Job ID = 2003710 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T04:33:37 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T04:33:37 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-1/SRR1267404/SRR1267404.2' 2019-07-05T04:33:42 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T04:33:42 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-1/SRR1267404/SRR1267404.2' 2019-07-05T04:33:42 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR1267404', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T04:33:46 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T04:33:46 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-1/SRR1267404/SRR1267404.2' 2019-07-05T04:33:46 fasterq-dump.2.9.6 err: invalid accession 'SRR1267404' 2019-07-05T04:34:02 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T04:34:02 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-1/SRR1267404/SRR1267404.2' 2019-07-05T04:34:02 fasterq-dump.2.9.6 err: invalid accession 'SRR1267404' 2019-07-05T04:34:16 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T04:34:16 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-1/SRR1267404/SRR1267404.2' 2019-07-05T04:34:16 fasterq-dump.2.9.6 err: invalid accession 'SRR1267404' 2019-07-05T04:34:31 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T04:34:31 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-1/SRR1267404/SRR1267404.2' 2019-07-05T04:34:31 fasterq-dump.2.9.6 err: invalid accession 'SRR1267404' spots read : 12,494,570 reads read : 12,494,570 reads written : 12,494,570 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1267404.sra.cache’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:01 12494570 reads; of these: 12494570 (100.00%) were unpaired; of these: 1739088 (13.92%) aligned 0 times 7702162 (61.64%) aligned exactly 1 time 3053320 (24.44%) aligned >1 times 86.08% overall alignment rate Time searching: 00:09:04 Overall time: 00:09:04 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_sort_core] merging from 8 files... [bam_rmdupse_core] 9273791 / 10755482 = 0.8622 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 @ Fri, 05 Jul 2019 13:50:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.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 @ Fri, 05 Jul 2019 13:50:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:50:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:50:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.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 @ Fri, 05 Jul 2019 13:50:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:50:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:50:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.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 @ Fri, 05 Jul 2019 13:50:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:50:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:50:32: 1000000 INFO @ Fri, 05 Jul 2019 13:50:32: 1000000 INFO @ Fri, 05 Jul 2019 13:50:33: 1000000 INFO @ Fri, 05 Jul 2019 13:50:37: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:50:37: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:50:37: #1 total tags in treatment: 1481691 INFO @ Fri, 05 Jul 2019 13:50:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:50:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 13:50:37: #1 tags after filtering in treatment: 1481340 INFO @ Fri, 05 Jul 2019 13:50:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:50:37: #1 finished! INFO @ Fri, 05 Jul 2019 13:50:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:50:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:50:37: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:50:37: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:50:37: #1 total tags in treatment: 1481691 INFO @ Fri, 05 Jul 2019 13:50:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:50:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 13:50:37: #1 tags after filtering in treatment: 1481340 INFO @ Fri, 05 Jul 2019 13:50:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:50:37: #1 finished! INFO @ Fri, 05 Jul 2019 13:50:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:50:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:50:38: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:50:38: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:50:38: #1 total tags in treatment: 1481691 INFO @ Fri, 05 Jul 2019 13:50:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:50:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 13:50:38: #1 tags after filtering in treatment: 1481340 INFO @ Fri, 05 Jul 2019 13:50:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:50:38: #1 finished! INFO @ Fri, 05 Jul 2019 13:50:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:50:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:50:42: #2 number of paired peaks: 69433 INFO @ Fri, 05 Jul 2019 13:50:42: start model_add_line... INFO @ Fri, 05 Jul 2019 13:50:42: start X-correlation... INFO @ Fri, 05 Jul 2019 13:50:42: end of X-cor INFO @ Fri, 05 Jul 2019 13:50:42: #2 finished! INFO @ Fri, 05 Jul 2019 13:50:42: #2 predicted fragment length is 295 bps INFO @ Fri, 05 Jul 2019 13:50:42: #2 alternative fragment length(s) may be 295 bps INFO @ Fri, 05 Jul 2019 13:50:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.05_model.r INFO @ Fri, 05 Jul 2019 13:50:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:50:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:50:42: #2 number of paired peaks: 69433 INFO @ Fri, 05 Jul 2019 13:50:42: start model_add_line... INFO @ Fri, 05 Jul 2019 13:50:42: start X-correlation... INFO @ Fri, 05 Jul 2019 13:50:42: end of X-cor INFO @ Fri, 05 Jul 2019 13:50:42: #2 finished! INFO @ Fri, 05 Jul 2019 13:50:42: #2 predicted fragment length is 295 bps INFO @ Fri, 05 Jul 2019 13:50:42: #2 alternative fragment length(s) may be 295 bps INFO @ Fri, 05 Jul 2019 13:50:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.10_model.r INFO @ Fri, 05 Jul 2019 13:50:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:50:42: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 13:50:43: #2 number of paired peaks: 69433 INFO @ Fri, 05 Jul 2019 13:50:43: start model_add_line... INFO @ Fri, 05 Jul 2019 13:50:43: start X-correlation... INFO @ Fri, 05 Jul 2019 13:50:43: end of X-cor INFO @ Fri, 05 Jul 2019 13:50:43: #2 finished! INFO @ Fri, 05 Jul 2019 13:50:43: #2 predicted fragment length is 295 bps INFO @ Fri, 05 Jul 2019 13:50:43: #2 alternative fragment length(s) may be 295 bps INFO @ Fri, 05 Jul 2019 13:50:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.20_model.r INFO @ Fri, 05 Jul 2019 13:50:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:50:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 13:50:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:50:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:50:48: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:50:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.05_peaks.xls INFO @ Fri, 05 Jul 2019 13:50:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:50:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.05_summits.bed INFO @ Fri, 05 Jul 2019 13:50:50: Done! INFO @ Fri, 05 Jul 2019 13:50:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.10_peaks.xls INFO @ Fri, 05 Jul 2019 13:50:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:50:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.10_summits.bed INFO @ Fri, 05 Jul 2019 13:50:50: Done! pass1 - making usageList (27 chroms): 2 millis pass2 - checking and writing primary data (251 records, 4 fields): 4 millis pass1 - making usageList (23 chroms): 2 millis pass2 - checking and writing primary data (120 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 13:50:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.20_peaks.xls INFO @ Fri, 05 Jul 2019 13:50:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:50:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX530450/SRX530450.20_summits.bed INFO @ Fri, 05 Jul 2019 13:50:51: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (41 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling