Job ID = 2010512 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 fasterq-dump.2.9.6 err: connection busy while validating within network system module - Failed to KHttpFileRead('https://sra-download.ncbi.nlm.nih.gov/traces/sra15/SRR/001011/SRR1035318' (), 32768) from '172.19.7.77' 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 fasterq-dump.2.9.6 err: connection busy while validating within network system module - Failed to KHttpFileRead('https://sra-download.ncbi.nlm.nih.gov/traces/sra15/SRR/001011/SRR1035318' (), 32768) from '172.19.7.77' 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 fasterq-dump.2.9.6 err: connection busy while validating within network system module - Failed to KHttpFileRead('https://sra-download.ncbi.nlm.nih.gov/traces/sra15/SRR/001011/SRR1035318' (), 32768) from '172.19.7.77' 2019-07-05T13:49:39 fasterq-dump.2.9.6 err: cmn_iter.c cmn_read_String( #1769473 ).VCursorCellDataDirect() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T13:49:39 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' 2019-07-05T13:49:39 fasterq-dump.2.9.6 err: connection busy while validating within network system module - Failed to KHttpFileRead('https://sra-download.ncbi.nlm.nih.gov/traces/sra15/SRR/001011/SRR1035318' (), 32768) from '172.19.7.77' 2019-07-05T13:49:39 fasterq-dump.2.9.6 err: cmn_iter.c cmn_read_String( #3522561 ).VCursorCellDataDirect() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) spots read : 10,550,270 reads read : 21,100,540 reads written : 21,100,540 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: 00:06:11 10550270 reads; of these: 10550270 (100.00%) were paired; of these: 4766188 (45.18%) aligned concordantly 0 times 3379950 (32.04%) aligned concordantly exactly 1 time 2404132 (22.79%) aligned concordantly >1 times ---- 4766188 pairs aligned concordantly 0 times; of these: 51002 (1.07%) aligned discordantly 1 time ---- 4715186 pairs aligned 0 times concordantly or discordantly; of these: 9430372 mates make up the pairs; of these: 9107964 (96.58%) aligned 0 times 157812 (1.67%) aligned exactly 1 time 164596 (1.75%) aligned >1 times 56.84% overall alignment rate Time searching: 00:06:11 Overall time: 00:06:11 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] 2458707 / 5831215 = 0.4216 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 23:23:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.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 23:23:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:23:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:23:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.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 23:23:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:23:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:23:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.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 23:23:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:23:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:23:34: 1000000 INFO @ Fri, 05 Jul 2019 23:23:35: 1000000 INFO @ Fri, 05 Jul 2019 23:23:36: 1000000 INFO @ Fri, 05 Jul 2019 23:23:41: 2000000 INFO @ Fri, 05 Jul 2019 23:23:42: 2000000 INFO @ Fri, 05 Jul 2019 23:23:45: 2000000 INFO @ Fri, 05 Jul 2019 23:23:49: 3000000 INFO @ Fri, 05 Jul 2019 23:23:49: 3000000 INFO @ Fri, 05 Jul 2019 23:23:54: 3000000 INFO @ Fri, 05 Jul 2019 23:23:56: 4000000 INFO @ Fri, 05 Jul 2019 23:23:56: 4000000 INFO @ Fri, 05 Jul 2019 23:24:03: 4000000 INFO @ Fri, 05 Jul 2019 23:24:03: 5000000 INFO @ Fri, 05 Jul 2019 23:24:04: 5000000 INFO @ Fri, 05 Jul 2019 23:24:10: 6000000 INFO @ Fri, 05 Jul 2019 23:24:12: 6000000 INFO @ Fri, 05 Jul 2019 23:24:12: 5000000 INFO @ Fri, 05 Jul 2019 23:24:17: 7000000 INFO @ Fri, 05 Jul 2019 23:24:17: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:24:17: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:24:17: #1 total tags in treatment: 3332029 INFO @ Fri, 05 Jul 2019 23:24:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:24:17: #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 23:24:17: #1 tags after filtering in treatment: 2144577 INFO @ Fri, 05 Jul 2019 23:24:17: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 05 Jul 2019 23:24:17: #1 finished! INFO @ Fri, 05 Jul 2019 23:24:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:24:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:24:17: #2 number of paired peaks: 172 WARNING @ Fri, 05 Jul 2019 23:24:17: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Fri, 05 Jul 2019 23:24:17: start model_add_line... INFO @ Fri, 05 Jul 2019 23:24:17: start X-correlation... INFO @ Fri, 05 Jul 2019 23:24:17: end of X-cor INFO @ Fri, 05 Jul 2019 23:24:17: #2 finished! INFO @ Fri, 05 Jul 2019 23:24:17: #2 predicted fragment length is 193 bps INFO @ Fri, 05 Jul 2019 23:24:17: #2 alternative fragment length(s) may be 4,193 bps INFO @ Fri, 05 Jul 2019 23:24:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.20_model.r INFO @ Fri, 05 Jul 2019 23:24:19: 7000000 INFO @ Fri, 05 Jul 2019 23:24:19: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:24:19: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:24:19: #1 total tags in treatment: 3332029 INFO @ Fri, 05 Jul 2019 23:24:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:24:19: #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 23:24:19: #1 tags after filtering in treatment: 2144577 INFO @ Fri, 05 Jul 2019 23:24:19: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 05 Jul 2019 23:24:19: #1 finished! INFO @ Fri, 05 Jul 2019 23:24:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:24:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:24:20: #2 number of paired peaks: 172 WARNING @ Fri, 05 Jul 2019 23:24:20: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Fri, 05 Jul 2019 23:24:20: start model_add_line... INFO @ Fri, 05 Jul 2019 23:24:20: start X-correlation... INFO @ Fri, 05 Jul 2019 23:24:20: end of X-cor INFO @ Fri, 05 Jul 2019 23:24:20: #2 finished! INFO @ Fri, 05 Jul 2019 23:24:20: #2 predicted fragment length is 193 bps INFO @ Fri, 05 Jul 2019 23:24:20: #2 alternative fragment length(s) may be 4,193 bps INFO @ Fri, 05 Jul 2019 23:24:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.05_model.r INFO @ Fri, 05 Jul 2019 23:24:21: 6000000 INFO @ Fri, 05 Jul 2019 23:24:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:24:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:24:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:24:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:24:28: 7000000 INFO @ Fri, 05 Jul 2019 23:24:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:24:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:24:28: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:24:28: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:24:28: #1 total tags in treatment: 3332029 INFO @ Fri, 05 Jul 2019 23:24:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:24:28: #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 23:24:28: #1 tags after filtering in treatment: 2144577 INFO @ Fri, 05 Jul 2019 23:24:28: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 05 Jul 2019 23:24:28: #1 finished! INFO @ Fri, 05 Jul 2019 23:24:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:24:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:24:29: #2 number of paired peaks: 172 WARNING @ Fri, 05 Jul 2019 23:24:29: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Fri, 05 Jul 2019 23:24:29: start model_add_line... INFO @ Fri, 05 Jul 2019 23:24:29: start X-correlation... INFO @ Fri, 05 Jul 2019 23:24:29: end of X-cor INFO @ Fri, 05 Jul 2019 23:24:29: #2 finished! INFO @ Fri, 05 Jul 2019 23:24:29: #2 predicted fragment length is 193 bps INFO @ Fri, 05 Jul 2019 23:24:29: #2 alternative fragment length(s) may be 4,193 bps INFO @ Fri, 05 Jul 2019 23:24:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.10_model.r INFO @ Fri, 05 Jul 2019 23:24:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:24:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:24:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:24:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:24:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.20_summits.bed INFO @ Fri, 05 Jul 2019 23:24:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:24:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:24:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.05_summits.bed INFO @ Fri, 05 Jul 2019 23:24:31: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (476 records, 4 fields): 85 millis INFO @ Fri, 05 Jul 2019 23:24:31: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (337 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:24:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:24:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:24:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:24:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381217/SRX381217.10_summits.bed INFO @ Fri, 05 Jul 2019 23:24:39: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (385 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。