Job ID = 2010828 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T15:52:23 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T15:52:23 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRR/007064/SRR7234528' 2019-07-05T15:52:23 fasterq-dump.2.9.6 err: invalid accession 'SRR7234528' 2019-07-05T15:52:38 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T15:52:38 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRR/007064/SRR7234528' 2019-07-05T15:52:38 fasterq-dump.2.9.6 err: invalid accession 'SRR7234528' 2019-07-05T15:52:53 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T15:52:53 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRR/007064/SRR7234528' 2019-07-05T15:52:53 fasterq-dump.2.9.6 err: invalid accession 'SRR7234528' 2019-07-05T15:53:18 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T15:53:18 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRR/007064/SRR7234528' 2019-07-05T15:53:18 fasterq-dump.2.9.6 err: invalid accession 'SRR7234528' 2019-07-05T15:53:33 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T15:53:33 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRR/007064/SRR7234528' 2019-07-05T15:53:33 fasterq-dump.2.9.6 err: invalid accession 'SRR7234528' 2019-07-05T15:53:49 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T15:53:49 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRR/007064/SRR7234528' 2019-07-05T15:53:49 fasterq-dump.2.9.6 err: invalid accession 'SRR7234528' 2019-07-05T15:54:04 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T15:54:04 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRR/007064/SRR7234528' 2019-07-05T15:54:04 fasterq-dump.2.9.6 err: invalid accession 'SRR7234528' spots read : 5,583,616 reads read : 11,167,232 reads written : 5,583,616 reads 0-length : 5,583,616 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: 00:02:07 5583616 reads; of these: 5583616 (100.00%) were unpaired; of these: 326243 (5.84%) aligned 0 times 4525230 (81.04%) aligned exactly 1 time 732143 (13.11%) aligned >1 times 94.16% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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_rmdupse_core] 1353651 / 5257373 = 0.2575 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, 06 Jul 2019 01:04:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140937/SRX4140937.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140937/SRX4140937.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140937/SRX4140937.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140937/SRX4140937.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, 06 Jul 2019 01:04:34: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:04:34: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:04:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140937/SRX4140937.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140937/SRX4140937.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140937/SRX4140937.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140937/SRX4140937.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, 06 Jul 2019 01:04:35: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:04:35: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:04:44: 1000000 INFO @ Sat, 06 Jul 2019 01:04:46: 1000000 INFO @ Sat, 06 Jul 2019 01:04:53: 2000000 INFO @ Sat, 06 Jul 2019 01:04:56: 2000000 INFO @ Sat, 06 Jul 2019 01:04:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140937/SRX4140937.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140937/SRX4140937.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140937/SRX4140937.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140937/SRX4140937.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, 06 Jul 2019 01:04:58: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:04:58: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:05:02: 3000000 INFO @ Sat, 06 Jul 2019 01:05:07: 3000000 INFO @ Sat, 06 Jul 2019 01:05:10: 1000000 INFO @ Sat, 06 Jul 2019 01:05:10: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 01:05:10: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 01:05:10: #1 total tags in treatment: 3903722 INFO @ Sat, 06 Jul 2019 01:05:10: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:05:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:05:11: #1 tags after filtering in treatment: 3903722 INFO @ Sat, 06 Jul 2019 01:05:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:05:11: #1 finished! INFO @ Sat, 06 Jul 2019 01:05:11: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:05:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:05:11: #2 number of paired peaks: 34 WARNING @ Sat, 06 Jul 2019 01:05:11: Too few paired peaks (34) 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, 06 Jul 2019 01:05:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4140937/SRX4140937.05_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/SRX4140937/SRX4140937.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140937/SRX4140937.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140937/SRX4140937.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:05:16: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 01:05:16: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 01:05:16: #1 total tags in treatment: 3903722 INFO @ Sat, 06 Jul 2019 01:05:16: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:05:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:05:16: #1 tags after filtering in treatment: 3903722 INFO @ Sat, 06 Jul 2019 01:05:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:05:16: #1 finished! INFO @ Sat, 06 Jul 2019 01:05:16: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:05:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:05:17: #2 number of paired peaks: 34 WARNING @ Sat, 06 Jul 2019 01:05:17: Too few paired peaks (34) 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, 06 Jul 2019 01:05:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4140937/SRX4140937.10_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/SRX4140937/SRX4140937.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140937/SRX4140937.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140937/SRX4140937.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:05:23: 2000000 INFO @ Sat, 06 Jul 2019 01:05:35: 3000000 INFO @ Sat, 06 Jul 2019 01:05:46: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 01:05:46: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 01:05:46: #1 total tags in treatment: 3903722 INFO @ Sat, 06 Jul 2019 01:05:46: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:05:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:05:46: #1 tags after filtering in treatment: 3903722 INFO @ Sat, 06 Jul 2019 01:05:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:05:46: #1 finished! INFO @ Sat, 06 Jul 2019 01:05:46: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:05:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:05:46: #2 number of paired peaks: 34 WARNING @ Sat, 06 Jul 2019 01:05:46: Too few paired peaks (34) 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, 06 Jul 2019 01:05:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4140937/SRX4140937.20_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/SRX4140937/SRX4140937.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140937/SRX4140937.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140937/SRX4140937.20_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。