Job ID = 10536534 sra ファイルのダウンロード中... Completed: 1358956K bytes transferred in 27 seconds (399659K bits/sec), in 1 file. 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 38638988 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671225/SRR6696977.sra Written 38638988 spots total rm: cannot remove `[DSE]RX*': 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 `[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: 00:21:07 38638988 reads; of these: 38638988 (100.00%) were paired; of these: 13867492 (35.89%) aligned concordantly 0 times 20909947 (54.12%) aligned concordantly exactly 1 time 3861549 (9.99%) aligned concordantly >1 times ---- 13867492 pairs aligned concordantly 0 times; of these: 232145 (1.67%) aligned discordantly 1 time ---- 13635347 pairs aligned 0 times concordantly or discordantly; of these: 27270694 mates make up the pairs; of these: 26990567 (98.97%) aligned 0 times 128432 (0.47%) aligned exactly 1 time 151695 (0.56%) aligned >1 times 65.07% overall alignment rate Time searching: 00:21:07 Overall time: 00:21:07 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] 8725082 / 24932742 = 0.3499 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 @ Thu, 05 Apr 2018 10:40:15: # Command line: callpeak -t SRX3671225.bam -f BAM -g 12100000 -n SRX3671225.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671225.20 # format = BAM # ChIP-seq file = ['SRX3671225.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 @ Thu, 05 Apr 2018 10:40:15: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:40:15: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:40:15: # Command line: callpeak -t SRX3671225.bam -f BAM -g 12100000 -n SRX3671225.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671225.05 # format = BAM # ChIP-seq file = ['SRX3671225.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 @ Thu, 05 Apr 2018 10:40:15: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:40:15: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:40:15: # Command line: callpeak -t SRX3671225.bam -f BAM -g 12100000 -n SRX3671225.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671225.10 # format = BAM # ChIP-seq file = ['SRX3671225.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 @ Thu, 05 Apr 2018 10:40:15: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:40:15: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:40:21: 1000000 INFO @ Thu, 05 Apr 2018 10:40:21: 1000000 INFO @ Thu, 05 Apr 2018 10:40:21: 1000000 INFO @ Thu, 05 Apr 2018 10:40:26: 2000000 INFO @ Thu, 05 Apr 2018 10:40:26: 2000000 INFO @ Thu, 05 Apr 2018 10:40:27: 2000000 INFO @ Thu, 05 Apr 2018 10:40:31: 3000000 INFO @ Thu, 05 Apr 2018 10:40:32: 3000000 INFO @ Thu, 05 Apr 2018 10:40:32: 3000000 INFO @ Thu, 05 Apr 2018 10:40:37: 4000000 INFO @ Thu, 05 Apr 2018 10:40:38: 4000000 INFO @ Thu, 05 Apr 2018 10:40:38: 4000000 INFO @ Thu, 05 Apr 2018 10:40:42: 5000000 INFO @ Thu, 05 Apr 2018 10:40:44: 5000000 INFO @ Thu, 05 Apr 2018 10:40:44: 5000000 INFO @ Thu, 05 Apr 2018 10:40:47: 6000000 INFO @ Thu, 05 Apr 2018 10:40:49: 6000000 INFO @ Thu, 05 Apr 2018 10:40:49: 6000000 INFO @ Thu, 05 Apr 2018 10:40:53: 7000000 INFO @ Thu, 05 Apr 2018 10:40:55: 7000000 INFO @ Thu, 05 Apr 2018 10:40:55: 7000000 INFO @ Thu, 05 Apr 2018 10:40:58: 8000000 INFO @ Thu, 05 Apr 2018 10:41:00: 8000000 INFO @ Thu, 05 Apr 2018 10:41:01: 8000000 INFO @ Thu, 05 Apr 2018 10:41:03: 9000000 INFO @ Thu, 05 Apr 2018 10:41:06: 9000000 INFO @ Thu, 05 Apr 2018 10:41:06: 9000000 INFO @ Thu, 05 Apr 2018 10:41:09: 10000000 INFO @ Thu, 05 Apr 2018 10:41:11: 10000000 INFO @ Thu, 05 Apr 2018 10:41:12: 10000000 INFO @ Thu, 05 Apr 2018 10:41:14: 11000000 INFO @ Thu, 05 Apr 2018 10:41:17: 11000000 INFO @ Thu, 05 Apr 2018 10:41:18: 11000000 INFO @ Thu, 05 Apr 2018 10:41:19: 12000000 INFO @ Thu, 05 Apr 2018 10:41:22: 12000000 INFO @ Thu, 05 Apr 2018 10:41:23: 12000000 INFO @ Thu, 05 Apr 2018 10:41:25: 13000000 INFO @ Thu, 05 Apr 2018 10:41:28: 13000000 INFO @ Thu, 05 Apr 2018 10:41:29: 13000000 INFO @ Thu, 05 Apr 2018 10:41:30: 14000000 INFO @ Thu, 05 Apr 2018 10:41:33: 14000000 INFO @ Thu, 05 Apr 2018 10:41:34: 14000000 INFO @ Thu, 05 Apr 2018 10:41:35: 15000000 INFO @ Thu, 05 Apr 2018 10:41:39: 15000000 INFO @ Thu, 05 Apr 2018 10:41:40: 15000000 INFO @ Thu, 05 Apr 2018 10:41:41: 16000000 INFO @ Thu, 05 Apr 2018 10:41:44: 16000000 INFO @ Thu, 05 Apr 2018 10:41:46: 16000000 INFO @ Thu, 05 Apr 2018 10:41:46: 17000000 INFO @ Thu, 05 Apr 2018 10:41:50: 17000000 INFO @ Thu, 05 Apr 2018 10:41:52: 18000000 INFO @ Thu, 05 Apr 2018 10:41:52: 17000000 INFO @ Thu, 05 Apr 2018 10:41:56: 18000000 INFO @ Thu, 05 Apr 2018 10:41:57: 19000000 INFO @ Thu, 05 Apr 2018 10:41:57: 18000000 INFO @ Thu, 05 Apr 2018 10:42:02: 19000000 INFO @ Thu, 05 Apr 2018 10:42:03: 20000000 INFO @ Thu, 05 Apr 2018 10:42:03: 19000000 INFO @ Thu, 05 Apr 2018 10:42:08: 20000000 INFO @ Thu, 05 Apr 2018 10:42:08: 21000000 INFO @ Thu, 05 Apr 2018 10:42:09: 20000000 INFO @ Thu, 05 Apr 2018 10:42:13: 21000000 INFO @ Thu, 05 Apr 2018 10:42:13: 22000000 INFO @ Thu, 05 Apr 2018 10:42:14: 21000000 INFO @ Thu, 05 Apr 2018 10:42:18: 22000000 INFO @ Thu, 05 Apr 2018 10:42:18: 23000000 INFO @ Thu, 05 Apr 2018 10:42:20: 22000000 INFO @ Thu, 05 Apr 2018 10:42:24: 24000000 INFO @ Thu, 05 Apr 2018 10:42:24: 23000000 INFO @ Thu, 05 Apr 2018 10:42:25: 23000000 INFO @ Thu, 05 Apr 2018 10:42:29: 25000000 INFO @ Thu, 05 Apr 2018 10:42:29: 24000000 INFO @ Thu, 05 Apr 2018 10:42:31: 24000000 INFO @ Thu, 05 Apr 2018 10:42:34: 26000000 INFO @ Thu, 05 Apr 2018 10:42:34: 25000000 INFO @ Thu, 05 Apr 2018 10:42:36: 25000000 INFO @ Thu, 05 Apr 2018 10:42:40: 27000000 INFO @ Thu, 05 Apr 2018 10:42:40: 26000000 INFO @ Thu, 05 Apr 2018 10:42:42: 26000000 INFO @ Thu, 05 Apr 2018 10:42:45: 28000000 INFO @ Thu, 05 Apr 2018 10:42:47: 27000000 INFO @ Thu, 05 Apr 2018 10:42:48: 27000000 INFO @ Thu, 05 Apr 2018 10:42:51: 29000000 INFO @ Thu, 05 Apr 2018 10:42:53: 28000000 INFO @ Thu, 05 Apr 2018 10:42:54: 28000000 INFO @ Thu, 05 Apr 2018 10:42:56: 30000000 INFO @ Thu, 05 Apr 2018 10:42:59: 29000000 INFO @ Thu, 05 Apr 2018 10:43:00: 29000000 INFO @ Thu, 05 Apr 2018 10:43:02: 31000000 INFO @ Thu, 05 Apr 2018 10:43:04: 30000000 INFO @ Thu, 05 Apr 2018 10:43:05: 30000000 INFO @ Thu, 05 Apr 2018 10:43:07: 32000000 INFO @ Thu, 05 Apr 2018 10:43:10: 31000000 INFO @ Thu, 05 Apr 2018 10:43:11: 31000000 INFO @ Thu, 05 Apr 2018 10:43:12: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:43:12: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:43:12: #1 total tags in treatment: 16123677 INFO @ Thu, 05 Apr 2018 10:43:12: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:43:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:43:12: #1 tags after filtering in treatment: 6443815 INFO @ Thu, 05 Apr 2018 10:43:12: #1 Redundant rate of treatment: 0.60 INFO @ Thu, 05 Apr 2018 10:43:12: #1 finished! INFO @ Thu, 05 Apr 2018 10:43:12: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:43:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:43:12: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:43:12: 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 @ Thu, 05 Apr 2018 10:43:12: Process for pairing-model is terminated! cat: SRX3671225.05_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 `SRX3671225.05_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 `SRX3671225.05_*.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 `SRX3671225.05_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 @ Thu, 05 Apr 2018 10:43:15: 32000000 INFO @ Thu, 05 Apr 2018 10:43:16: 32000000 INFO @ Thu, 05 Apr 2018 10:43:20: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:43:20: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:43:20: #1 total tags in treatment: 16123677 INFO @ Thu, 05 Apr 2018 10:43:20: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:43:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:43:21: #1 tags after filtering in treatment: 6443815 INFO @ Thu, 05 Apr 2018 10:43:21: #1 Redundant rate of treatment: 0.60 INFO @ Thu, 05 Apr 2018 10:43:21: #1 finished! INFO @ Thu, 05 Apr 2018 10:43:21: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:43:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:43:21: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:43:21: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:43:21: #1 total tags in treatment: 16123677 INFO @ Thu, 05 Apr 2018 10:43:21: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:43:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:43:21: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:43:21: 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 @ Thu, 05 Apr 2018 10:43:21: Process for pairing-model is terminated! cat: SRX3671225.10_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 `SRX3671225.10_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 `SRX3671225.10_*.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 `SRX3671225.10_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 @ Thu, 05 Apr 2018 10:43:21: #1 tags after filtering in treatment: 6443815 INFO @ Thu, 05 Apr 2018 10:43:21: #1 Redundant rate of treatment: 0.60 INFO @ Thu, 05 Apr 2018 10:43:21: #1 finished! INFO @ Thu, 05 Apr 2018 10:43:21: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:43:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:43:22: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:43:22: 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 @ Thu, 05 Apr 2018 10:43:22: Process for pairing-model is terminated! cat: SRX3671225.20_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 `SRX3671225.20_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 `SRX3671225.20_*.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 `SRX3671225.20_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。