Job ID = 2010519 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T13:49:49 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' 2019-07-05T13:49:49 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/traces/sra15/SRR/001011/SRR1035324' 2019-07-05T13:49:53 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' 2019-07-05T13:49:53 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/traces/sra15/SRR/001011/SRR1035324' 2019-07-05T13:49:53 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1035324' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T13:49:58 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' 2019-07-05T13:49:58 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/traces/sra15/SRR/001011/SRR1035324' 2019-07-05T13:49:58 fasterq-dump.2.9.6 err: invalid accession 'SRR1035324' 2019-07-05T13:50:13 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' 2019-07-05T13:50:13 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/traces/sra15/SRR/001011/SRR1035324' 2019-07-05T13:50:13 fasterq-dump.2.9.6 err: invalid accession 'SRR1035324' 2019-07-05T13:50:28 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' 2019-07-05T13:50:28 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/traces/sra15/SRR/001011/SRR1035324' 2019-07-05T13:50:28 fasterq-dump.2.9.6 err: invalid accession 'SRR1035324' 2019-07-05T14:05:02 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 ) 2019-07-05T14:05:02 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 : 13,560,806 reads read : 27,121,612 reads written : 27,121,612 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:57 13560806 reads; of these: 13560806 (100.00%) were paired; of these: 6609342 (48.74%) aligned concordantly 0 times 4200035 (30.97%) aligned concordantly exactly 1 time 2751429 (20.29%) aligned concordantly >1 times ---- 6609342 pairs aligned concordantly 0 times; of these: 84304 (1.28%) aligned discordantly 1 time ---- 6525038 pairs aligned 0 times concordantly or discordantly; of these: 13050076 mates make up the pairs; of these: 12569522 (96.32%) aligned 0 times 245540 (1.88%) aligned exactly 1 time 235014 (1.80%) aligned >1 times 53.65% overall alignment rate Time searching: 00:07:57 Overall time: 00:07:57 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 2812044 / 7027740 = 0.4001 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 23:20:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 23:20:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:20:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:20:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 23:20:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:20:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:20:39: 1000000 INFO @ Fri, 05 Jul 2019 23:20:40: 1000000 INFO @ Fri, 05 Jul 2019 23:20:46: 2000000 INFO @ Fri, 05 Jul 2019 23:20:47: 2000000 INFO @ Fri, 05 Jul 2019 23:20:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 23:20:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:20:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:20:53: 3000000 INFO @ Fri, 05 Jul 2019 23:20:54: 3000000 INFO @ Fri, 05 Jul 2019 23:20:55: 1000000 INFO @ Fri, 05 Jul 2019 23:21:00: 4000000 INFO @ Fri, 05 Jul 2019 23:21:01: 4000000 INFO @ Fri, 05 Jul 2019 23:21:02: 2000000 INFO @ Fri, 05 Jul 2019 23:21:06: 5000000 INFO @ Fri, 05 Jul 2019 23:21:08: 5000000 INFO @ Fri, 05 Jul 2019 23:21:08: 3000000 INFO @ Fri, 05 Jul 2019 23:21:13: 6000000 INFO @ Fri, 05 Jul 2019 23:21:15: 6000000 INFO @ Fri, 05 Jul 2019 23:21:15: 4000000 INFO @ Fri, 05 Jul 2019 23:21:20: 7000000 INFO @ Fri, 05 Jul 2019 23:21:21: 7000000 INFO @ Fri, 05 Jul 2019 23:21:22: 5000000 INFO @ Fri, 05 Jul 2019 23:21:26: 8000000 INFO @ Fri, 05 Jul 2019 23:21:28: 8000000 INFO @ Fri, 05 Jul 2019 23:21:29: 6000000 INFO @ Fri, 05 Jul 2019 23:21:32: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:21:32: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:21:32: #1 total tags in treatment: 4153355 INFO @ Fri, 05 Jul 2019 23:21:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:21:32: #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 23:21:32: #1 tags after filtering in treatment: 2442024 INFO @ Fri, 05 Jul 2019 23:21:32: #1 Redundant rate of treatment: 0.41 INFO @ Fri, 05 Jul 2019 23:21:32: #1 finished! INFO @ Fri, 05 Jul 2019 23:21:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:21:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:21:33: #2 number of paired peaks: 450 WARNING @ Fri, 05 Jul 2019 23:21:33: Fewer paired peaks (450) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 450 pairs to build model! INFO @ Fri, 05 Jul 2019 23:21:33: start model_add_line... INFO @ Fri, 05 Jul 2019 23:21:33: start X-correlation... INFO @ Fri, 05 Jul 2019 23:21:33: end of X-cor INFO @ Fri, 05 Jul 2019 23:21:33: #2 finished! INFO @ Fri, 05 Jul 2019 23:21:33: #2 predicted fragment length is 176 bps INFO @ Fri, 05 Jul 2019 23:21:33: #2 alternative fragment length(s) may be 3,176 bps INFO @ Fri, 05 Jul 2019 23:21:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.05_model.r INFO @ Fri, 05 Jul 2019 23:21:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:21:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:21:34: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:21:34: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:21:34: #1 total tags in treatment: 4153355 INFO @ Fri, 05 Jul 2019 23:21:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:21:34: #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 23:21:34: #1 tags after filtering in treatment: 2442024 INFO @ Fri, 05 Jul 2019 23:21:34: #1 Redundant rate of treatment: 0.41 INFO @ Fri, 05 Jul 2019 23:21:34: #1 finished! INFO @ Fri, 05 Jul 2019 23:21:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:21:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:21:34: #2 number of paired peaks: 450 WARNING @ Fri, 05 Jul 2019 23:21:34: Fewer paired peaks (450) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 450 pairs to build model! INFO @ Fri, 05 Jul 2019 23:21:34: start model_add_line... INFO @ Fri, 05 Jul 2019 23:21:34: start X-correlation... INFO @ Fri, 05 Jul 2019 23:21:34: end of X-cor INFO @ Fri, 05 Jul 2019 23:21:34: #2 finished! INFO @ Fri, 05 Jul 2019 23:21:34: #2 predicted fragment length is 176 bps INFO @ Fri, 05 Jul 2019 23:21:34: #2 alternative fragment length(s) may be 3,176 bps INFO @ Fri, 05 Jul 2019 23:21:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.10_model.r INFO @ Fri, 05 Jul 2019 23:21:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:21:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:21:35: 7000000 INFO @ Fri, 05 Jul 2019 23:21:42: 8000000 INFO @ Fri, 05 Jul 2019 23:21:43: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:21:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:21:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:21:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:21:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.05_summits.bed INFO @ Fri, 05 Jul 2019 23:21:46: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (609 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:21:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:21:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:21:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.10_summits.bed INFO @ Fri, 05 Jul 2019 23:21:47: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (551 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:21:48: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:21:48: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:21:48: #1 total tags in treatment: 4153355 INFO @ Fri, 05 Jul 2019 23:21:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:21:48: #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 23:21:48: #1 tags after filtering in treatment: 2442024 INFO @ Fri, 05 Jul 2019 23:21:48: #1 Redundant rate of treatment: 0.41 INFO @ Fri, 05 Jul 2019 23:21:48: #1 finished! INFO @ Fri, 05 Jul 2019 23:21:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:21:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:21:48: #2 number of paired peaks: 450 WARNING @ Fri, 05 Jul 2019 23:21:48: Fewer paired peaks (450) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 450 pairs to build model! INFO @ Fri, 05 Jul 2019 23:21:48: start model_add_line... INFO @ Fri, 05 Jul 2019 23:21:48: start X-correlation... INFO @ Fri, 05 Jul 2019 23:21:48: end of X-cor INFO @ Fri, 05 Jul 2019 23:21:48: #2 finished! INFO @ Fri, 05 Jul 2019 23:21:48: #2 predicted fragment length is 176 bps INFO @ Fri, 05 Jul 2019 23:21:48: #2 alternative fragment length(s) may be 3,176 bps INFO @ Fri, 05 Jul 2019 23:21:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.20_model.r INFO @ Fri, 05 Jul 2019 23:21:48: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:21:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:21:58: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:22:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:22:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:22:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381223/SRX381223.20_summits.bed INFO @ Fri, 05 Jul 2019 23:22:01: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (562 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。