Job ID = 2007940 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:40:29 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-05T07:40:38 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' 2019-07-05T07:40:43 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' 2019-07-05T07:40:43 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/ERR506376/ERR506376.1' 2019-07-05T07:40:43 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506376' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:41:00 fasterq-dump.2.9.6 err: sorter.c run_producer_pool() : processed lookup rows: 2681390 of 3217667 2019-07-05T07:41:00 fasterq-dump.2.9.6 err: sorter.c execute_lookup_production() -> RC(rcVDB,rcNoTarg,rcConstructing,rcSize,rcInvalid) 2019-07-05T07:41:00 fasterq-dump.2.9.6 err: fasterq-dump.c produce_lookup_files() -> RC(rcVDB,rcNoTarg,rcConstructing,rcSize,rcInvalid) 2019-07-05T07:41:04 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' 2019-07-05T07:41:04 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/ERR506376/ERR506376.1' 2019-07-05T07:41:04 fasterq-dump.2.9.6 err: invalid accession 'ERR506376' 2019-07-05T07:41:19 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' 2019-07-05T07:41:19 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/ERR506376/ERR506376.1' 2019-07-05T07:41:19 fasterq-dump.2.9.6 err: invalid accession 'ERR506376' spots read : 1,671,466 reads read : 3,342,932 reads written : 3,342,932 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: 00:02:31 1671466 reads; of these: 1671466 (100.00%) were paired; of these: 198052 (11.85%) aligned concordantly 0 times 1359852 (81.36%) aligned concordantly exactly 1 time 113562 (6.79%) aligned concordantly >1 times ---- 198052 pairs aligned concordantly 0 times; of these: 105769 (53.40%) aligned discordantly 1 time ---- 92283 pairs aligned 0 times concordantly or discordantly; of these: 184566 mates make up the pairs; of these: 127724 (69.20%) aligned 0 times 33631 (18.22%) aligned exactly 1 time 23211 (12.58%) aligned >1 times 96.18% overall alignment rate Time searching: 00:02:31 Overall time: 00:02:31 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] 44528 / 1548406 = 0.0288 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 16:53:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.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 16:53:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:53:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:53:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.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 16:53:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:53:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:53:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.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 16:53:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:53:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:54:09: 1000000 INFO @ Fri, 05 Jul 2019 16:54:10: 1000000 INFO @ Fri, 05 Jul 2019 16:54:14: 1000000 INFO @ Fri, 05 Jul 2019 16:54:21: 2000000 INFO @ Fri, 05 Jul 2019 16:54:22: 2000000 INFO @ Fri, 05 Jul 2019 16:54:29: 2000000 INFO @ Fri, 05 Jul 2019 16:54:33: 3000000 INFO @ Fri, 05 Jul 2019 16:54:34: 3000000 INFO @ Fri, 05 Jul 2019 16:54:34: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:54:34: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:54:34: #1 total tags in treatment: 1430253 INFO @ Fri, 05 Jul 2019 16:54:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:54:34: #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 16:54:34: #1 tags after filtering in treatment: 1327437 INFO @ Fri, 05 Jul 2019 16:54:34: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 16:54:34: #1 finished! INFO @ Fri, 05 Jul 2019 16:54:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:54:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:54:34: #2 number of paired peaks: 208 WARNING @ Fri, 05 Jul 2019 16:54:34: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Fri, 05 Jul 2019 16:54:34: start model_add_line... INFO @ Fri, 05 Jul 2019 16:54:34: start X-correlation... INFO @ Fri, 05 Jul 2019 16:54:34: end of X-cor INFO @ Fri, 05 Jul 2019 16:54:34: #2 finished! INFO @ Fri, 05 Jul 2019 16:54:34: #2 predicted fragment length is 208 bps INFO @ Fri, 05 Jul 2019 16:54:34: #2 alternative fragment length(s) may be 208 bps INFO @ Fri, 05 Jul 2019 16:54:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.05_model.r INFO @ Fri, 05 Jul 2019 16:54:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:54:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:54:35: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:54:35: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:54:35: #1 total tags in treatment: 1430253 INFO @ Fri, 05 Jul 2019 16:54:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:54:35: #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 16:54:35: #1 tags after filtering in treatment: 1327437 INFO @ Fri, 05 Jul 2019 16:54:35: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 16:54:35: #1 finished! INFO @ Fri, 05 Jul 2019 16:54:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:54:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:54:35: #2 number of paired peaks: 208 WARNING @ Fri, 05 Jul 2019 16:54:35: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Fri, 05 Jul 2019 16:54:35: start model_add_line... INFO @ Fri, 05 Jul 2019 16:54:35: start X-correlation... INFO @ Fri, 05 Jul 2019 16:54:35: end of X-cor INFO @ Fri, 05 Jul 2019 16:54:35: #2 finished! INFO @ Fri, 05 Jul 2019 16:54:35: #2 predicted fragment length is 208 bps INFO @ Fri, 05 Jul 2019 16:54:35: #2 alternative fragment length(s) may be 208 bps INFO @ Fri, 05 Jul 2019 16:54:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.10_model.r INFO @ Fri, 05 Jul 2019 16:54:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:54:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:54:39: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:54:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:54:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:54:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:54:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.05_summits.bed INFO @ Fri, 05 Jul 2019 16:54:41: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (636 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 16:54:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:54:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:54:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.10_summits.bed INFO @ Fri, 05 Jul 2019 16:54:42: Done! INFO @ Fri, 05 Jul 2019 16:54:42: 3000000 pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (414 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:54:44: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:54:44: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:54:44: #1 total tags in treatment: 1430253 INFO @ Fri, 05 Jul 2019 16:54:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:54:44: #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 16:54:44: #1 tags after filtering in treatment: 1327437 INFO @ Fri, 05 Jul 2019 16:54:44: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 16:54:44: #1 finished! INFO @ Fri, 05 Jul 2019 16:54:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:54:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:54:44: #2 number of paired peaks: 208 WARNING @ Fri, 05 Jul 2019 16:54:44: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Fri, 05 Jul 2019 16:54:44: start model_add_line... INFO @ Fri, 05 Jul 2019 16:54:44: start X-correlation... INFO @ Fri, 05 Jul 2019 16:54:44: end of X-cor INFO @ Fri, 05 Jul 2019 16:54:44: #2 finished! INFO @ Fri, 05 Jul 2019 16:54:44: #2 predicted fragment length is 208 bps INFO @ Fri, 05 Jul 2019 16:54:44: #2 alternative fragment length(s) may be 208 bps INFO @ Fri, 05 Jul 2019 16:54:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.20_model.r INFO @ Fri, 05 Jul 2019 16:54:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:54:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:54:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:54:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:54:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:54:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471733/ERX471733.20_summits.bed INFO @ Fri, 05 Jul 2019 16:54:50: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (275 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。