Job ID = 2007953 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:40:37 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' 2019-07-05T07:40:37 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-2/ERR506389/ERR506389.1' 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_db_type().VDBManagerOpenDBRead( 'ERR506389' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: invalid accession 'ERR506389' 2019-07-05T07:40:52 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' 2019-07-05T07:40:52 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-2/ERR506389/ERR506389.1' 2019-07-05T07:40:52 fasterq-dump.2.9.6 err: invalid accession 'ERR506389' 2019-07-05T07:41:07 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' 2019-07-05T07:41:07 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-2/ERR506389/ERR506389.1' 2019-07-05T07:41:07 fasterq-dump.2.9.6 err: invalid accession 'ERR506389' 2019-07-05T07:41:22 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' 2019-07-05T07:41:22 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-2/ERR506389/ERR506389.1' 2019-07-05T07:41:22 fasterq-dump.2.9.6 err: invalid accession 'ERR506389' spots read : 1,768,730 reads read : 3,537,460 reads written : 3,537,460 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: 00:02:10 1768730 reads; of these: 1768730 (100.00%) were paired; of these: 197709 (11.18%) aligned concordantly 0 times 1441157 (81.48%) aligned concordantly exactly 1 time 129864 (7.34%) aligned concordantly >1 times ---- 197709 pairs aligned concordantly 0 times; of these: 49005 (24.79%) aligned discordantly 1 time ---- 148704 pairs aligned 0 times concordantly or discordantly; of these: 297408 mates make up the pairs; of these: 263524 (88.61%) aligned 0 times 20357 (6.84%) aligned exactly 1 time 13527 (4.55%) aligned >1 times 92.55% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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_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] 100152 / 1610041 = 0.0622 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 16:53:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.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 16:53:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:53:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:53:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.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 16:53:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:53:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:53:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.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 16:53:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:53:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:53:36: 1000000 INFO @ Fri, 05 Jul 2019 16:53:37: 1000000 INFO @ Fri, 05 Jul 2019 16:53:37: 1000000 INFO @ Fri, 05 Jul 2019 16:53:46: 2000000 INFO @ Fri, 05 Jul 2019 16:53:47: 2000000 INFO @ Fri, 05 Jul 2019 16:53:49: 2000000 INFO @ Fri, 05 Jul 2019 16:53:55: 3000000 INFO @ Fri, 05 Jul 2019 16:53:56: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:56: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:56: #1 total tags in treatment: 1472479 INFO @ Fri, 05 Jul 2019 16:53:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:56: #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 16:53:56: #1 tags after filtering in treatment: 1386974 INFO @ Fri, 05 Jul 2019 16:53:56: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 05 Jul 2019 16:53:56: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:56: #2 number of paired peaks: 177 WARNING @ Fri, 05 Jul 2019 16:53:56: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Fri, 05 Jul 2019 16:53:56: start model_add_line... INFO @ Fri, 05 Jul 2019 16:53:56: start X-correlation... INFO @ Fri, 05 Jul 2019 16:53:56: end of X-cor INFO @ Fri, 05 Jul 2019 16:53:56: #2 finished! INFO @ Fri, 05 Jul 2019 16:53:56: #2 predicted fragment length is 213 bps INFO @ Fri, 05 Jul 2019 16:53:56: #2 alternative fragment length(s) may be 1,29,65,102,129,148,189,213,255,278,300,320,331,366,395,411,452,480,517,543,587 bps INFO @ Fri, 05 Jul 2019 16:53:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.20_model.r INFO @ Fri, 05 Jul 2019 16:53:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:53:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:53:58: 3000000 INFO @ Fri, 05 Jul 2019 16:53:58: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:58: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:58: #1 total tags in treatment: 1472479 INFO @ Fri, 05 Jul 2019 16:53:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:58: #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 16:53:59: #1 tags after filtering in treatment: 1386974 INFO @ Fri, 05 Jul 2019 16:53:59: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 05 Jul 2019 16:53:59: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:59: #2 number of paired peaks: 177 WARNING @ Fri, 05 Jul 2019 16:53:59: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Fri, 05 Jul 2019 16:53:59: start model_add_line... INFO @ Fri, 05 Jul 2019 16:53:59: start X-correlation... INFO @ Fri, 05 Jul 2019 16:53:59: end of X-cor INFO @ Fri, 05 Jul 2019 16:53:59: #2 finished! INFO @ Fri, 05 Jul 2019 16:53:59: #2 predicted fragment length is 213 bps INFO @ Fri, 05 Jul 2019 16:53:59: #2 alternative fragment length(s) may be 1,29,65,102,129,148,189,213,255,278,300,320,331,366,395,411,452,480,517,543,587 bps INFO @ Fri, 05 Jul 2019 16:53:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.05_model.r INFO @ Fri, 05 Jul 2019 16:53:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:53:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:54:00: 3000000 INFO @ Fri, 05 Jul 2019 16:54:01: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:54:01: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:54:01: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:54:01: #1 total tags in treatment: 1472479 INFO @ Fri, 05 Jul 2019 16:54:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:54:01: #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 16:54:01: #1 tags after filtering in treatment: 1386974 INFO @ Fri, 05 Jul 2019 16:54:01: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 05 Jul 2019 16:54:01: #1 finished! INFO @ Fri, 05 Jul 2019 16:54:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:54:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:54:01: #2 number of paired peaks: 177 WARNING @ Fri, 05 Jul 2019 16:54:01: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Fri, 05 Jul 2019 16:54:01: start model_add_line... INFO @ Fri, 05 Jul 2019 16:54:01: start X-correlation... INFO @ Fri, 05 Jul 2019 16:54:01: end of X-cor INFO @ Fri, 05 Jul 2019 16:54:01: #2 finished! INFO @ Fri, 05 Jul 2019 16:54:01: #2 predicted fragment length is 213 bps INFO @ Fri, 05 Jul 2019 16:54:01: #2 alternative fragment length(s) may be 1,29,65,102,129,148,189,213,255,278,300,320,331,366,395,411,452,480,517,543,587 bps INFO @ Fri, 05 Jul 2019 16:54:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.10_model.r INFO @ Fri, 05 Jul 2019 16:54:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:54:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:54:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:54:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:54:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.20_summits.bed INFO @ Fri, 05 Jul 2019 16:54:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:54:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:54:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:54:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:54:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.05_summits.bed INFO @ Fri, 05 Jul 2019 16:54:05: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (102 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 16:54:06: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:54:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:54:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:54:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471746/ERX471746.10_summits.bed INFO @ Fri, 05 Jul 2019 16:54:07: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (35 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。