Job ID = 4289525 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T05:36:54 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 : 8,764,332 reads read : 8,764,332 reads written : 8,764,332 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: 00:01:19 8764332 reads; of these: 8764332 (100.00%) were unpaired; of these: 660892 (7.54%) aligned 0 times 7592589 (86.63%) aligned exactly 1 time 510851 (5.83%) aligned >1 times 92.46% overall alignment rate Time searching: 00:01:19 Overall time: 00:01:19 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_rmdupse_core] 6265938 / 8103440 = 0.7732 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:43:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.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 @ Tue, 10 Dec 2019 14:43:01: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:43:01: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:43:10: 1000000 INFO @ Tue, 10 Dec 2019 14:43:17: #1 tag size is determined as 41 bps INFO @ Tue, 10 Dec 2019 14:43:17: #1 tag size = 41 INFO @ Tue, 10 Dec 2019 14:43:17: #1 total tags in treatment: 1837502 INFO @ Tue, 10 Dec 2019 14:43:17: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:43:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 14:43:17: #1 tags after filtering in treatment: 1837502 INFO @ Tue, 10 Dec 2019 14:43:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:43:17: #1 finished! INFO @ Tue, 10 Dec 2019 14:43:17: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:43:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:43:17: #2 number of paired peaks: 112 WARNING @ Tue, 10 Dec 2019 14:43:17: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Tue, 10 Dec 2019 14:43:17: start model_add_line... INFO @ Tue, 10 Dec 2019 14:43:17: start X-correlation... INFO @ Tue, 10 Dec 2019 14:43:17: end of X-cor INFO @ Tue, 10 Dec 2019 14:43:17: #2 finished! INFO @ Tue, 10 Dec 2019 14:43:17: #2 predicted fragment length is 88 bps INFO @ Tue, 10 Dec 2019 14:43:17: #2 alternative fragment length(s) may be 4,88 bps INFO @ Tue, 10 Dec 2019 14:43:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.05_model.r INFO @ Tue, 10 Dec 2019 14:43:17: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:43:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:43:22: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:43:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.05_peaks.xls INFO @ Tue, 10 Dec 2019 14:43:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:43:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.05_summits.bed INFO @ Tue, 10 Dec 2019 14:43:25: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (5087 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:43:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.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 @ Tue, 10 Dec 2019 14:43:31: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:43:31: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:43:42: 1000000 INFO @ Tue, 10 Dec 2019 14:43:50: #1 tag size is determined as 41 bps INFO @ Tue, 10 Dec 2019 14:43:50: #1 tag size = 41 INFO @ Tue, 10 Dec 2019 14:43:50: #1 total tags in treatment: 1837502 INFO @ Tue, 10 Dec 2019 14:43:50: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:43:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 14:43:50: #1 tags after filtering in treatment: 1837502 INFO @ Tue, 10 Dec 2019 14:43:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:43:50: #1 finished! INFO @ Tue, 10 Dec 2019 14:43:50: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:43:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:43:50: #2 number of paired peaks: 112 WARNING @ Tue, 10 Dec 2019 14:43:50: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Tue, 10 Dec 2019 14:43:50: start model_add_line... INFO @ Tue, 10 Dec 2019 14:43:50: start X-correlation... INFO @ Tue, 10 Dec 2019 14:43:50: end of X-cor INFO @ Tue, 10 Dec 2019 14:43:50: #2 finished! INFO @ Tue, 10 Dec 2019 14:43:50: #2 predicted fragment length is 88 bps INFO @ Tue, 10 Dec 2019 14:43:50: #2 alternative fragment length(s) may be 4,88 bps INFO @ Tue, 10 Dec 2019 14:43:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.10_model.r INFO @ Tue, 10 Dec 2019 14:43:50: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:43:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:43:55: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:43:57: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.10_peaks.xls INFO @ Tue, 10 Dec 2019 14:43:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:43:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.10_summits.bed INFO @ Tue, 10 Dec 2019 14:43:57: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (3189 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:44:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.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 @ Tue, 10 Dec 2019 14:44:01: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:44:01: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:44:10: 1000000 INFO @ Tue, 10 Dec 2019 14:44:16: #1 tag size is determined as 41 bps INFO @ Tue, 10 Dec 2019 14:44:16: #1 tag size = 41 INFO @ Tue, 10 Dec 2019 14:44:16: #1 total tags in treatment: 1837502 INFO @ Tue, 10 Dec 2019 14:44:16: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:44:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 14:44:17: #1 tags after filtering in treatment: 1837502 INFO @ Tue, 10 Dec 2019 14:44:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:44:17: #1 finished! INFO @ Tue, 10 Dec 2019 14:44:17: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:44:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:44:17: #2 number of paired peaks: 112 WARNING @ Tue, 10 Dec 2019 14:44:17: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Tue, 10 Dec 2019 14:44:17: start model_add_line... INFO @ Tue, 10 Dec 2019 14:44:17: start X-correlation... INFO @ Tue, 10 Dec 2019 14:44:17: end of X-cor INFO @ Tue, 10 Dec 2019 14:44:17: #2 finished! INFO @ Tue, 10 Dec 2019 14:44:17: #2 predicted fragment length is 88 bps INFO @ Tue, 10 Dec 2019 14:44:17: #2 alternative fragment length(s) may be 4,88 bps INFO @ Tue, 10 Dec 2019 14:44:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.20_model.r INFO @ Tue, 10 Dec 2019 14:44:17: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:44:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:44:22: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:44:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.20_peaks.xls INFO @ Tue, 10 Dec 2019 14:44:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:44:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6932529/SRX6932529.20_summits.bed INFO @ Tue, 10 Dec 2019 14:44:24: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (912 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。