Job ID = 4289562 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T05:47:42 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 : 7,807,818 reads read : 7,807,818 reads written : 7,807,818 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: 00:01:14 7807818 reads; of these: 7807818 (100.00%) were unpaired; of these: 763056 (9.77%) aligned 0 times 6580188 (84.28%) aligned exactly 1 time 464574 (5.95%) aligned >1 times 90.23% overall alignment rate Time searching: 00:01:14 Overall time: 00:01:14 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] 5750723 / 7044762 = 0.8163 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:52:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.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 14:52:16: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:52:16: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:52:24: 1000000 INFO @ Tue, 10 Dec 2019 14:52:26: #1 tag size is determined as 41 bps INFO @ Tue, 10 Dec 2019 14:52:26: #1 tag size = 41 INFO @ Tue, 10 Dec 2019 14:52:26: #1 total tags in treatment: 1294039 INFO @ Tue, 10 Dec 2019 14:52:26: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:52:26: #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 14:52:26: #1 tags after filtering in treatment: 1294039 INFO @ Tue, 10 Dec 2019 14:52:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:52:26: #1 finished! INFO @ Tue, 10 Dec 2019 14:52:26: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:52:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:52:26: #2 number of paired peaks: 115 WARNING @ Tue, 10 Dec 2019 14:52:26: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 10 Dec 2019 14:52:26: start model_add_line... INFO @ Tue, 10 Dec 2019 14:52:26: start X-correlation... INFO @ Tue, 10 Dec 2019 14:52:26: end of X-cor INFO @ Tue, 10 Dec 2019 14:52:26: #2 finished! INFO @ Tue, 10 Dec 2019 14:52:26: #2 predicted fragment length is 93 bps INFO @ Tue, 10 Dec 2019 14:52:26: #2 alternative fragment length(s) may be 2,93,455,526,536,575 bps INFO @ Tue, 10 Dec 2019 14:52:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.05_model.r INFO @ Tue, 10 Dec 2019 14:52:26: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:52:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:52:30: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:52:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.05_peaks.xls INFO @ Tue, 10 Dec 2019 14:52:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:52:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.05_summits.bed INFO @ Tue, 10 Dec 2019 14:52:32: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (3039 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:52:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.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 14:52:46: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:52:46: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:52:54: 1000000 INFO @ Tue, 10 Dec 2019 14:52:56: #1 tag size is determined as 41 bps INFO @ Tue, 10 Dec 2019 14:52:56: #1 tag size = 41 INFO @ Tue, 10 Dec 2019 14:52:56: #1 total tags in treatment: 1294039 INFO @ Tue, 10 Dec 2019 14:52:56: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:52:56: #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 14:52:56: #1 tags after filtering in treatment: 1294039 INFO @ Tue, 10 Dec 2019 14:52:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:52:56: #1 finished! INFO @ Tue, 10 Dec 2019 14:52:56: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:52:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:52:56: #2 number of paired peaks: 115 WARNING @ Tue, 10 Dec 2019 14:52:56: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 10 Dec 2019 14:52:56: start model_add_line... INFO @ Tue, 10 Dec 2019 14:52:56: start X-correlation... INFO @ Tue, 10 Dec 2019 14:52:56: end of X-cor INFO @ Tue, 10 Dec 2019 14:52:56: #2 finished! INFO @ Tue, 10 Dec 2019 14:52:56: #2 predicted fragment length is 93 bps INFO @ Tue, 10 Dec 2019 14:52:56: #2 alternative fragment length(s) may be 2,93,455,526,536,575 bps INFO @ Tue, 10 Dec 2019 14:52:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.10_model.r INFO @ Tue, 10 Dec 2019 14:52:56: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:52:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:53:00: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:53:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.10_peaks.xls INFO @ Tue, 10 Dec 2019 14:53:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:53:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.10_summits.bed INFO @ Tue, 10 Dec 2019 14:53:02: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (849 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:53:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.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 14:53:16: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:53:16: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:53:31: 1000000 INFO @ Tue, 10 Dec 2019 14:53:34: #1 tag size is determined as 41 bps INFO @ Tue, 10 Dec 2019 14:53:34: #1 tag size = 41 INFO @ Tue, 10 Dec 2019 14:53:34: #1 total tags in treatment: 1294039 INFO @ Tue, 10 Dec 2019 14:53:34: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:53:34: #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 14:53:35: #1 tags after filtering in treatment: 1294039 INFO @ Tue, 10 Dec 2019 14:53:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:53:35: #1 finished! INFO @ Tue, 10 Dec 2019 14:53:35: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:53:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:53:35: #2 number of paired peaks: 115 WARNING @ Tue, 10 Dec 2019 14:53:35: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 10 Dec 2019 14:53:35: start model_add_line... INFO @ Tue, 10 Dec 2019 14:53:35: start X-correlation... INFO @ Tue, 10 Dec 2019 14:53:35: end of X-cor INFO @ Tue, 10 Dec 2019 14:53:35: #2 finished! INFO @ Tue, 10 Dec 2019 14:53:35: #2 predicted fragment length is 93 bps INFO @ Tue, 10 Dec 2019 14:53:35: #2 alternative fragment length(s) may be 2,93,455,526,536,575 bps INFO @ Tue, 10 Dec 2019 14:53:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.20_model.r INFO @ Tue, 10 Dec 2019 14:53:35: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:53:35: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:53:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 10 Dec 2019 14:53:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.20_peaks.xls INFO @ Tue, 10 Dec 2019 14:53:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:53:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6932546/SRX6932546.20_summits.bed INFO @ Tue, 10 Dec 2019 14:53:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (88 records, 4 fields): 2 millis CompletedMACS2peakCalling