Job ID = 2640577 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:48:39 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 ) 2019-08-24T08:48:39 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 : 3,614,647 reads read : 7,229,294 reads written : 3,614,647 reads 0-length : 3,614,647 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:13 3614647 reads; of these: 3614647 (100.00%) were unpaired; of these: 300194 (8.30%) aligned 0 times 2541451 (70.31%) aligned exactly 1 time 773002 (21.39%) aligned >1 times 91.70% overall alignment rate Time searching: 00:03:14 Overall time: 00:03:14 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 88626 / 3314453 = 0.0267 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:53:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.bam'] # control file = None # effective genome size = 2.15e+09 # 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 17:53:46: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:53:46: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:53:53: 1000000 INFO @ Sat, 24 Aug 2019 17:53:59: 2000000 INFO @ Sat, 24 Aug 2019 17:54:06: 3000000 INFO @ Sat, 24 Aug 2019 17:54:08: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:54:08: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:54:08: #1 total tags in treatment: 3225827 INFO @ Sat, 24 Aug 2019 17:54:08: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:54:08: #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 17:54:08: #1 tags after filtering in treatment: 3225503 INFO @ Sat, 24 Aug 2019 17:54:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:54:08: #1 finished! INFO @ Sat, 24 Aug 2019 17:54:08: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:54:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:54:12: #2 number of paired peaks: 60631 INFO @ Sat, 24 Aug 2019 17:54:12: start model_add_line... INFO @ Sat, 24 Aug 2019 17:54:13: start X-correlation... INFO @ Sat, 24 Aug 2019 17:54:13: end of X-cor INFO @ Sat, 24 Aug 2019 17:54:13: #2 finished! INFO @ Sat, 24 Aug 2019 17:54:13: #2 predicted fragment length is 229 bps INFO @ Sat, 24 Aug 2019 17:54:13: #2 alternative fragment length(s) may be 229 bps INFO @ Sat, 24 Aug 2019 17:54:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.05_model.r INFO @ Sat, 24 Aug 2019 17:54:13: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:54:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:54:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.bam'] # control file = None # effective genome size = 2.15e+09 # 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 17:54:16: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:54:16: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:54:23: 1000000 INFO @ Sat, 24 Aug 2019 17:54:23: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:54:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:54:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:54:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.05_summits.bed INFO @ Sat, 24 Aug 2019 17:54:28: Done! pass1 - making usageList (31 chroms): 2 millis pass2 - checking and writing primary data (1588 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:54:29: 2000000 INFO @ Sat, 24 Aug 2019 17:54:36: 3000000 INFO @ Sat, 24 Aug 2019 17:54:37: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:54:37: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:54:37: #1 total tags in treatment: 3225827 INFO @ Sat, 24 Aug 2019 17:54:37: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:54:37: #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 17:54:38: #1 tags after filtering in treatment: 3225503 INFO @ Sat, 24 Aug 2019 17:54:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:54:38: #1 finished! INFO @ Sat, 24 Aug 2019 17:54:38: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:54:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:54:42: #2 number of paired peaks: 60631 INFO @ Sat, 24 Aug 2019 17:54:42: start model_add_line... INFO @ Sat, 24 Aug 2019 17:54:42: start X-correlation... INFO @ Sat, 24 Aug 2019 17:54:42: end of X-cor INFO @ Sat, 24 Aug 2019 17:54:42: #2 finished! INFO @ Sat, 24 Aug 2019 17:54:42: #2 predicted fragment length is 229 bps INFO @ Sat, 24 Aug 2019 17:54:42: #2 alternative fragment length(s) may be 229 bps INFO @ Sat, 24 Aug 2019 17:54:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.10_model.r INFO @ Sat, 24 Aug 2019 17:54:42: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:54:42: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:54:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.bam'] # control file = None # effective genome size = 2.15e+09 # 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 17:54:46: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:54:46: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:54:53: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:54:53: 1000000 INFO @ Sat, 24 Aug 2019 17:54:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:54:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:54:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.10_summits.bed INFO @ Sat, 24 Aug 2019 17:54:58: Done! pass1 - making usageList (21 chroms): 1 millis pass2 - checking and writing primary data (219 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:55:01: 2000000 INFO @ Sat, 24 Aug 2019 17:55:08: 3000000 INFO @ Sat, 24 Aug 2019 17:55:10: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:55:10: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:55:10: #1 total tags in treatment: 3225827 INFO @ Sat, 24 Aug 2019 17:55:10: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:55:10: #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 17:55:10: #1 tags after filtering in treatment: 3225503 INFO @ Sat, 24 Aug 2019 17:55:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:55:10: #1 finished! INFO @ Sat, 24 Aug 2019 17:55:10: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:55:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:55:15: #2 number of paired peaks: 60631 INFO @ Sat, 24 Aug 2019 17:55:15: start model_add_line... INFO @ Sat, 24 Aug 2019 17:55:15: start X-correlation... INFO @ Sat, 24 Aug 2019 17:55:15: end of X-cor INFO @ Sat, 24 Aug 2019 17:55:15: #2 finished! INFO @ Sat, 24 Aug 2019 17:55:15: #2 predicted fragment length is 229 bps INFO @ Sat, 24 Aug 2019 17:55:15: #2 alternative fragment length(s) may be 229 bps INFO @ Sat, 24 Aug 2019 17:55:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.20_model.r INFO @ Sat, 24 Aug 2019 17:55:15: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:55:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:55:25: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:55:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:55:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:55:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375020/SRX5375020.20_summits.bed INFO @ Sat, 24 Aug 2019 17:55:30: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (33 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。