Job ID = 11193114 sra ファイルのダウンロード中... Completed: 258782K bytes transferred in 5 seconds (362767K 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 12898577 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4234133/SRR7360968.sra Written 12898577 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4234133/SRR7360968.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: 00:02:05 12898577 reads; of these: 12898577 (100.00%) were unpaired; of these: 884597 (6.86%) aligned 0 times 10999085 (85.27%) aligned exactly 1 time 1014895 (7.87%) aligned >1 times 93.14% overall alignment rate Time searching: 00:02:05 Overall time: 00:02:05 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_rmdupse_core] 3672412 / 12013980 = 0.3057 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 @ Sat, 15 Sep 2018 11:02:29: # Command line: callpeak -t SRX4234133.bam -f BAM -g 12100000 -n SRX4234133.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4234133.10 # format = BAM # ChIP-seq file = ['SRX4234133.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 @ Sat, 15 Sep 2018 11:02:29: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:02:29: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:02:29: # Command line: callpeak -t SRX4234133.bam -f BAM -g 12100000 -n SRX4234133.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4234133.20 # format = BAM # ChIP-seq file = ['SRX4234133.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 @ Sat, 15 Sep 2018 11:02:29: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:02:29: # Command line: callpeak -t SRX4234133.bam -f BAM -g 12100000 -n SRX4234133.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4234133.05 # format = BAM # ChIP-seq file = ['SRX4234133.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 @ Sat, 15 Sep 2018 11:02:29: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:02:29: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:02:29: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:02:36: 1000000 INFO @ Sat, 15 Sep 2018 11:02:36: 1000000 INFO @ Sat, 15 Sep 2018 11:02:36: 1000000 INFO @ Sat, 15 Sep 2018 11:02:42: 2000000 INFO @ Sat, 15 Sep 2018 11:02:43: 2000000 INFO @ Sat, 15 Sep 2018 11:02:43: 2000000 INFO @ Sat, 15 Sep 2018 11:02:49: 3000000 INFO @ Sat, 15 Sep 2018 11:02:50: 3000000 INFO @ Sat, 15 Sep 2018 11:02:50: 3000000 INFO @ Sat, 15 Sep 2018 11:02:56: 4000000 INFO @ Sat, 15 Sep 2018 11:02:57: 4000000 INFO @ Sat, 15 Sep 2018 11:02:57: 4000000 INFO @ Sat, 15 Sep 2018 11:03:03: 5000000 INFO @ Sat, 15 Sep 2018 11:03:03: 5000000 INFO @ Sat, 15 Sep 2018 11:03:04: 5000000 INFO @ Sat, 15 Sep 2018 11:03:10: 6000000 INFO @ Sat, 15 Sep 2018 11:03:10: 6000000 INFO @ Sat, 15 Sep 2018 11:03:11: 6000000 INFO @ Sat, 15 Sep 2018 11:03:16: 7000000 INFO @ Sat, 15 Sep 2018 11:03:17: 7000000 INFO @ Sat, 15 Sep 2018 11:03:19: 7000000 INFO @ Sat, 15 Sep 2018 11:03:23: 8000000 INFO @ Sat, 15 Sep 2018 11:03:24: 8000000 INFO @ Sat, 15 Sep 2018 11:03:25: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 11:03:25: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 11:03:25: #1 total tags in treatment: 8341568 INFO @ Sat, 15 Sep 2018 11:03:25: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:03:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:03:25: #1 tags after filtering in treatment: 8341568 INFO @ Sat, 15 Sep 2018 11:03:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:03:25: #1 finished! INFO @ Sat, 15 Sep 2018 11:03:25: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:03:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:03:26: 8000000 INFO @ Sat, 15 Sep 2018 11:03:26: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 11:03:26: 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 @ Sat, 15 Sep 2018 11:03:26: Process for pairing-model is terminated! cat: SRX4234133.20_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 `SRX4234133.20_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 `SRX4234133.20_*.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 `SRX4234133.20_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 @ Sat, 15 Sep 2018 11:03:26: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 11:03:26: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 11:03:26: #1 total tags in treatment: 8341568 INFO @ Sat, 15 Sep 2018 11:03:26: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:03:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:03:27: #1 tags after filtering in treatment: 8341568 INFO @ Sat, 15 Sep 2018 11:03:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:03:27: #1 finished! INFO @ Sat, 15 Sep 2018 11:03:27: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:03:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:03:27: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 11:03:27: 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 @ Sat, 15 Sep 2018 11:03:27: Process for pairing-model is terminated! cat: SRX4234133.05_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 `SRX4234133.05_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 `SRX4234133.05_*.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 `SRX4234133.05_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 @ Sat, 15 Sep 2018 11:03:28: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 11:03:28: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 11:03:28: #1 total tags in treatment: 8341568 INFO @ Sat, 15 Sep 2018 11:03:28: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:03:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:03:28: #1 tags after filtering in treatment: 8341568 INFO @ Sat, 15 Sep 2018 11:03:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:03:28: #1 finished! INFO @ Sat, 15 Sep 2018 11:03:28: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:03:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:03:29: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 11:03:29: 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 @ Sat, 15 Sep 2018 11:03:29: Process for pairing-model is terminated! cat: SRX4234133.10_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 `SRX4234133.10_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 `SRX4234133.10_*.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 `SRX4234133.10_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。