Job ID = 2640932 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T11:05:01 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 18,519,405 reads read : 18,519,405 reads written : 18,519,405 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:05:49 18519405 reads; of these: 18519405 (100.00%) were unpaired; of these: 612005 (3.30%) aligned 0 times 16205941 (87.51%) aligned exactly 1 time 1701459 (9.19%) aligned >1 times 96.70% overall alignment rate Time searching: 00:05:49 Overall time: 00:05:49 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] 8576466 / 17907400 = 0.4789 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:24:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.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, 24 Aug 2019 20:24:20: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:24:20: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:24:31: 1000000 INFO @ Sat, 24 Aug 2019 20:24:41: 2000000 INFO @ Sat, 24 Aug 2019 20:24:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.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, 24 Aug 2019 20:24:50: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:24:50: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:24:52: 3000000 INFO @ Sat, 24 Aug 2019 20:25:00: 1000000 INFO @ Sat, 24 Aug 2019 20:25:02: 4000000 INFO @ Sat, 24 Aug 2019 20:25:09: 2000000 INFO @ Sat, 24 Aug 2019 20:25:13: 5000000 INFO @ Sat, 24 Aug 2019 20:25:17: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:25:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.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, 24 Aug 2019 20:25:20: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:25:20: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:25:23: 6000000 INFO @ Sat, 24 Aug 2019 20:25:26: 4000000 INFO @ Sat, 24 Aug 2019 20:25:30: 1000000 INFO @ Sat, 24 Aug 2019 20:25:34: 7000000 INFO @ Sat, 24 Aug 2019 20:25:34: 5000000 INFO @ Sat, 24 Aug 2019 20:25:39: 2000000 INFO @ Sat, 24 Aug 2019 20:25:43: 6000000 INFO @ Sat, 24 Aug 2019 20:25:44: 8000000 INFO @ Sat, 24 Aug 2019 20:25:48: 3000000 INFO @ Sat, 24 Aug 2019 20:25:51: 7000000 INFO @ Sat, 24 Aug 2019 20:25:55: 9000000 INFO @ Sat, 24 Aug 2019 20:25:58: 4000000 INFO @ Sat, 24 Aug 2019 20:25:58: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:25:58: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:25:58: #1 total tags in treatment: 9330934 INFO @ Sat, 24 Aug 2019 20:25:58: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:25:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 20:25:58: #1 tags after filtering in treatment: 9330934 INFO @ Sat, 24 Aug 2019 20:25:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:25:58: #1 finished! INFO @ Sat, 24 Aug 2019 20:25:58: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:25:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:25:59: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:25:59: 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, 24 Aug 2019 20:25:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:25:59: 8000000 INFO @ Sat, 24 Aug 2019 20:26:07: 5000000 INFO @ Sat, 24 Aug 2019 20:26:08: 9000000 INFO @ Sat, 24 Aug 2019 20:26:10: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:26:10: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:26:10: #1 total tags in treatment: 9330934 INFO @ Sat, 24 Aug 2019 20:26:10: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:26:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 20:26:11: #1 tags after filtering in treatment: 9330934 INFO @ Sat, 24 Aug 2019 20:26:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:26:11: #1 finished! INFO @ Sat, 24 Aug 2019 20:26:11: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:26:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:26:11: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:26:11: 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, 24 Aug 2019 20:26:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:26:15: 6000000 INFO @ Sat, 24 Aug 2019 20:26:24: 7000000 INFO @ Sat, 24 Aug 2019 20:26:33: 8000000 INFO @ Sat, 24 Aug 2019 20:26:41: 9000000 INFO @ Sat, 24 Aug 2019 20:26:44: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:26:44: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:26:44: #1 total tags in treatment: 9330934 INFO @ Sat, 24 Aug 2019 20:26:44: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:26:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 20:26:44: #1 tags after filtering in treatment: 9330934 INFO @ Sat, 24 Aug 2019 20:26:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:26:44: #1 finished! INFO @ Sat, 24 Aug 2019 20:26:44: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:26:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:26:45: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:26:45: 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, 24 Aug 2019 20:26:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703454/SRX4703454.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。