Job ID = 11634711 sra ファイルのダウンロード中... Completed: 466873K bytes transferred in 10 seconds (374955K 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: SINGLE fastq に変換中... Read 25458874 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4957447/SRR8136461.sra Written 25458874 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4957447/SRR8136461.sra 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: 00:04:21 25458874 reads; of these: 25458874 (100.00%) were unpaired; of these: 1525271 (5.99%) aligned 0 times 21541777 (84.61%) aligned exactly 1 time 2391826 (9.39%) aligned >1 times 94.01% overall alignment rate Time searching: 00:04:21 Overall time: 00:04:21 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_rmdupse_core] 13417338 / 23933603 = 0.5606 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, 15 Feb 2019 10:38:57: # Command line: callpeak -t SRX4957447.bam -f BAM -g 12100000 -n SRX4957447.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4957447.20 # format = BAM # ChIP-seq file = ['SRX4957447.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, 15 Feb 2019 10:38:57: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:38:57: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:38:57: # Command line: callpeak -t SRX4957447.bam -f BAM -g 12100000 -n SRX4957447.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4957447.05 # format = BAM # ChIP-seq file = ['SRX4957447.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, 15 Feb 2019 10:38:57: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:38:57: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:38:57: # Command line: callpeak -t SRX4957447.bam -f BAM -g 12100000 -n SRX4957447.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4957447.10 # format = BAM # ChIP-seq file = ['SRX4957447.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, 15 Feb 2019 10:38:57: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:38:57: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:39:03: 1000000 INFO @ Fri, 15 Feb 2019 10:39:03: 1000000 INFO @ Fri, 15 Feb 2019 10:39:03: 1000000 INFO @ Fri, 15 Feb 2019 10:39:08: 2000000 INFO @ Fri, 15 Feb 2019 10:39:08: 2000000 INFO @ Fri, 15 Feb 2019 10:39:09: 2000000 INFO @ Fri, 15 Feb 2019 10:39:14: 3000000 INFO @ Fri, 15 Feb 2019 10:39:14: 3000000 INFO @ Fri, 15 Feb 2019 10:39:15: 3000000 INFO @ Fri, 15 Feb 2019 10:39:19: 4000000 INFO @ Fri, 15 Feb 2019 10:39:20: 4000000 INFO @ Fri, 15 Feb 2019 10:39:21: 4000000 INFO @ Fri, 15 Feb 2019 10:39:25: 5000000 INFO @ Fri, 15 Feb 2019 10:39:25: 5000000 INFO @ Fri, 15 Feb 2019 10:39:27: 5000000 INFO @ Fri, 15 Feb 2019 10:39:30: 6000000 INFO @ Fri, 15 Feb 2019 10:39:31: 6000000 INFO @ Fri, 15 Feb 2019 10:39:33: 6000000 INFO @ Fri, 15 Feb 2019 10:39:36: 7000000 INFO @ Fri, 15 Feb 2019 10:39:37: 7000000 INFO @ Fri, 15 Feb 2019 10:39:39: 7000000 INFO @ Fri, 15 Feb 2019 10:39:42: 8000000 INFO @ Fri, 15 Feb 2019 10:39:43: 8000000 INFO @ Fri, 15 Feb 2019 10:39:45: 8000000 INFO @ Fri, 15 Feb 2019 10:39:47: 9000000 INFO @ Fri, 15 Feb 2019 10:39:49: 9000000 INFO @ Fri, 15 Feb 2019 10:39:51: 9000000 INFO @ Fri, 15 Feb 2019 10:39:53: 10000000 INFO @ Fri, 15 Feb 2019 10:39:54: 10000000 INFO @ Fri, 15 Feb 2019 10:39:56: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:39:56: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:39:56: #1 total tags in treatment: 10516265 INFO @ Fri, 15 Feb 2019 10:39:56: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:39:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:39:56: #1 tags after filtering in treatment: 10516265 INFO @ Fri, 15 Feb 2019 10:39:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:39:56: #1 finished! INFO @ Fri, 15 Feb 2019 10:39:56: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:39:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:39:57: 10000000 INFO @ Fri, 15 Feb 2019 10:39:57: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:39:57: 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, 15 Feb 2019 10:39:57: Process for pairing-model is terminated! cat: SRX4957447.05_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4957447.05_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 `SRX4957447.05_*.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 `SRX4957447.05_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, 15 Feb 2019 10:39:57: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:39:57: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:39:57: #1 total tags in treatment: 10516265 INFO @ Fri, 15 Feb 2019 10:39:57: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:39:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:39:58: #1 tags after filtering in treatment: 10516265 INFO @ Fri, 15 Feb 2019 10:39:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:39:58: #1 finished! INFO @ Fri, 15 Feb 2019 10:39:58: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:39:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:39:58: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:39:58: 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, 15 Feb 2019 10:39:58: Process for pairing-model is terminated! cat: SRX4957447.10_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): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4957447.10_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 `SRX4957447.10_*.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 `SRX4957447.10_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, 15 Feb 2019 10:40:00: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:40:00: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:40:00: #1 total tags in treatment: 10516265 INFO @ Fri, 15 Feb 2019 10:40:00: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:40:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:40:00: #1 tags after filtering in treatment: 10516265 INFO @ Fri, 15 Feb 2019 10:40:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:40:00: #1 finished! INFO @ Fri, 15 Feb 2019 10:40:00: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:40:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:40:00: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:40:00: 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, 15 Feb 2019 10:40:00: Process for pairing-model is terminated! cat: SRX4957447.20_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4957447.20_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 `SRX4957447.20_*.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 `SRX4957447.20_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。