Job ID = 1293230 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T13:25:30 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' 2019-06-02T13:25:30 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/SRR1301065/SRR1301065.1' 2019-06-02T13:25:41 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1301065' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T13:25:41 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 2,717,950 reads read : 2,717,950 reads written : 2,717,950 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: 00:00:57 2717950 reads; of these: 2717950 (100.00%) were unpaired; of these: 77938 (2.87%) aligned 0 times 2332867 (85.83%) aligned exactly 1 time 307145 (11.30%) aligned >1 times 97.13% overall alignment rate Time searching: 00:00:57 Overall time: 00:00:57 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] 150759 / 2640012 = 0.0571 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 22:29:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.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 22:29:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:29:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:29:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.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 22:29:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:29:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:29:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.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 22:29:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:29:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:29:16: 1000000 INFO @ Sun, 02 Jun 2019 22:29:17: 1000000 INFO @ Sun, 02 Jun 2019 22:29:18: 1000000 INFO @ Sun, 02 Jun 2019 22:29:28: 2000000 INFO @ Sun, 02 Jun 2019 22:29:30: 2000000 INFO @ Sun, 02 Jun 2019 22:29:32: 2000000 INFO @ Sun, 02 Jun 2019 22:29:33: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:29:33: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:29:33: #1 total tags in treatment: 2489253 INFO @ Sun, 02 Jun 2019 22:29:33: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:29:33: #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 22:29:33: #1 tags after filtering in treatment: 2489253 INFO @ Sun, 02 Jun 2019 22:29:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:29:33: #1 finished! INFO @ Sun, 02 Jun 2019 22:29:33: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:29:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:29:34: #2 number of paired peaks: 2068 INFO @ Sun, 02 Jun 2019 22:29:34: start model_add_line... INFO @ Sun, 02 Jun 2019 22:29:34: start X-correlation... INFO @ Sun, 02 Jun 2019 22:29:34: end of X-cor INFO @ Sun, 02 Jun 2019 22:29:34: #2 finished! INFO @ Sun, 02 Jun 2019 22:29:34: #2 predicted fragment length is 140 bps INFO @ Sun, 02 Jun 2019 22:29:34: #2 alternative fragment length(s) may be 140 bps INFO @ Sun, 02 Jun 2019 22:29:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.10_model.r INFO @ Sun, 02 Jun 2019 22:29:34: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:29:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:29:36: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:29:36: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:29:36: #1 total tags in treatment: 2489253 INFO @ Sun, 02 Jun 2019 22:29:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:29:36: #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 22:29:36: #1 tags after filtering in treatment: 2489253 INFO @ Sun, 02 Jun 2019 22:29:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:29:36: #1 finished! INFO @ Sun, 02 Jun 2019 22:29:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:29:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:29:37: #2 number of paired peaks: 2068 INFO @ Sun, 02 Jun 2019 22:29:37: start model_add_line... INFO @ Sun, 02 Jun 2019 22:29:37: start X-correlation... INFO @ Sun, 02 Jun 2019 22:29:37: end of X-cor INFO @ Sun, 02 Jun 2019 22:29:37: #2 finished! INFO @ Sun, 02 Jun 2019 22:29:37: #2 predicted fragment length is 140 bps INFO @ Sun, 02 Jun 2019 22:29:37: #2 alternative fragment length(s) may be 140 bps INFO @ Sun, 02 Jun 2019 22:29:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.05_model.r INFO @ Sun, 02 Jun 2019 22:29:37: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:29:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:29:39: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:29:39: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:29:39: #1 total tags in treatment: 2489253 INFO @ Sun, 02 Jun 2019 22:29:39: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:29:39: #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 22:29:39: #1 tags after filtering in treatment: 2489253 INFO @ Sun, 02 Jun 2019 22:29:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:29:39: #1 finished! INFO @ Sun, 02 Jun 2019 22:29:39: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:29:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:29:39: #2 number of paired peaks: 2068 INFO @ Sun, 02 Jun 2019 22:29:39: start model_add_line... INFO @ Sun, 02 Jun 2019 22:29:39: start X-correlation... INFO @ Sun, 02 Jun 2019 22:29:40: end of X-cor INFO @ Sun, 02 Jun 2019 22:29:40: #2 finished! INFO @ Sun, 02 Jun 2019 22:29:40: #2 predicted fragment length is 140 bps INFO @ Sun, 02 Jun 2019 22:29:40: #2 alternative fragment length(s) may be 140 bps INFO @ Sun, 02 Jun 2019 22:29:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.20_model.r INFO @ Sun, 02 Jun 2019 22:29:40: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:29:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:29:43: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:29:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:29:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:29:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:29:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.10_summits.bed INFO @ Sun, 02 Jun 2019 22:29:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (712 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:29:49: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:29:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:29:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:29:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.05_summits.bed INFO @ Sun, 02 Jun 2019 22:29:50: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1976 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 02 Jun 2019 22:29:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:29:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:29:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX554717/SRX554717.20_summits.bed INFO @ Sun, 02 Jun 2019 22:29:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (152 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。