Job ID = 11634707 sra ファイルのダウンロード中... Completed: 651560K bytes transferred in 10 seconds (489496K 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 35738862 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4957443/SRR8136457.sra Written 35738862 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4957443/SRR8136457.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: 00:06:03 35738862 reads; of these: 35738862 (100.00%) were unpaired; of these: 1990395 (5.57%) aligned 0 times 30410070 (85.09%) aligned exactly 1 time 3338397 (9.34%) aligned >1 times 94.43% overall alignment rate Time searching: 00:06:03 Overall time: 00:06:03 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 16 files... [bam_rmdupse_core] 20842310 / 33748467 = 0.6176 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 10:42:06: # Command line: callpeak -t SRX4957443.bam -f BAM -g 12100000 -n SRX4957443.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4957443.20 # format = BAM # ChIP-seq file = ['SRX4957443.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 10:42:06: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:42:06: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:42:06: # Command line: callpeak -t SRX4957443.bam -f BAM -g 12100000 -n SRX4957443.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4957443.10 # format = BAM # ChIP-seq file = ['SRX4957443.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 10:42:06: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:42:06: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:42:06: # Command line: callpeak -t SRX4957443.bam -f BAM -g 12100000 -n SRX4957443.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4957443.05 # format = BAM # ChIP-seq file = ['SRX4957443.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 10:42:06: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:42:06: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:42:13: 1000000 INFO @ Fri, 15 Feb 2019 10:42:13: 1000000 INFO @ Fri, 15 Feb 2019 10:42:13: 1000000 INFO @ Fri, 15 Feb 2019 10:42:20: 2000000 INFO @ Fri, 15 Feb 2019 10:42:20: 2000000 INFO @ Fri, 15 Feb 2019 10:42:21: 2000000 INFO @ Fri, 15 Feb 2019 10:42:26: 3000000 INFO @ Fri, 15 Feb 2019 10:42:28: 3000000 INFO @ Fri, 15 Feb 2019 10:42:29: 3000000 INFO @ Fri, 15 Feb 2019 10:42:33: 4000000 INFO @ Fri, 15 Feb 2019 10:42:37: 4000000 INFO @ Fri, 15 Feb 2019 10:42:37: 4000000 INFO @ Fri, 15 Feb 2019 10:42:40: 5000000 INFO @ Fri, 15 Feb 2019 10:42:45: 5000000 INFO @ Fri, 15 Feb 2019 10:42:45: 5000000 INFO @ Fri, 15 Feb 2019 10:42:46: 6000000 INFO @ Fri, 15 Feb 2019 10:42:53: 6000000 INFO @ Fri, 15 Feb 2019 10:42:53: 6000000 INFO @ Fri, 15 Feb 2019 10:42:53: 7000000 INFO @ Fri, 15 Feb 2019 10:43:00: 7000000 INFO @ Fri, 15 Feb 2019 10:43:00: 8000000 INFO @ Fri, 15 Feb 2019 10:43:00: 7000000 INFO @ Fri, 15 Feb 2019 10:43:07: 9000000 INFO @ Fri, 15 Feb 2019 10:43:07: 8000000 INFO @ Fri, 15 Feb 2019 10:43:07: 8000000 INFO @ Fri, 15 Feb 2019 10:43:13: 10000000 INFO @ Fri, 15 Feb 2019 10:43:14: 9000000 INFO @ Fri, 15 Feb 2019 10:43:15: 9000000 INFO @ Fri, 15 Feb 2019 10:43:20: 11000000 INFO @ Fri, 15 Feb 2019 10:43:22: 10000000 INFO @ Fri, 15 Feb 2019 10:43:22: 10000000 INFO @ Fri, 15 Feb 2019 10:43:27: 12000000 INFO @ Fri, 15 Feb 2019 10:43:29: 11000000 INFO @ Fri, 15 Feb 2019 10:43:29: 11000000 INFO @ Fri, 15 Feb 2019 10:43:33: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:43:33: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:43:33: #1 total tags in treatment: 12906157 INFO @ Fri, 15 Feb 2019 10:43:33: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:43:33: #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 10:43:33: #1 tags after filtering in treatment: 12906157 INFO @ Fri, 15 Feb 2019 10:43:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:43:33: #1 finished! INFO @ Fri, 15 Feb 2019 10:43:33: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:43:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:43:34: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:43:34: 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 10:43:34: Process for pairing-model is terminated! cat: SRX4957443.05_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): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4957443.05_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 `SRX4957443.05_*.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 `SRX4957443.05_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 10:43:37: 12000000 INFO @ Fri, 15 Feb 2019 10:43:37: 12000000 INFO @ Fri, 15 Feb 2019 10:43:43: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:43:43: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:43:43: #1 total tags in treatment: 12906157 INFO @ Fri, 15 Feb 2019 10:43:43: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:43:43: #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 10:43:43: #1 tags after filtering in treatment: 12906157 INFO @ Fri, 15 Feb 2019 10:43:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:43:43: #1 finished! INFO @ Fri, 15 Feb 2019 10:43:43: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:43:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:43:43: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:43:43: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:43:43: #1 total tags in treatment: 12906157 INFO @ Fri, 15 Feb 2019 10:43:43: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:43:43: #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 10:43:43: #1 tags after filtering in treatment: 12906157 INFO @ Fri, 15 Feb 2019 10:43:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:43:43: #1 finished! INFO @ Fri, 15 Feb 2019 10:43:43: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:43:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:43:44: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:43:44: 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 10:43:44: Process for pairing-model is terminated! cat: SRX4957443.20_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 `SRX4957443.20_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 `SRX4957443.20_*.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 `SRX4957443.20_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 @ Fri, 15 Feb 2019 10:43:44: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:43:44: 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 10:43:44: Process for pairing-model is terminated! cat: SRX4957443.10_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4957443.10_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 `SRX4957443.10_*.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 `SRX4957443.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。