Job ID = 2007932 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:40:35 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' 2019-07-05T07:40:35 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/era10/ERR/ERR506/ERR506368' 2019-07-05T07:40:35 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'ERR506368', 'SEQUENCE', 'NAME' ).VDBManagerOpenDBRead() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:40 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' 2019-07-05T07:40:40 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/era10/ERR/ERR506/ERR506368' 2019-07-05T07:40:40 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506368' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:46 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' 2019-07-05T07:40:46 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/era10/ERR/ERR506/ERR506368' 2019-07-05T07:40:46 fasterq-dump.2.9.6 err: invalid accession 'ERR506368' 2019-07-05T07:41:01 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' 2019-07-05T07:41:01 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/era10/ERR/ERR506/ERR506368' 2019-07-05T07:41:01 fasterq-dump.2.9.6 err: invalid accession 'ERR506368' 2019-07-05T07:41:16 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' 2019-07-05T07:41:16 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/era10/ERR/ERR506/ERR506368' 2019-07-05T07:41:16 fasterq-dump.2.9.6 err: invalid accession 'ERR506368' spots read : 1,793,488 reads read : 3,586,976 reads written : 3,586,976 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: 00:03:36 1793488 reads; of these: 1793488 (100.00%) were paired; of these: 158265 (8.82%) aligned concordantly 0 times 1502703 (83.79%) aligned concordantly exactly 1 time 132520 (7.39%) aligned concordantly >1 times ---- 158265 pairs aligned concordantly 0 times; of these: 68926 (43.55%) aligned discordantly 1 time ---- 89339 pairs aligned 0 times concordantly or discordantly; of these: 178678 mates make up the pairs; of these: 142115 (79.54%) aligned 0 times 21661 (12.12%) aligned exactly 1 time 14902 (8.34%) aligned >1 times 96.04% overall alignment rate Time searching: 00:03:36 Overall time: 00:03:36 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] 31070 / 1690846 = 0.0184 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 16:53:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.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 16:53:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:53:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:53:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.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 16:53:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:53:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:53:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.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 16:53:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:53:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:53:58: 1000000 INFO @ Fri, 05 Jul 2019 16:54:00: 1000000 INFO @ Fri, 05 Jul 2019 16:54:00: 1000000 INFO @ Fri, 05 Jul 2019 16:54:07: 2000000 INFO @ Fri, 05 Jul 2019 16:54:14: 2000000 INFO @ Fri, 05 Jul 2019 16:54:14: 2000000 INFO @ Fri, 05 Jul 2019 16:54:17: 3000000 INFO @ Fri, 05 Jul 2019 16:54:20: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:54:20: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:54:20: #1 total tags in treatment: 1604806 INFO @ Fri, 05 Jul 2019 16:54:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:54:20: #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 16:54:20: #1 tags after filtering in treatment: 1457427 INFO @ Fri, 05 Jul 2019 16:54:20: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 05 Jul 2019 16:54:20: #1 finished! INFO @ Fri, 05 Jul 2019 16:54:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:54:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:54:20: #2 number of paired peaks: 343 WARNING @ Fri, 05 Jul 2019 16:54:20: Fewer paired peaks (343) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 343 pairs to build model! INFO @ Fri, 05 Jul 2019 16:54:20: start model_add_line... INFO @ Fri, 05 Jul 2019 16:54:20: start X-correlation... INFO @ Fri, 05 Jul 2019 16:54:20: end of X-cor INFO @ Fri, 05 Jul 2019 16:54:20: #2 finished! INFO @ Fri, 05 Jul 2019 16:54:20: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 16:54:20: #2 alternative fragment length(s) may be 4,123,135,153 bps INFO @ Fri, 05 Jul 2019 16:54:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.20_model.r WARNING @ Fri, 05 Jul 2019 16:54:20: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:54:20: #2 You may need to consider one of the other alternative d(s): 4,123,135,153 WARNING @ Fri, 05 Jul 2019 16:54:20: #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 16:54:20: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:54:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:54:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:54:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:54:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:54:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.20_summits.bed INFO @ Fri, 05 Jul 2019 16:54:27: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (260 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 16:54:28: 3000000 INFO @ Fri, 05 Jul 2019 16:54:28: 3000000 CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:54:33: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:54:33: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:54:33: #1 total tags in treatment: 1604806 INFO @ Fri, 05 Jul 2019 16:54:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:54:33: #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 16:54:33: #1 tags after filtering in treatment: 1457427 INFO @ Fri, 05 Jul 2019 16:54:33: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 05 Jul 2019 16:54:33: #1 finished! INFO @ Fri, 05 Jul 2019 16:54:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:54:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:54:33: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:54:33: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:54:33: #1 total tags in treatment: 1604806 INFO @ Fri, 05 Jul 2019 16:54:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:54:33: #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 16:54:33: #2 number of paired peaks: 343 WARNING @ Fri, 05 Jul 2019 16:54:33: Fewer paired peaks (343) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 343 pairs to build model! INFO @ Fri, 05 Jul 2019 16:54:33: start model_add_line... INFO @ Fri, 05 Jul 2019 16:54:33: start X-correlation... INFO @ Fri, 05 Jul 2019 16:54:33: #1 tags after filtering in treatment: 1457427 INFO @ Fri, 05 Jul 2019 16:54:33: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 05 Jul 2019 16:54:33: #1 finished! INFO @ Fri, 05 Jul 2019 16:54:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:54:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:54:33: end of X-cor INFO @ Fri, 05 Jul 2019 16:54:33: #2 finished! INFO @ Fri, 05 Jul 2019 16:54:33: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 16:54:33: #2 alternative fragment length(s) may be 4,123,135,153 bps INFO @ Fri, 05 Jul 2019 16:54:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.05_model.r WARNING @ Fri, 05 Jul 2019 16:54:33: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:54:33: #2 You may need to consider one of the other alternative d(s): 4,123,135,153 WARNING @ Fri, 05 Jul 2019 16:54:33: #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 16:54:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:54:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:54:33: #2 number of paired peaks: 343 WARNING @ Fri, 05 Jul 2019 16:54:33: Fewer paired peaks (343) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 343 pairs to build model! INFO @ Fri, 05 Jul 2019 16:54:33: start model_add_line... INFO @ Fri, 05 Jul 2019 16:54:33: start X-correlation... INFO @ Fri, 05 Jul 2019 16:54:33: end of X-cor INFO @ Fri, 05 Jul 2019 16:54:33: #2 finished! INFO @ Fri, 05 Jul 2019 16:54:33: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 16:54:33: #2 alternative fragment length(s) may be 4,123,135,153 bps INFO @ Fri, 05 Jul 2019 16:54:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.10_model.r WARNING @ Fri, 05 Jul 2019 16:54:34: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:54:34: #2 You may need to consider one of the other alternative d(s): 4,123,135,153 WARNING @ Fri, 05 Jul 2019 16:54:34: #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 16:54:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:54:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:54:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:54:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:54:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:54:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:54:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.10_summits.bed INFO @ Fri, 05 Jul 2019 16:54:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:54:40: Done! INFO @ Fri, 05 Jul 2019 16:54:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:54:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471725/ERX471725.05_summits.bed INFO @ Fri, 05 Jul 2019 16:54:40: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (410 records, 4 fields): 3 millis pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (624 records, 4 fields): 5 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。