Job ID = 1292528 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T10:15:43 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' 2019-06-02T10:15:43 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/SRR1163608/SRR1163608.1' 2019-06-02T10:15:43 fasterq-dump.2.9.6 err: invalid accession 'SRR1163608' 2019-06-02T10:16:11 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' 2019-06-02T10:16:11 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/SRR1163608/SRR1163608.1' 2019-06-02T10:16:22 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR1163608', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 9,402,304 reads read : 9,402,304 reads written : 9,402,304 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: 00:01:42 9402304 reads; of these: 9402304 (100.00%) were unpaired; of these: 4480424 (47.65%) aligned 0 times 4168047 (44.33%) aligned exactly 1 time 753833 (8.02%) aligned >1 times 52.35% overall alignment rate Time searching: 00:01:42 Overall time: 00:01:42 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] 2907832 / 4921880 = 0.5908 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 19:20:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.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 19:20:55: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:20:55: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:20:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.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 19:20:55: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:20:55: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:20:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.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 19:20:55: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:20:55: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:21:03: 1000000 INFO @ Sun, 02 Jun 2019 19:21:04: 1000000 INFO @ Sun, 02 Jun 2019 19:21:04: 1000000 INFO @ Sun, 02 Jun 2019 19:21:11: 2000000 INFO @ Sun, 02 Jun 2019 19:21:11: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:21:11: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:21:11: #1 total tags in treatment: 2014048 INFO @ Sun, 02 Jun 2019 19:21:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:21:11: #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 19:21:11: #1 tags after filtering in treatment: 2014048 INFO @ Sun, 02 Jun 2019 19:21:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:21:11: #1 finished! INFO @ Sun, 02 Jun 2019 19:21:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:21:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:21:11: #2 number of paired peaks: 1564 INFO @ Sun, 02 Jun 2019 19:21:11: start model_add_line... INFO @ Sun, 02 Jun 2019 19:21:11: start X-correlation... INFO @ Sun, 02 Jun 2019 19:21:11: end of X-cor INFO @ Sun, 02 Jun 2019 19:21:11: #2 finished! INFO @ Sun, 02 Jun 2019 19:21:11: #2 predicted fragment length is 141 bps INFO @ Sun, 02 Jun 2019 19:21:11: #2 alternative fragment length(s) may be 141,592 bps INFO @ Sun, 02 Jun 2019 19:21:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.10_model.r INFO @ Sun, 02 Jun 2019 19:21:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:21:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:21:13: 2000000 INFO @ Sun, 02 Jun 2019 19:21:13: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:21:13: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:21:13: #1 total tags in treatment: 2014048 INFO @ Sun, 02 Jun 2019 19:21:13: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:21:13: #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 19:21:13: #1 tags after filtering in treatment: 2014048 INFO @ Sun, 02 Jun 2019 19:21:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:21:13: #1 finished! INFO @ Sun, 02 Jun 2019 19:21:13: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:21:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:21:13: 2000000 INFO @ Sun, 02 Jun 2019 19:21:14: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:21:14: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:21:14: #1 total tags in treatment: 2014048 INFO @ Sun, 02 Jun 2019 19:21:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:21:14: #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 19:21:14: #2 number of paired peaks: 1564 INFO @ Sun, 02 Jun 2019 19:21:14: start model_add_line... INFO @ Sun, 02 Jun 2019 19:21:14: start X-correlation... INFO @ Sun, 02 Jun 2019 19:21:14: #1 tags after filtering in treatment: 2014048 INFO @ Sun, 02 Jun 2019 19:21:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:21:14: #1 finished! INFO @ Sun, 02 Jun 2019 19:21:14: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:21:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:21:14: end of X-cor INFO @ Sun, 02 Jun 2019 19:21:14: #2 finished! INFO @ Sun, 02 Jun 2019 19:21:14: #2 predicted fragment length is 141 bps INFO @ Sun, 02 Jun 2019 19:21:14: #2 alternative fragment length(s) may be 141,592 bps INFO @ Sun, 02 Jun 2019 19:21:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.05_model.r INFO @ Sun, 02 Jun 2019 19:21:14: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:21:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:21:14: #2 number of paired peaks: 1564 INFO @ Sun, 02 Jun 2019 19:21:14: start model_add_line... INFO @ Sun, 02 Jun 2019 19:21:14: start X-correlation... INFO @ Sun, 02 Jun 2019 19:21:14: end of X-cor INFO @ Sun, 02 Jun 2019 19:21:14: #2 finished! INFO @ Sun, 02 Jun 2019 19:21:14: #2 predicted fragment length is 141 bps INFO @ Sun, 02 Jun 2019 19:21:14: #2 alternative fragment length(s) may be 141,592 bps INFO @ Sun, 02 Jun 2019 19:21:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.20_model.r INFO @ Sun, 02 Jun 2019 19:21:14: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:21:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:21:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:21:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:21:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:21:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:21:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:21:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.10_summits.bed INFO @ Sun, 02 Jun 2019 19:21:21: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (787 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:21:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:21:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:21:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.05_summits.bed INFO @ Sun, 02 Jun 2019 19:21:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2239 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:21:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:21:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:21:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466542/SRX466542.20_summits.bed INFO @ Sun, 02 Jun 2019 19:21:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (128 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。