Job ID = 2007925 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/traces/era10/ERR/ERR506/ERR506362' 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506362' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: perform_fastq_split_file_join().make_fastq_csra_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 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/traces/era10/ERR/ERR506/ERR506362' 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506362' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: perform_fastq_split_file_join().make_fastq_csra_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 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/traces/era10/ERR/ERR506/ERR506362' 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506362' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: perform_fastq_split_file_join().make_fastq_csra_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 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/traces/era10/ERR/ERR506/ERR506362' 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506362' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: perform_fastq_split_file_join().make_fastq_csra_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 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/traces/era10/ERR/ERR506/ERR506362' 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506362' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 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/traces/era10/ERR/ERR506/ERR506362' 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506362' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: perform_fastq_split_file_join().make_fastq_csra_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: perform_fastq_split_file_join().make_fastq_csra_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:42 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' 2019-07-05T07:40:42 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/traces/era10/ERR/ERR506/ERR506362' 2019-07-05T07:40:42 fasterq-dump.2.9.6 err: invalid accession 'ERR506362' 2019-07-05T07:40:57 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' 2019-07-05T07:40:57 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/era10/ERR/ERR506/ERR506362' 2019-07-05T07:40:57 fasterq-dump.2.9.6 err: invalid accession 'ERR506362' 2019-07-05T07:41:12 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' 2019-07-05T07:41:12 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/era10/ERR/ERR506/ERR506362' 2019-07-05T07:41:12 fasterq-dump.2.9.6 err: invalid accession 'ERR506362' spots read : 1,716,477 reads read : 3,432,954 reads written : 3,432,954 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: 00:02:11 1716477 reads; of these: 1716477 (100.00%) were paired; of these: 278916 (16.25%) aligned concordantly 0 times 1314739 (76.60%) aligned concordantly exactly 1 time 122822 (7.16%) aligned concordantly >1 times ---- 278916 pairs aligned concordantly 0 times; of these: 26867 (9.63%) aligned discordantly 1 time ---- 252049 pairs aligned 0 times concordantly or discordantly; of these: 504098 mates make up the pairs; of these: 480101 (95.24%) aligned 0 times 15742 (3.12%) aligned exactly 1 time 8255 (1.64%) aligned >1 times 86.01% overall alignment rate Time searching: 00:02:11 Overall time: 00:02:11 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_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] 273796 / 1461295 = 0.1874 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 16:52:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.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 16:52:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:52:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:52:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.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 16:52:44: #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/ERX471719/ERX471719.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.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 16:52:45: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:52:45: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:52:54: 1000000 INFO @ Fri, 05 Jul 2019 16:52:55: 1000000 INFO @ Fri, 05 Jul 2019 16:52:55: 1000000 INFO @ Fri, 05 Jul 2019 16:53:04: 2000000 INFO @ Fri, 05 Jul 2019 16:53:04: 2000000 INFO @ Fri, 05 Jul 2019 16:53:06: 2000000 INFO @ Fri, 05 Jul 2019 16:53:07: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:07: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:07: #1 total tags in treatment: 1166261 INFO @ Fri, 05 Jul 2019 16:53:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:07: #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 16:53:07: #1 tags after filtering in treatment: 1109721 INFO @ Fri, 05 Jul 2019 16:53:07: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 16:53:07: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:08: #2 number of paired peaks: 161 WARNING @ Fri, 05 Jul 2019 16:53:08: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 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: 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 181 bps INFO @ Fri, 05 Jul 2019 16:53:08: #2 alternative fragment length(s) may be 2,162,166,181,190,215,235,290,539,587 bps INFO @ Fri, 05 Jul 2019 16:53:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.10_model.r WARNING @ Fri, 05 Jul 2019 16:53:08: #2 Since the d (181) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:53:08: #2 You may need to consider one of the other alternative d(s): 2,162,166,181,190,215,235,290,539,587 WARNING @ Fri, 05 Jul 2019 16:53:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. 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 16:53:08: #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: 1166261 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: 1109721 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: 161 WARNING @ Fri, 05 Jul 2019 16:53:08: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 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: 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 181 bps INFO @ Fri, 05 Jul 2019 16:53:08: #2 alternative fragment length(s) may be 2,162,166,181,190,215,235,290,539,587 bps INFO @ Fri, 05 Jul 2019 16:53:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.20_model.r WARNING @ Fri, 05 Jul 2019 16:53:08: #2 Since the d (181) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:53:08: #2 You may need to consider one of the other alternative d(s): 2,162,166,181,190,215,235,290,539,587 WARNING @ Fri, 05 Jul 2019 16:53:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. 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: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:10: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:10: #1 total tags in treatment: 1166261 INFO @ Fri, 05 Jul 2019 16:53:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:10: #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 16:53:10: #1 tags after filtering in treatment: 1109721 INFO @ Fri, 05 Jul 2019 16:53:10: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 16:53:10: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:11: #2 number of paired peaks: 161 WARNING @ Fri, 05 Jul 2019 16:53:11: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Fri, 05 Jul 2019 16:53:11: start model_add_line... INFO @ Fri, 05 Jul 2019 16:53:11: start X-correlation... INFO @ Fri, 05 Jul 2019 16:53:11: end of X-cor INFO @ Fri, 05 Jul 2019 16:53:11: #2 finished! INFO @ Fri, 05 Jul 2019 16:53:11: #2 predicted fragment length is 181 bps INFO @ Fri, 05 Jul 2019 16:53:11: #2 alternative fragment length(s) may be 2,162,166,181,190,215,235,290,539,587 bps INFO @ Fri, 05 Jul 2019 16:53:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.05_model.r WARNING @ Fri, 05 Jul 2019 16:53:11: #2 Since the d (181) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:53:11: #2 You may need to consider one of the other alternative d(s): 2,162,166,181,190,215,235,290,539,587 WARNING @ Fri, 05 Jul 2019 16:53:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:53:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:53:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:53:12: #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 16:53:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:53:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:53:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.10_summits.bed INFO @ Fri, 05 Jul 2019 16:53:13: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (32 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:53:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:53:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:53:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.20_summits.bed INFO @ Fri, 05 Jul 2019 16:53:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (8 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:53:15: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:53:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:53:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:53:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471719/ERX471719.05_summits.bed INFO @ Fri, 05 Jul 2019 16:53:16: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (78 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。