Job ID = 2007949 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:40:38 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' 2019-07-05T07:40:38 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/sos/sra-pub-run-2/ERR506385/ERR506385.1' 2019-07-05T07:40:38 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506385' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:38 fasterq-dump.2.9.6 err: sorter.c run_producer_pool(): row_count == 0! 2019-07-05T07:40:38 fasterq-dump.2.9.6 err: sorter.c execute_lookup_production() -> RC(rcVDB,rcNoTarg,rcConstructing,rcParam,rcInvalid) 2019-07-05T07:40:38 fasterq-dump.2.9.6 err: fasterq-dump.c produce_lookup_files() -> RC(rcVDB,rcNoTarg,rcConstructing,rcParam,rcInvalid) 2019-07-05T07:40:43 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' 2019-07-05T07:40:43 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/sos/sra-pub-run-2/ERR506385/ERR506385.1' 2019-07-05T07:40:43 fasterq-dump.2.9.6 err: invalid accession 'ERR506385' 2019-07-05T07:40:58 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' 2019-07-05T07:40:58 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/sos/sra-pub-run-2/ERR506385/ERR506385.1' 2019-07-05T07:40:58 fasterq-dump.2.9.6 err: invalid accession 'ERR506385' 2019-07-05T07:41:13 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' 2019-07-05T07:41:13 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/sos/sra-pub-run-2/ERR506385/ERR506385.1' 2019-07-05T07:41:13 fasterq-dump.2.9.6 err: invalid accession 'ERR506385' spots read : 1,814,062 reads read : 3,628,124 reads written : 3,628,124 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: 00:01:48 1814062 reads; of these: 1814062 (100.00%) were paired; of these: 433365 (23.89%) aligned concordantly 0 times 1262577 (69.60%) aligned concordantly exactly 1 time 118120 (6.51%) aligned concordantly >1 times ---- 433365 pairs aligned concordantly 0 times; of these: 29416 (6.79%) aligned discordantly 1 time ---- 403949 pairs aligned 0 times concordantly or discordantly; of these: 807898 mates make up the pairs; of these: 783264 (96.95%) aligned 0 times 15585 (1.93%) aligned exactly 1 time 9049 (1.12%) aligned >1 times 78.41% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 245876 / 1406913 = 0.1748 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 16:53:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.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 16:53:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:53:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:53:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.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 16:53:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:53:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:53:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.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 16:53:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:53:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:53:35: 1000000 INFO @ Fri, 05 Jul 2019 16:53:36: 1000000 INFO @ Fri, 05 Jul 2019 16:53:38: 1000000 INFO @ Fri, 05 Jul 2019 16:53:44: 2000000 INFO @ Fri, 05 Jul 2019 16:53:46: 2000000 INFO @ Fri, 05 Jul 2019 16:53:47: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:47: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:47: #1 total tags in treatment: 1137607 INFO @ Fri, 05 Jul 2019 16:53:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:47: #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 16:53:47: #1 tags after filtering in treatment: 1085097 INFO @ Fri, 05 Jul 2019 16:53:47: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 16:53:47: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:47: #2 number of paired peaks: 164 WARNING @ Fri, 05 Jul 2019 16:53:47: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 05 Jul 2019 16:53:47: start model_add_line... INFO @ Fri, 05 Jul 2019 16:53:47: start X-correlation... INFO @ Fri, 05 Jul 2019 16:53:47: end of X-cor INFO @ Fri, 05 Jul 2019 16:53:47: #2 finished! INFO @ Fri, 05 Jul 2019 16:53:47: #2 predicted fragment length is 198 bps INFO @ Fri, 05 Jul 2019 16:53:47: #2 alternative fragment length(s) may be 1,198,245,525,558,561,581 bps INFO @ Fri, 05 Jul 2019 16:53:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.10_model.r WARNING @ Fri, 05 Jul 2019 16:53:47: #2 Since the d (198) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:53:47: #2 You may need to consider one of the other alternative d(s): 1,198,245,525,558,561,581 WARNING @ Fri, 05 Jul 2019 16:53:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:53:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:53:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:53:48: 2000000 INFO @ Fri, 05 Jul 2019 16:53:49: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:49: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:49: #1 total tags in treatment: 1137607 INFO @ Fri, 05 Jul 2019 16:53:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:49: #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 16:53:50: #1 tags after filtering in treatment: 1085097 INFO @ Fri, 05 Jul 2019 16:53:50: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 16:53:50: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:50: #2 number of paired peaks: 164 WARNING @ Fri, 05 Jul 2019 16:53:50: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 05 Jul 2019 16:53:50: start model_add_line... INFO @ Fri, 05 Jul 2019 16:53:50: start X-correlation... INFO @ Fri, 05 Jul 2019 16:53:50: end of X-cor INFO @ Fri, 05 Jul 2019 16:53:50: #2 finished! INFO @ Fri, 05 Jul 2019 16:53:50: #2 predicted fragment length is 198 bps INFO @ Fri, 05 Jul 2019 16:53:50: #2 alternative fragment length(s) may be 1,198,245,525,558,561,581 bps INFO @ Fri, 05 Jul 2019 16:53:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.05_model.r WARNING @ Fri, 05 Jul 2019 16:53:50: #2 Since the d (198) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:53:50: #2 You may need to consider one of the other alternative d(s): 1,198,245,525,558,561,581 WARNING @ Fri, 05 Jul 2019 16:53:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:53:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:53:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:53:51: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:53:52: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:52: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:52: #1 total tags in treatment: 1137607 INFO @ Fri, 05 Jul 2019 16:53:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:52: #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 16:53:52: #1 tags after filtering in treatment: 1085097 INFO @ Fri, 05 Jul 2019 16:53:52: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 16:53:52: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:52: #2 number of paired peaks: 164 WARNING @ Fri, 05 Jul 2019 16:53:52: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 05 Jul 2019 16:53:52: start model_add_line... INFO @ Fri, 05 Jul 2019 16:53:52: start X-correlation... INFO @ Fri, 05 Jul 2019 16:53:52: end of X-cor INFO @ Fri, 05 Jul 2019 16:53:52: #2 finished! INFO @ Fri, 05 Jul 2019 16:53:52: #2 predicted fragment length is 198 bps INFO @ Fri, 05 Jul 2019 16:53:52: #2 alternative fragment length(s) may be 1,198,245,525,558,561,581 bps INFO @ Fri, 05 Jul 2019 16:53:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.20_model.r WARNING @ Fri, 05 Jul 2019 16:53:52: #2 Since the d (198) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:53:52: #2 You may need to consider one of the other alternative d(s): 1,198,245,525,558,561,581 WARNING @ Fri, 05 Jul 2019 16:53:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:53:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:53:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:53:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:53:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:53:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.10_summits.bed INFO @ Fri, 05 Jul 2019 16:53:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (40 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:53:53: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:53:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:53:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:53:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.05_summits.bed INFO @ Fri, 05 Jul 2019 16:53:55: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (83 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:53:55: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:53:57: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:53:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:53:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471742/ERX471742.20_summits.bed INFO @ Fri, 05 Jul 2019 16:53:57: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (15 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。