Job ID = 2640756 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T09:54:53 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 : 10,845,128 reads read : 21,690,256 reads written : 21,690,256 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: 00:00:01 Multiseed full-index search: 00:02:33 10845128 reads; of these: 10845128 (100.00%) were paired; of these: 9090330 (83.82%) aligned concordantly 0 times 1384584 (12.77%) aligned concordantly exactly 1 time 370214 (3.41%) aligned concordantly >1 times ---- 9090330 pairs aligned concordantly 0 times; of these: 7714 (0.08%) aligned discordantly 1 time ---- 9082616 pairs aligned 0 times concordantly or discordantly; of these: 18165232 mates make up the pairs; of these: 18119298 (99.75%) aligned 0 times 12439 (0.07%) aligned exactly 1 time 33495 (0.18%) aligned >1 times 16.46% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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] 192460 / 1760394 = 0.1093 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:04:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.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 @ Sat, 24 Aug 2019 19:04:08: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:04:08: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:04:17: 1000000 INFO @ Sat, 24 Aug 2019 19:04:24: 2000000 INFO @ Sat, 24 Aug 2019 19:04:32: 3000000 INFO @ Sat, 24 Aug 2019 19:04:34: #1 tag size is determined as 39 bps INFO @ Sat, 24 Aug 2019 19:04:34: #1 tag size = 39 INFO @ Sat, 24 Aug 2019 19:04:34: #1 total tags in treatment: 1562550 INFO @ Sat, 24 Aug 2019 19:04:34: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:04:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:04:34: #1 tags after filtering in treatment: 1306016 INFO @ Sat, 24 Aug 2019 19:04:34: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 24 Aug 2019 19:04:34: #1 finished! INFO @ Sat, 24 Aug 2019 19:04:34: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:04:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:04:34: #2 number of paired peaks: 110 WARNING @ Sat, 24 Aug 2019 19:04:34: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sat, 24 Aug 2019 19:04:34: start model_add_line... INFO @ Sat, 24 Aug 2019 19:04:34: start X-correlation... INFO @ Sat, 24 Aug 2019 19:04:34: end of X-cor INFO @ Sat, 24 Aug 2019 19:04:34: #2 finished! INFO @ Sat, 24 Aug 2019 19:04:34: #2 predicted fragment length is 243 bps INFO @ Sat, 24 Aug 2019 19:04:34: #2 alternative fragment length(s) may be 243 bps INFO @ Sat, 24 Aug 2019 19:04:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.05_model.r INFO @ Sat, 24 Aug 2019 19:04:34: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:04:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:04:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.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 @ Sat, 24 Aug 2019 19:04:37: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:04:37: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:04:38: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:04:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.05_peaks.xls INFO @ Sat, 24 Aug 2019 19:04:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:04:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.05_summits.bed INFO @ Sat, 24 Aug 2019 19:04:40: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (317 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:04:45: 1000000 INFO @ Sat, 24 Aug 2019 19:04:53: 2000000 INFO @ Sat, 24 Aug 2019 19:05:00: 3000000 INFO @ Sat, 24 Aug 2019 19:05:02: #1 tag size is determined as 39 bps INFO @ Sat, 24 Aug 2019 19:05:02: #1 tag size = 39 INFO @ Sat, 24 Aug 2019 19:05:02: #1 total tags in treatment: 1562550 INFO @ Sat, 24 Aug 2019 19:05:02: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:05:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:05:02: #1 tags after filtering in treatment: 1306016 INFO @ Sat, 24 Aug 2019 19:05:02: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 24 Aug 2019 19:05:02: #1 finished! INFO @ Sat, 24 Aug 2019 19:05:02: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:05:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:05:02: #2 number of paired peaks: 110 WARNING @ Sat, 24 Aug 2019 19:05:02: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sat, 24 Aug 2019 19:05:02: start model_add_line... INFO @ Sat, 24 Aug 2019 19:05:02: start X-correlation... INFO @ Sat, 24 Aug 2019 19:05:02: end of X-cor INFO @ Sat, 24 Aug 2019 19:05:02: #2 finished! INFO @ Sat, 24 Aug 2019 19:05:02: #2 predicted fragment length is 243 bps INFO @ Sat, 24 Aug 2019 19:05:02: #2 alternative fragment length(s) may be 243 bps INFO @ Sat, 24 Aug 2019 19:05:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.10_model.r INFO @ Sat, 24 Aug 2019 19:05:02: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:05:02: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:05:06: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:05:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.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 @ Sat, 24 Aug 2019 19:05:07: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:05:07: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:05:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.10_peaks.xls INFO @ Sat, 24 Aug 2019 19:05:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:05:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.10_summits.bed INFO @ Sat, 24 Aug 2019 19:05:08: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (215 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:05:19: 1000000 INFO @ Sat, 24 Aug 2019 19:05:30: 2000000 INFO @ Sat, 24 Aug 2019 19:05:42: 3000000 INFO @ Sat, 24 Aug 2019 19:05:44: #1 tag size is determined as 39 bps INFO @ Sat, 24 Aug 2019 19:05:44: #1 tag size = 39 INFO @ Sat, 24 Aug 2019 19:05:44: #1 total tags in treatment: 1562550 INFO @ Sat, 24 Aug 2019 19:05:44: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:05:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:05:44: #1 tags after filtering in treatment: 1306016 INFO @ Sat, 24 Aug 2019 19:05:44: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 24 Aug 2019 19:05:44: #1 finished! INFO @ Sat, 24 Aug 2019 19:05:44: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:05:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:05:44: #2 number of paired peaks: 110 WARNING @ Sat, 24 Aug 2019 19:05:44: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sat, 24 Aug 2019 19:05:44: start model_add_line... INFO @ Sat, 24 Aug 2019 19:05:44: start X-correlation... INFO @ Sat, 24 Aug 2019 19:05:44: end of X-cor INFO @ Sat, 24 Aug 2019 19:05:44: #2 finished! INFO @ Sat, 24 Aug 2019 19:05:44: #2 predicted fragment length is 243 bps INFO @ Sat, 24 Aug 2019 19:05:44: #2 alternative fragment length(s) may be 243 bps INFO @ Sat, 24 Aug 2019 19:05:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.20_model.r INFO @ Sat, 24 Aug 2019 19:05:44: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:05:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:05:48: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:05:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.20_peaks.xls INFO @ Sat, 24 Aug 2019 19:05:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:05:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2732447/ERX2732447.20_summits.bed INFO @ Sat, 24 Aug 2019 19:05:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (144 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。