Job ID = 2007934 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:40:39 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' 2019-07-05T07:40:39 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/ERR506370' 2019-07-05T07:40:39 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'ERR506370', 'SEQUENCE', 'NAME' ).VDBManagerOpenDBRead() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:44 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' 2019-07-05T07:40:44 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/ERR506370' 2019-07-05T07:40:44 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506370' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:54 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' 2019-07-05T07:40:54 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/ERR506370' 2019-07-05T07:40:54 fasterq-dump.2.9.6 err: invalid accession 'ERR506370' 2019-07-05T07:41:09 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' 2019-07-05T07:41:09 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/ERR506370' 2019-07-05T07:41:09 fasterq-dump.2.9.6 err: invalid accession 'ERR506370' 2019-07-05T07:41:24 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' 2019-07-05T07:41:24 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/ERR506370' 2019-07-05T07:41:24 fasterq-dump.2.9.6 err: invalid accession 'ERR506370' spots read : 1,716,211 reads read : 3,432,422 reads written : 3,432,422 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: 00:02:00 1716211 reads; of these: 1716211 (100.00%) were paired; of these: 173479 (10.11%) aligned concordantly 0 times 1415645 (82.49%) aligned concordantly exactly 1 time 127087 (7.41%) aligned concordantly >1 times ---- 173479 pairs aligned concordantly 0 times; of these: 27030 (15.58%) aligned discordantly 1 time ---- 146449 pairs aligned 0 times concordantly or discordantly; of these: 292898 mates make up the pairs; of these: 269010 (91.84%) aligned 0 times 15948 (5.44%) aligned exactly 1 time 7940 (2.71%) aligned >1 times 92.16% overall alignment rate Time searching: 00:02:00 Overall time: 00:02:00 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] 214445 / 1564742 = 0.1370 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 16:53:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.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 16:53:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:53:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:53:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.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 16:53:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:53:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:53:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.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 16:53:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:53:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:53:20: 1000000 INFO @ Fri, 05 Jul 2019 16:53:21: 1000000 INFO @ Fri, 05 Jul 2019 16:53:21: 1000000 INFO @ Fri, 05 Jul 2019 16:53:33: 2000000 INFO @ Fri, 05 Jul 2019 16:53:34: 2000000 INFO @ Fri, 05 Jul 2019 16:53:35: 2000000 INFO @ Fri, 05 Jul 2019 16:53:41: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:41: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:41: #1 total tags in treatment: 1329888 INFO @ Fri, 05 Jul 2019 16:53:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:41: #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 16:53:41: #1 tags after filtering in treatment: 1268252 INFO @ Fri, 05 Jul 2019 16:53:41: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 16:53:41: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:41: #2 number of paired peaks: 160 WARNING @ Fri, 05 Jul 2019 16:53:41: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Fri, 05 Jul 2019 16:53:41: start model_add_line... INFO @ Fri, 05 Jul 2019 16:53:41: start X-correlation... INFO @ Fri, 05 Jul 2019 16:53:41: end of X-cor INFO @ Fri, 05 Jul 2019 16:53:41: #2 finished! INFO @ Fri, 05 Jul 2019 16:53:41: #2 predicted fragment length is 181 bps INFO @ Fri, 05 Jul 2019 16:53:41: #2 alternative fragment length(s) may be 1,85,103,137,181,203,237,278,296,321,527,559,576 bps INFO @ Fri, 05 Jul 2019 16:53:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.10_model.r WARNING @ Fri, 05 Jul 2019 16:53:41: #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 16:53:41: #2 You may need to consider one of the other alternative d(s): 1,85,103,137,181,203,237,278,296,321,527,559,576 WARNING @ Fri, 05 Jul 2019 16:53:41: #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 16:53:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:53:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:53:42: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:42: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:42: #1 total tags in treatment: 1329888 INFO @ Fri, 05 Jul 2019 16:53:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:42: #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 16:53:42: #1 tags after filtering in treatment: 1268252 INFO @ Fri, 05 Jul 2019 16:53:42: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 16:53:42: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:42: #2 number of paired peaks: 160 WARNING @ Fri, 05 Jul 2019 16:53:42: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Fri, 05 Jul 2019 16:53:42: start model_add_line... INFO @ Fri, 05 Jul 2019 16:53:42: start X-correlation... INFO @ Fri, 05 Jul 2019 16:53:42: end of X-cor INFO @ Fri, 05 Jul 2019 16:53:42: #2 finished! INFO @ Fri, 05 Jul 2019 16:53:42: #2 predicted fragment length is 181 bps INFO @ Fri, 05 Jul 2019 16:53:42: #2 alternative fragment length(s) may be 1,85,103,137,181,203,237,278,296,321,527,559,576 bps INFO @ Fri, 05 Jul 2019 16:53:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.20_model.r WARNING @ Fri, 05 Jul 2019 16:53:42: #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 16:53:42: #2 You may need to consider one of the other alternative d(s): 1,85,103,137,181,203,237,278,296,321,527,559,576 WARNING @ Fri, 05 Jul 2019 16:53:42: #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 16:53:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:53:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:53:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:53:45: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:45: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:45: #1 total tags in treatment: 1329888 INFO @ Fri, 05 Jul 2019 16:53:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:45: #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 16:53:45: #1 tags after filtering in treatment: 1268252 INFO @ Fri, 05 Jul 2019 16:53:45: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 16:53:45: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:46: #2 number of paired peaks: 160 WARNING @ Fri, 05 Jul 2019 16:53:46: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Fri, 05 Jul 2019 16:53:46: start model_add_line... INFO @ Fri, 05 Jul 2019 16:53:46: start X-correlation... INFO @ Fri, 05 Jul 2019 16:53:46: end of X-cor INFO @ Fri, 05 Jul 2019 16:53:46: #2 finished! INFO @ Fri, 05 Jul 2019 16:53:46: #2 predicted fragment length is 181 bps INFO @ Fri, 05 Jul 2019 16:53:46: #2 alternative fragment length(s) may be 1,85,103,137,181,203,237,278,296,321,527,559,576 bps INFO @ Fri, 05 Jul 2019 16:53:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.05_model.r WARNING @ Fri, 05 Jul 2019 16:53:46: #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 16:53:46: #2 You may need to consider one of the other alternative d(s): 1,85,103,137,181,203,237,278,296,321,527,559,576 WARNING @ Fri, 05 Jul 2019 16:53:46: #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 16:53:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:53:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:53:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:53:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:53:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:53:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.10_summits.bed INFO @ Fri, 05 Jul 2019 16:53:47: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (23 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 16:53:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:53:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:53:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.20_summits.bed INFO @ Fri, 05 Jul 2019 16:53:48: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (7 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:53:50: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:53:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:53:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:53:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471727/ERX471727.05_summits.bed INFO @ Fri, 05 Jul 2019 16:53:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (58 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。