Job ID = 1291660 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T07:10:21 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T07:10:21 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/sos/sra-pub-run-1/SRR3535766/SRR3535766.1' 2019-06-02T07:10:31 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR3535766' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 6,113,677 reads read : 6,113,677 reads written : 6,113,677 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:01:27 6113677 reads; of these: 6113677 (100.00%) were unpaired; of these: 523722 (8.57%) aligned 0 times 4711377 (77.06%) aligned exactly 1 time 878578 (14.37%) aligned >1 times 91.43% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1905306 / 5589955 = 0.3408 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 @ Sun, 02 Jun 2019 16:15:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 16:15:01: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:15:01: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:15:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 16:15:01: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:15:01: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:15:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 16:15:01: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:15:01: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:15:11: 1000000 INFO @ Sun, 02 Jun 2019 16:15:11: 1000000 INFO @ Sun, 02 Jun 2019 16:15:12: 1000000 INFO @ Sun, 02 Jun 2019 16:15:21: 2000000 INFO @ Sun, 02 Jun 2019 16:15:21: 2000000 INFO @ Sun, 02 Jun 2019 16:15:23: 2000000 INFO @ Sun, 02 Jun 2019 16:15:30: 3000000 INFO @ Sun, 02 Jun 2019 16:15:31: 3000000 INFO @ Sun, 02 Jun 2019 16:15:34: 3000000 INFO @ Sun, 02 Jun 2019 16:15:37: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:15:37: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:15:37: #1 total tags in treatment: 3684649 INFO @ Sun, 02 Jun 2019 16:15:37: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:15:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:15:37: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:15:37: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:15:37: #1 total tags in treatment: 3684649 INFO @ Sun, 02 Jun 2019 16:15:37: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:15:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:15:37: #1 tags after filtering in treatment: 3684649 INFO @ Sun, 02 Jun 2019 16:15:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:15:37: #1 finished! INFO @ Sun, 02 Jun 2019 16:15:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:15:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:15:37: #1 tags after filtering in treatment: 3684649 INFO @ Sun, 02 Jun 2019 16:15:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:15:37: #1 finished! INFO @ Sun, 02 Jun 2019 16:15:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:15:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:15:37: #2 number of paired peaks: 3061 INFO @ Sun, 02 Jun 2019 16:15:37: start model_add_line... INFO @ Sun, 02 Jun 2019 16:15:37: start X-correlation... INFO @ Sun, 02 Jun 2019 16:15:37: #2 number of paired peaks: 3061 INFO @ Sun, 02 Jun 2019 16:15:37: start model_add_line... INFO @ Sun, 02 Jun 2019 16:15:37: end of X-cor INFO @ Sun, 02 Jun 2019 16:15:37: #2 finished! INFO @ Sun, 02 Jun 2019 16:15:37: #2 predicted fragment length is 230 bps INFO @ Sun, 02 Jun 2019 16:15:37: #2 alternative fragment length(s) may be 230 bps INFO @ Sun, 02 Jun 2019 16:15:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.10_model.r INFO @ Sun, 02 Jun 2019 16:15:37: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:15:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:15:37: start X-correlation... INFO @ Sun, 02 Jun 2019 16:15:37: end of X-cor INFO @ Sun, 02 Jun 2019 16:15:37: #2 finished! INFO @ Sun, 02 Jun 2019 16:15:37: #2 predicted fragment length is 230 bps INFO @ Sun, 02 Jun 2019 16:15:37: #2 alternative fragment length(s) may be 230 bps INFO @ Sun, 02 Jun 2019 16:15:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.05_model.r INFO @ Sun, 02 Jun 2019 16:15:37: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:15:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:15:41: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:15:41: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:15:41: #1 total tags in treatment: 3684649 INFO @ Sun, 02 Jun 2019 16:15:41: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:15:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:15:41: #1 tags after filtering in treatment: 3684649 INFO @ Sun, 02 Jun 2019 16:15:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:15:41: #1 finished! INFO @ Sun, 02 Jun 2019 16:15:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:15:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:15:42: #2 number of paired peaks: 3061 INFO @ Sun, 02 Jun 2019 16:15:42: start model_add_line... INFO @ Sun, 02 Jun 2019 16:15:42: start X-correlation... INFO @ Sun, 02 Jun 2019 16:15:42: end of X-cor INFO @ Sun, 02 Jun 2019 16:15:42: #2 finished! INFO @ Sun, 02 Jun 2019 16:15:42: #2 predicted fragment length is 230 bps INFO @ Sun, 02 Jun 2019 16:15:42: #2 alternative fragment length(s) may be 230 bps INFO @ Sun, 02 Jun 2019 16:15:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.20_model.r INFO @ Sun, 02 Jun 2019 16:15:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:15:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:15:52: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:15:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:15:56: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:15:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:15:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:15:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.05_summits.bed INFO @ Sun, 02 Jun 2019 16:15:58: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (3890 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:15:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:15:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:15:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.10_summits.bed INFO @ Sun, 02 Jun 2019 16:15:59: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2621 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:16:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:16:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:16:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769988/SRX1769988.20_summits.bed INFO @ Sun, 02 Jun 2019 16:16:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1622 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。