Job ID = 1296485 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T07:25:24 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-03T07:25:24 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra70/SRR/007616/SRR7798955' 2019-06-03T07:25:24 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_table_names( 'SRR7798955' ).VDBManagerOpenDBRead() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T07:25:49 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-03T07:25:49 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra70/SRR/007616/SRR7798955' 2019-06-03T07:25:49 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR7798955' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T07:25:49 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 12,825,907 reads read : 25,651,814 reads written : 25,651,814 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:00:01 Multiseed full-index search: 00:03:14 12825907 reads; of these: 12825907 (100.00%) were paired; of these: 12584425 (98.12%) aligned concordantly 0 times 171834 (1.34%) aligned concordantly exactly 1 time 69648 (0.54%) aligned concordantly >1 times ---- 12584425 pairs aligned concordantly 0 times; of these: 1106 (0.01%) aligned discordantly 1 time ---- 12583319 pairs aligned 0 times concordantly or discordantly; of these: 25166638 mates make up the pairs; of these: 24835572 (98.68%) aligned 0 times 104935 (0.42%) aligned exactly 1 time 226131 (0.90%) aligned >1 times 3.18% overall alignment rate Time searching: 00:03:15 Overall time: 00:03:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 5513 / 241667 = 0.0228 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 @ Mon, 03 Jun 2019 16:42:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 16:42:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:42:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:42:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 16:42:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:42:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:42:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 16:42:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:42:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:42:34: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 16:42:34: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 16:42:34: #1 total tags in treatment: 235975 INFO @ Mon, 03 Jun 2019 16:42:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:42:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 16:42:34: #1 tags after filtering in treatment: 233428 INFO @ Mon, 03 Jun 2019 16:42:34: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 03 Jun 2019 16:42:34: #1 finished! INFO @ Mon, 03 Jun 2019 16:42:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:42:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:42:34: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 16:42:34: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 16:42:34: #1 total tags in treatment: 235975 INFO @ Mon, 03 Jun 2019 16:42:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:42:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 16:42:34: #1 tags after filtering in treatment: 233428 INFO @ Mon, 03 Jun 2019 16:42:34: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 03 Jun 2019 16:42:34: #1 finished! INFO @ Mon, 03 Jun 2019 16:42:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:42:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:42:34: #2 number of paired peaks: 935 WARNING @ Mon, 03 Jun 2019 16:42:34: Fewer paired peaks (935) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 935 pairs to build model! INFO @ Mon, 03 Jun 2019 16:42:34: start model_add_line... INFO @ Mon, 03 Jun 2019 16:42:34: start X-correlation... INFO @ Mon, 03 Jun 2019 16:42:34: end of X-cor INFO @ Mon, 03 Jun 2019 16:42:34: #2 finished! INFO @ Mon, 03 Jun 2019 16:42:34: #2 predicted fragment length is 90 bps INFO @ Mon, 03 Jun 2019 16:42:34: #2 alternative fragment length(s) may be 90,196,285 bps INFO @ Mon, 03 Jun 2019 16:42:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.10_model.r INFO @ Mon, 03 Jun 2019 16:42:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:42:34: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 16:42:34: #2 number of paired peaks: 935 WARNING @ Mon, 03 Jun 2019 16:42:34: Fewer paired peaks (935) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 935 pairs to build model! INFO @ Mon, 03 Jun 2019 16:42:34: start model_add_line... INFO @ Mon, 03 Jun 2019 16:42:34: start X-correlation... INFO @ Mon, 03 Jun 2019 16:42:34: end of X-cor INFO @ Mon, 03 Jun 2019 16:42:34: #2 finished! INFO @ Mon, 03 Jun 2019 16:42:34: #2 predicted fragment length is 90 bps INFO @ Mon, 03 Jun 2019 16:42:34: #2 alternative fragment length(s) may be 90,196,285 bps INFO @ Mon, 03 Jun 2019 16:42:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.05_model.r INFO @ Mon, 03 Jun 2019 16:42:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:42:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:42:34: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 16:42:34: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 16:42:34: #1 total tags in treatment: 235975 INFO @ Mon, 03 Jun 2019 16:42:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:42:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 16:42:34: #1 tags after filtering in treatment: 233428 INFO @ Mon, 03 Jun 2019 16:42:34: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 03 Jun 2019 16:42:34: #1 finished! INFO @ Mon, 03 Jun 2019 16:42:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:42:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:42:35: #2 number of paired peaks: 935 WARNING @ Mon, 03 Jun 2019 16:42:35: Fewer paired peaks (935) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 935 pairs to build model! INFO @ Mon, 03 Jun 2019 16:42:35: start model_add_line... INFO @ Mon, 03 Jun 2019 16:42:35: start X-correlation... INFO @ Mon, 03 Jun 2019 16:42:35: end of X-cor INFO @ Mon, 03 Jun 2019 16:42:35: #2 finished! INFO @ Mon, 03 Jun 2019 16:42:35: #2 predicted fragment length is 90 bps INFO @ Mon, 03 Jun 2019 16:42:35: #2 alternative fragment length(s) may be 90,196,285 bps INFO @ Mon, 03 Jun 2019 16:42:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.20_model.r INFO @ Mon, 03 Jun 2019 16:42:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:42:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:42:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:42:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:42:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.10_peaks.xls INFO @ Mon, 03 Jun 2019 16:42:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:42:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.10_summits.bed INFO @ Mon, 03 Jun 2019 16:42:35: Done! INFO @ Mon, 03 Jun 2019 16:42:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.05_peaks.xls INFO @ Mon, 03 Jun 2019 16:42:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:42:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.05_summits.bed INFO @ Mon, 03 Jun 2019 16:42:35: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (43 records, 4 fields): 1 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (65 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:42:35: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 16:42:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.20_peaks.xls INFO @ Mon, 03 Jun 2019 16:42:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:42:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650796/SRX4650796.20_summits.bed INFO @ Mon, 03 Jun 2019 16:42:36: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (27 records, 4 fields): 2 millis CompletedMACS2peakCalling