Job ID = 2010524 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T13:50:22 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' 2019-07-05T13:50:22 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/sra15/SRR/001011/SRR1035328' 2019-07-05T13:50:22 fasterq-dump.2.9.6 err: invalid accession 'SRR1035328' spots read : 10,253,289 reads read : 20,506,578 reads written : 20,506,578 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: 00:02:32 10253289 reads; of these: 10253289 (100.00%) were paired; of these: 9708110 (94.68%) aligned concordantly 0 times 381861 (3.72%) aligned concordantly exactly 1 time 163318 (1.59%) aligned concordantly >1 times ---- 9708110 pairs aligned concordantly 0 times; of these: 7054 (0.07%) aligned discordantly 1 time ---- 9701056 pairs aligned 0 times concordantly or discordantly; of these: 19402112 mates make up the pairs; of these: 19083557 (98.36%) aligned 0 times 189176 (0.98%) aligned exactly 1 time 129379 (0.67%) aligned >1 times 6.94% overall alignment rate Time searching: 00:02:32 Overall time: 00:02:32 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] 243468 / 550751 = 0.4421 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 23:08:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.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 23:08:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:08:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:08:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.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 23:08:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:08:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:08:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.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 23:08:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:08:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:08:24: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:08:24: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:08:24: #1 total tags in treatment: 302768 INFO @ Fri, 05 Jul 2019 23:08:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:08:24: #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 23:08:24: #1 tags after filtering in treatment: 222666 INFO @ Fri, 05 Jul 2019 23:08:24: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 05 Jul 2019 23:08:24: #1 finished! INFO @ Fri, 05 Jul 2019 23:08:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:08:24: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:08:24: #2 number of paired peaks: 262 WARNING @ Fri, 05 Jul 2019 23:08:24: Fewer paired peaks (262) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 262 pairs to build model! INFO @ Fri, 05 Jul 2019 23:08:24: start model_add_line... INFO @ Fri, 05 Jul 2019 23:08:24: start X-correlation... INFO @ Fri, 05 Jul 2019 23:08:24: end of X-cor INFO @ Fri, 05 Jul 2019 23:08:24: #2 finished! INFO @ Fri, 05 Jul 2019 23:08:24: #2 predicted fragment length is 103 bps INFO @ Fri, 05 Jul 2019 23:08:24: #2 alternative fragment length(s) may be 21,49,103,124,238,531,566 bps INFO @ Fri, 05 Jul 2019 23:08:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.05_model.r INFO @ Fri, 05 Jul 2019 23:08:24: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:08:24: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:08:24: #1 total tags in treatment: 302768 INFO @ Fri, 05 Jul 2019 23:08:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:08:24: #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 23:08:24: #1 tags after filtering in treatment: 222666 INFO @ Fri, 05 Jul 2019 23:08:24: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 05 Jul 2019 23:08:24: #1 finished! INFO @ Fri, 05 Jul 2019 23:08:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:08:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:08:24: #2 number of paired peaks: 262 WARNING @ Fri, 05 Jul 2019 23:08:24: Fewer paired peaks (262) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 262 pairs to build model! INFO @ Fri, 05 Jul 2019 23:08:24: start model_add_line... INFO @ Fri, 05 Jul 2019 23:08:24: start X-correlation... INFO @ Fri, 05 Jul 2019 23:08:24: end of X-cor INFO @ Fri, 05 Jul 2019 23:08:24: #2 finished! INFO @ Fri, 05 Jul 2019 23:08:24: #2 predicted fragment length is 103 bps INFO @ Fri, 05 Jul 2019 23:08:24: #2 alternative fragment length(s) may be 21,49,103,124,238,531,566 bps INFO @ Fri, 05 Jul 2019 23:08:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.10_model.r INFO @ Fri, 05 Jul 2019 23:08:25: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:08:25: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:08:25: #1 total tags in treatment: 302768 INFO @ Fri, 05 Jul 2019 23:08:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:08:25: #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 23:08:25: #1 tags after filtering in treatment: 222666 INFO @ Fri, 05 Jul 2019 23:08:25: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 05 Jul 2019 23:08:25: #1 finished! INFO @ Fri, 05 Jul 2019 23:08:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:08:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:08:25: #2 number of paired peaks: 262 WARNING @ Fri, 05 Jul 2019 23:08:25: Fewer paired peaks (262) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 262 pairs to build model! INFO @ Fri, 05 Jul 2019 23:08:25: start model_add_line... INFO @ Fri, 05 Jul 2019 23:08:25: start X-correlation... INFO @ Fri, 05 Jul 2019 23:08:25: end of X-cor INFO @ Fri, 05 Jul 2019 23:08:25: #2 finished! INFO @ Fri, 05 Jul 2019 23:08:25: #2 predicted fragment length is 103 bps INFO @ Fri, 05 Jul 2019 23:08:25: #2 alternative fragment length(s) may be 21,49,103,124,238,531,566 bps INFO @ Fri, 05 Jul 2019 23:08:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.20_model.r INFO @ Fri, 05 Jul 2019 23:08:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:08:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:08:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:08:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:08:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:08:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:08:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:08:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:08:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:08:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:08:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:08:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:08:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.20_summits.bed INFO @ Fri, 05 Jul 2019 23:08:28: Done! INFO @ Fri, 05 Jul 2019 23:08:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:08:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.05_summits.bed INFO @ Fri, 05 Jul 2019 23:08:28: Done! INFO @ Fri, 05 Jul 2019 23:08:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:08:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:08:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381227/SRX381227.10_summits.bed INFO @ Fri, 05 Jul 2019 23:08:29: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (271 records, 4 fields): 4 millis pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (37 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (149 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling