Job ID = 2010213 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T12:47:52 fasterq-dump.2.9.6 fatal: SIGNAL - Segmentation fault *** Error in `/home/okishinya/chipatlas/bin/sratoolkit.2.9.6-1-ubuntu64/bin/fasterq-dump': corrupted double-linked list: 0x00007fffd8002da0 *** 2019-07-05T12:48:14 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' 2019-07-05T12:48:14 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/sra53/SRR/006039/SRR6184437' 2019-07-05T12:48:14 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_db_type().VDBManagerOpenDBRead( 'SRR6184437' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T12:48:14 fasterq-dump.2.9.6 err: invalid accession 'SRR6184437' 2019-07-05T12:48:30 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' 2019-07-05T12:48:30 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/sra53/SRR/006039/SRR6184437' 2019-07-05T12:48:30 fasterq-dump.2.9.6 err: invalid accession 'SRR6184437' 2019-07-05T12:48:45 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' 2019-07-05T12:48:45 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/sra53/SRR/006039/SRR6184437' 2019-07-05T12:48:45 fasterq-dump.2.9.6 err: invalid accession 'SRR6184437' 2019-07-05T12:49:00 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' 2019-07-05T12:49:00 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/sra53/SRR/006039/SRR6184437' 2019-07-05T12:49:00 fasterq-dump.2.9.6 err: invalid accession 'SRR6184437' spots read : 7,849,242 reads read : 15,698,484 reads written : 7,849,242 reads 0-length : 7,849,242 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: 00:01:24 7849242 reads; of these: 7849242 (100.00%) were unpaired; of these: 448069 (5.71%) aligned 0 times 6696112 (85.31%) aligned exactly 1 time 705061 (8.98%) aligned >1 times 94.29% overall alignment rate Time searching: 00:01:24 Overall time: 00:01:24 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] 2192151 / 7401173 = 0.2962 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, 05 Jul 2019 21:58:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.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, 05 Jul 2019 21:58:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:58:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:58:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.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, 05 Jul 2019 21:58:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:58:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:58:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.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, 05 Jul 2019 21:58:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:58:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:58:42: 1000000 INFO @ Fri, 05 Jul 2019 21:58:43: 1000000 INFO @ Fri, 05 Jul 2019 21:58:44: 1000000 INFO @ Fri, 05 Jul 2019 21:58:50: 2000000 INFO @ Fri, 05 Jul 2019 21:58:52: 2000000 INFO @ Fri, 05 Jul 2019 21:58:52: 2000000 INFO @ Fri, 05 Jul 2019 21:58:58: 3000000 INFO @ Fri, 05 Jul 2019 21:59:00: 3000000 INFO @ Fri, 05 Jul 2019 21:59:02: 3000000 INFO @ Fri, 05 Jul 2019 21:59:07: 4000000 INFO @ Fri, 05 Jul 2019 21:59:08: 4000000 INFO @ Fri, 05 Jul 2019 21:59:11: 4000000 INFO @ Fri, 05 Jul 2019 21:59:14: 5000000 INFO @ Fri, 05 Jul 2019 21:59:16: 5000000 INFO @ Fri, 05 Jul 2019 21:59:16: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 21:59:16: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 21:59:16: #1 total tags in treatment: 5209022 INFO @ Fri, 05 Jul 2019 21:59:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:59:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:59:16: #1 tags after filtering in treatment: 5209022 INFO @ Fri, 05 Jul 2019 21:59:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:59:16: #1 finished! INFO @ Fri, 05 Jul 2019 21:59:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:59:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:59:16: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:59:16: 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, 05 Jul 2019 21:59:16: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 21:59:17: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 21:59:17: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 21:59:17: #1 total tags in treatment: 5209022 INFO @ Fri, 05 Jul 2019 21:59:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:59:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:59:17: #1 tags after filtering in treatment: 5209022 INFO @ Fri, 05 Jul 2019 21:59:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:59:17: #1 finished! INFO @ Fri, 05 Jul 2019 21:59:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:59:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:59:18: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:59:18: 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, 05 Jul 2019 21:59:18: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 21:59:19: 5000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.10_*.xls’: No such file or directoryrm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.10_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:59:21: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 21:59:21: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 21:59:21: #1 total tags in treatment: 5209022 INFO @ Fri, 05 Jul 2019 21:59:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:59:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:59:21: #1 tags after filtering in treatment: 5209022 INFO @ Fri, 05 Jul 2019 21:59:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:59:21: #1 finished! INFO @ Fri, 05 Jul 2019 21:59:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:59:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:59:21: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:59:21: 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, 05 Jul 2019 21:59:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.20_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/SRX3294585/SRX3294585.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294585/SRX3294585.20_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。