Job ID = 1298988 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:40:42 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-03T08:40:42 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra36/SRR/001137/SRR1164489' 2019-06-03T08:40:53 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1164489' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T08:40:53 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 7,340 reads read : 7,340 reads written : 7,340 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:00:00 7340 reads; of these: 7340 (100.00%) were unpaired; of these: 1887 (25.71%) aligned 0 times 4459 (60.75%) aligned exactly 1 time 994 (13.54%) aligned >1 times 74.29% overall alignment rate Time searching: 00:00:00 Overall time: 00:00:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 1095 / 5453 = 0.2008 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 17:40:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 17:40:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:40:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:40:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 17:40:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:40:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:40:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:40:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:40:56: #1 total tags in treatment: 4358 INFO @ Mon, 03 Jun 2019 17:40:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:40:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 17:40:56: #1 tags after filtering in treatment: 4355 INFO @ Mon, 03 Jun 2019 17:40:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:40:56: #1 finished! INFO @ Mon, 03 Jun 2019 17:40:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:40:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:40:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:40:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:40:56: #1 total tags in treatment: 4358 INFO @ Mon, 03 Jun 2019 17:40:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:40:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 17:40:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 17:40:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:40:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:40:56: #1 tags after filtering in treatment: 4355 INFO @ Mon, 03 Jun 2019 17:40:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:40:56: #1 finished! INFO @ Mon, 03 Jun 2019 17:40:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:40:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:40:56: #2 number of paired peaks: 28 WARNING @ Mon, 03 Jun 2019 17:40:56: Too few paired peaks (28) 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 @ Mon, 03 Jun 2019 17:40:56: Process for pairing-model is terminated! INFO @ Mon, 03 Jun 2019 17:40:56: #2 number of paired peaks: 28 WARNING @ Mon, 03 Jun 2019 17:40:56: Too few paired peaks (28) 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 @ Mon, 03 Jun 2019 17:40:56: Process for pairing-model is terminated! INFO @ Mon, 03 Jun 2019 17:40:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:40:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:40:56: #1 total tags in treatment: 4358 INFO @ Mon, 03 Jun 2019 17:40:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:40:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 17:40:56: #1 tags after filtering in treatment: 4355 INFO @ Mon, 03 Jun 2019 17:40:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:40:56: #1 finished! INFO @ Mon, 03 Jun 2019 17:40:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:40:56: #2 looking for paired plus/minus strand peaks... cut: /home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.20_peaks.narrowPeak: No such file or directory INFO @ Mon, 03 Jun 2019 17:40:56: #2 number of paired peaks: 28 WARNING @ Mon, 03 Jun 2019 17:40:56: Too few paired peaks (28) 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 @ Mon, 03 Jun 2019 17:40:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling cut: /home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.10_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/dm3/SRX467065/SRX467065.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467065/SRX467065.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling