Job ID = 2010641 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:45:50 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 1,495,217 reads read : 2,990,434 reads written : 2,990,434 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: 00:00:47 1495217 reads; of these: 1495217 (100.00%) were paired; of these: 919454 (61.49%) aligned concordantly 0 times 477602 (31.94%) aligned concordantly exactly 1 time 98161 (6.57%) aligned concordantly >1 times ---- 919454 pairs aligned concordantly 0 times; of these: 15775 (1.72%) aligned discordantly 1 time ---- 903679 pairs aligned 0 times concordantly or discordantly; of these: 1807358 mates make up the pairs; of these: 1710271 (94.63%) aligned 0 times 77075 (4.26%) aligned exactly 1 time 20012 (1.11%) aligned >1 times 42.81% overall alignment rate Time searching: 00:00:47 Overall time: 00:00:47 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] 28937 / 582781 = 0.0497 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 23:48:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.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 23:48:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:48:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:48:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.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 23:48:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:48:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:48:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.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 23:48:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:48:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:48:43: 1000000 INFO @ Fri, 05 Jul 2019 23:48:44: #1 tag size is determined as 70 bps INFO @ Fri, 05 Jul 2019 23:48:44: #1 tag size = 70 INFO @ Fri, 05 Jul 2019 23:48:44: #1 total tags in treatment: 547722 INFO @ Fri, 05 Jul 2019 23:48:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:48:44: #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 23:48:44: #1 tags after filtering in treatment: 507099 INFO @ Fri, 05 Jul 2019 23:48:44: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 23:48:44: #1 finished! INFO @ Fri, 05 Jul 2019 23:48:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:48:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:48:44: #2 number of paired peaks: 250 WARNING @ Fri, 05 Jul 2019 23:48:44: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Fri, 05 Jul 2019 23:48:44: start model_add_line... INFO @ Fri, 05 Jul 2019 23:48:44: start X-correlation... INFO @ Fri, 05 Jul 2019 23:48:45: end of X-cor INFO @ Fri, 05 Jul 2019 23:48:45: #2 finished! INFO @ Fri, 05 Jul 2019 23:48:45: #2 predicted fragment length is 257 bps INFO @ Fri, 05 Jul 2019 23:48:45: #2 alternative fragment length(s) may be 257 bps INFO @ Fri, 05 Jul 2019 23:48:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.05_model.r INFO @ Fri, 05 Jul 2019 23:48:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:48:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:48:46: 1000000 INFO @ Fri, 05 Jul 2019 23:48:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:48:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:48:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:48:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.05_summits.bed INFO @ Fri, 05 Jul 2019 23:48:47: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (778 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 23:48:48: 1000000 INFO @ Fri, 05 Jul 2019 23:48:48: #1 tag size is determined as 70 bps INFO @ Fri, 05 Jul 2019 23:48:48: #1 tag size = 70 INFO @ Fri, 05 Jul 2019 23:48:48: #1 total tags in treatment: 547722 INFO @ Fri, 05 Jul 2019 23:48:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:48:48: #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 23:48:48: #1 tags after filtering in treatment: 507099 INFO @ Fri, 05 Jul 2019 23:48:48: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 23:48:48: #1 finished! INFO @ Fri, 05 Jul 2019 23:48:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:48:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:48:48: #2 number of paired peaks: 250 WARNING @ Fri, 05 Jul 2019 23:48:48: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Fri, 05 Jul 2019 23:48:48: start model_add_line... INFO @ Fri, 05 Jul 2019 23:48:48: start X-correlation... INFO @ Fri, 05 Jul 2019 23:48:48: end of X-cor INFO @ Fri, 05 Jul 2019 23:48:48: #2 finished! INFO @ Fri, 05 Jul 2019 23:48:48: #2 predicted fragment length is 257 bps INFO @ Fri, 05 Jul 2019 23:48:48: #2 alternative fragment length(s) may be 257 bps INFO @ Fri, 05 Jul 2019 23:48:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.20_model.r INFO @ Fri, 05 Jul 2019 23:48:48: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:48:48: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:48:50: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:48:50: #1 tag size is determined as 70 bps INFO @ Fri, 05 Jul 2019 23:48:50: #1 tag size = 70 INFO @ Fri, 05 Jul 2019 23:48:50: #1 total tags in treatment: 547722 INFO @ Fri, 05 Jul 2019 23:48:50: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:48:50: #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 23:48:50: #1 tags after filtering in treatment: 507099 INFO @ Fri, 05 Jul 2019 23:48:50: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 23:48:50: #1 finished! INFO @ Fri, 05 Jul 2019 23:48:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:48:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:48:50: #2 number of paired peaks: 250 WARNING @ Fri, 05 Jul 2019 23:48:50: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Fri, 05 Jul 2019 23:48:50: start model_add_line... INFO @ Fri, 05 Jul 2019 23:48:50: start X-correlation... INFO @ Fri, 05 Jul 2019 23:48:50: end of X-cor INFO @ Fri, 05 Jul 2019 23:48:50: #2 finished! INFO @ Fri, 05 Jul 2019 23:48:50: #2 predicted fragment length is 257 bps INFO @ Fri, 05 Jul 2019 23:48:50: #2 alternative fragment length(s) may be 257 bps INFO @ Fri, 05 Jul 2019 23:48:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.10_model.r INFO @ Fri, 05 Jul 2019 23:48:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:48:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:48:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:48:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:48:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.20_summits.bed INFO @ Fri, 05 Jul 2019 23:48:51: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (202 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:48:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:48:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:48:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:48:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX386369/SRX386369.10_summits.bed INFO @ Fri, 05 Jul 2019 23:48:53: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (431 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。