFO @ Sun, 03 Sep 2017 19:18:09: 7000000 INFO @ Sun, 03 Sep 2017 19:18:09: 7000000 INFO @ Sun, 03 Sep 2017 19:18:12: 8000000 INFO @ Sun, 03 Sep 2017 19:18:14: 8000000 INFO @ Sun, 03 Sep 2017 19:18:15: 8000000 INFO @ Sun, 03 Sep 2017 19:18:17: 9000000 INFO @ Sun, 03 Sep 2017 19:18:19: 9000000 INFO @ Sun, 03 Sep 2017 19:18:20: 9000000 INFO @ Sun, 03 Sep 2017 19:18:22: 10000000 INFO @ Sun, 03 Sep 2017 19:18:24: 10000000 INFO @ Sun, 03 Sep 2017 19:18:25: 10000000 INFO @ Sun, 03 Sep 2017 19:18:27: 11000000 INFO @ Sun, 03 Sep 2017 19:18:30: 11000000 INFO @ Sun, 03 Sep 2017 19:18:30: 11000000 INFO @ Sun, 03 Sep 2017 19:18:32: 12000000 INFO @ Sun, 03 Sep 2017 19:18:35: 12000000 INFO @ Sun, 03 Sep 2017 19:18:35: 12000000 INFO @ Sun, 03 Sep 2017 19:18:36: 13000000 INFO @ Sun, 03 Sep 2017 19:18:40: 13000000 INFO @ Sun, 03 Sep 2017 19:18:41: 13000000 INFO @ Sun, 03 Sep 2017 19:18:41: 14000000 INFO @ Sun, 03 Sep 2017 19:18:45: 14000000 INFO @ Sun, 03 Sep 2017 19:18:46: 15000000 INFO @ Sun, 03 Sep 2017 19:18:46: 14000000 INFO @ Sun, 03 Sep 2017 19:18:50: 15000000 INFO @ Sun, 03 Sep 2017 19:18:51: 16000000 INFO @ Sun, 03 Sep 2017 19:18:51: 15000000 INFO @ Sun, 03 Sep 2017 19:18:56: 17000000 INFO @ Sun, 03 Sep 2017 19:18:56: 16000000 INFO @ Sun, 03 Sep 2017 19:18:57: 16000000 INFO @ Sun, 03 Sep 2017 19:19:00: 18000000 INFO @ Sun, 03 Sep 2017 19:19:01: 17000000 INFO @ Sun, 03 Sep 2017 19:19:02: 17000000 INFO @ Sun, 03 Sep 2017 19:19:05: 19000000 INFO @ Sun, 03 Sep 2017 19:19:06: 18000000 INFO @ Sun, 03 Sep 2017 19:19:07: 18000000 INFO @ Sun, 03 Sep 2017 19:19:10: 20000000 INFO @ Sun, 03 Sep 2017 19:19:12: 19000000 INFO @ Sun, 03 Sep 2017 19:19:13: 19000000 INFO @ Sun, 03 Sep 2017 19:19:15: 21000000 INFO @ Sun, 03 Sep 2017 19:19:17: 20000000 INFO @ Sun, 03 Sep 2017 19:19:18: 20000000 INFO @ Sun, 03 Sep 2017 19:19:20: 22000000 INFO @ Sun, 03 Sep 2017 19:19:22: 21000000 INFO @ Sun, 03 Sep 2017 19:19:23: 21000000 INFO @ Sun, 03 Sep 2017 19:19:25: 23000000 INFO @ Sun, 03 Sep 2017 19:19:27: 22000000 INFO @ Sun, 03 Sep 2017 19:19:29: 22000000 INFO @ Sun, 03 Sep 2017 19:19:29: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:19:29: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:19:29: #1 total tags in treatment: 10555461 INFO @ Sun, 03 Sep 2017 19:19:29: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:19:29: #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 19:19:29: #1 tags after filtering in treatment: 4639620 INFO @ Sun, 03 Sep 2017 19:19:29: #1 Redundant rate of treatment: 0.56 INFO @ Sun, 03 Sep 2017 19:19:29: #1 finished! INFO @ Sun, 03 Sep 2017 19:19:29: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:19:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:19:29: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:19:29: 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 @ Sun, 03 Sep 2017 19:19:29: Process for pairing-model is terminated! cat: SRX2675844.10_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): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675844.10_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 `SRX2675844.10_*.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 `SRX2675844.10_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 19:19:33: 23000000 INFO @ Sun, 03 Sep 2017 19:19:34: 23000000 INFO @ Sun, 03 Sep 2017 19:19:37: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:19:37: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:19:37: #1 total tags in treatment: 10555461 INFO @ Sun, 03 Sep 2017 19:19:37: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:19:37: #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 19:19:38: #1 tags after filtering in treatment: 4639620 INFO @ Sun, 03 Sep 2017 19:19:38: #1 Redundant rate of treatment: 0.56 INFO @ Sun, 03 Sep 2017 19:19:38: #1 finished! INFO @ Sun, 03 Sep 2017 19:19:38: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:19:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:19:38: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:19:38: 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 19:19:38: Process for pairing-model is terminated! cat: SRX2675844.20_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675844.20_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 `SRX2675844.20_*.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 `SRX2675844.20_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 19:19:39: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:19:39: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:19:39: #1 total tags in treatment: 10555461 INFO @ Sun, 03 Sep 2017 19:19:39: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:19:39: #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 19:19:39: #1 tags after filtering in treatment: 4639620 INFO @ Sun, 03 Sep 2017 19:19:39: #1 Redundant rate of treatment: 0.56 INFO @ Sun, 03 Sep 2017 19:19:39: #1 finished! INFO @ Sun, 03 Sep 2017 19:19:39: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:19:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:19:39: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:19:39: 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 @ Sun, 03 Sep 2017 19:19:39: Process for pairing-model is terminated! cat: SRX2675844.05_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 `SRX2675844.05_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 `SRX2675844.05_*.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 `SRX2675844.05_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。