Job ID = 2007945 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/ERR506381/ERR506381.1' 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506381' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:47 fasterq-dump.2.9.6 err: sorter.c run_producer_pool() : processed lookup rows: 485594 of 2913559 2019-07-05T07:40:47 fasterq-dump.2.9.6 err: sorter.c execute_lookup_production() -> RC(rcVDB,rcNoTarg,rcConstructing,rcSize,rcInvalid) 2019-07-05T07:40:47 fasterq-dump.2.9.6 err: fasterq-dump.c produce_lookup_files() -> RC(rcVDB,rcNoTarg,rcConstructing,rcSize,rcInvalid) 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/ERR506381/ERR506381.1' 2019-07-05T07:40:52 fasterq-dump.2.9.6 err: invalid accession 'ERR506381' 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/ERR506381/ERR506381.1' 2019-07-05T07:41:07 fasterq-dump.2.9.6 err: invalid accession 'ERR506381' 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/ERR506381/ERR506381.1' 2019-07-05T07:41:22 fasterq-dump.2.9.6 err: invalid accession 'ERR506381' spots read : 1,649,753 reads read : 3,299,506 reads written : 3,299,506 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: 00:01:46 1649753 reads; of these: 1649753 (100.00%) were paired; of these: 230787 (13.99%) aligned concordantly 0 times 1299873 (78.79%) aligned concordantly exactly 1 time 119093 (7.22%) aligned concordantly >1 times ---- 230787 pairs aligned concordantly 0 times; of these: 26754 (11.59%) aligned discordantly 1 time ---- 204033 pairs aligned 0 times concordantly or discordantly; of these: 408066 mates make up the pairs; of these: 383866 (94.07%) aligned 0 times 16424 (4.02%) aligned exactly 1 time 7776 (1.91%) aligned >1 times 88.37% overall alignment rate Time searching: 00:01:46 Overall time: 00:01:46 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] 223495 / 1441844 = 0.1550 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 16:52:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.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 16:52:44: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:52:44: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:52:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.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 16:52:45: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:52:45: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:52:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.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 16:52:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:52:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:52:53: 1000000 INFO @ Fri, 05 Jul 2019 16:52:54: 1000000 INFO @ Fri, 05 Jul 2019 16:52:57: 1000000 INFO @ Fri, 05 Jul 2019 16:53:02: 2000000 INFO @ Fri, 05 Jul 2019 16:53:03: 2000000 INFO @ Fri, 05 Jul 2019 16:53:06: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:06: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:06: #1 total tags in treatment: 1197310 INFO @ Fri, 05 Jul 2019 16:53:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:06: #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 16:53:06: #1 tags after filtering in treatment: 1143040 INFO @ Fri, 05 Jul 2019 16:53:06: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 16:53:06: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:06: #2 number of paired peaks: 168 WARNING @ Fri, 05 Jul 2019 16:53:06: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 05 Jul 2019 16:53:06: start model_add_line... INFO @ Fri, 05 Jul 2019 16:53:06: start X-correlation... INFO @ Fri, 05 Jul 2019 16:53:07: end of X-cor INFO @ Fri, 05 Jul 2019 16:53:07: #2 finished! INFO @ Fri, 05 Jul 2019 16:53:07: #2 predicted fragment length is 247 bps INFO @ Fri, 05 Jul 2019 16:53:07: #2 alternative fragment length(s) may be 0,24,63,108,130,163,185,221,226,247,271,275,311,342,372,409,458,485,518,537,582 bps INFO @ Fri, 05 Jul 2019 16:53:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.05_model.r INFO @ Fri, 05 Jul 2019 16:53:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:53:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:53:08: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:08: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:08: #1 total tags in treatment: 1197310 INFO @ Fri, 05 Jul 2019 16:53:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:08: #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 16:53:08: #1 tags after filtering in treatment: 1143040 INFO @ Fri, 05 Jul 2019 16:53:08: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 16:53:08: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:08: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:08: #2 number of paired peaks: 168 WARNING @ Fri, 05 Jul 2019 16:53:08: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 05 Jul 2019 16:53:08: start model_add_line... INFO @ Fri, 05 Jul 2019 16:53:08: start X-correlation... INFO @ Fri, 05 Jul 2019 16:53:08: 2000000 INFO @ Fri, 05 Jul 2019 16:53:08: end of X-cor INFO @ Fri, 05 Jul 2019 16:53:08: #2 finished! INFO @ Fri, 05 Jul 2019 16:53:08: #2 predicted fragment length is 247 bps INFO @ Fri, 05 Jul 2019 16:53:08: #2 alternative fragment length(s) may be 0,24,63,108,130,163,185,221,226,247,271,275,311,342,372,409,458,485,518,537,582 bps INFO @ Fri, 05 Jul 2019 16:53:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.10_model.r INFO @ Fri, 05 Jul 2019 16:53:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:53:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:53:10: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:53:12: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:53:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:53:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:53:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.05_summits.bed INFO @ Fri, 05 Jul 2019 16:53:12: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (56 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:53:13: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:13: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:13: #1 total tags in treatment: 1197310 INFO @ Fri, 05 Jul 2019 16:53:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:13: #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 16:53:13: #1 tags after filtering in treatment: 1143040 INFO @ Fri, 05 Jul 2019 16:53:13: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 16:53:13: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:13: #2 number of paired peaks: 168 WARNING @ Fri, 05 Jul 2019 16:53:13: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 05 Jul 2019 16:53:13: start model_add_line... INFO @ Fri, 05 Jul 2019 16:53:13: start X-correlation... INFO @ Fri, 05 Jul 2019 16:53:13: end of X-cor INFO @ Fri, 05 Jul 2019 16:53:13: #2 finished! INFO @ Fri, 05 Jul 2019 16:53:13: #2 predicted fragment length is 247 bps INFO @ Fri, 05 Jul 2019 16:53:13: #2 alternative fragment length(s) may be 0,24,63,108,130,163,185,221,226,247,271,275,311,342,372,409,458,485,518,537,582 bps INFO @ Fri, 05 Jul 2019 16:53:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.20_model.r INFO @ Fri, 05 Jul 2019 16:53:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:53:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:53:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:53:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:53:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.10_summits.bed INFO @ Fri, 05 Jul 2019 16:53:13: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (21 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:53:17: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:53:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:53:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:53:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471738/ERX471738.20_summits.bed INFO @ Fri, 05 Jul 2019 16:53:18: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。