Job ID = 1296486 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T07:25:47 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' 2019-06-03T07:25:47 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/SRR7798956' 2019-06-03T07:25:47 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR7798956' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T07:26:11 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' 2019-06-03T07:26:11 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/SRR7798956' 2019-06-03T07:26:11 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_table_names( 'SRR7798956' ).VDBManagerOpenDBRead() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 31,042,840 reads read : 62,085,680 reads written : 62,085,680 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: 00:00:00 Multiseed full-index search: 00:05:30 31042840 reads; of these: 31042840 (100.00%) were paired; of these: 30680874 (98.83%) aligned concordantly 0 times 291412 (0.94%) aligned concordantly exactly 1 time 70554 (0.23%) aligned concordantly >1 times ---- 30680874 pairs aligned concordantly 0 times; of these: 1516 (0.00%) aligned discordantly 1 time ---- 30679358 pairs aligned 0 times concordantly or discordantly; of these: 61358716 mates make up the pairs; of these: 60760153 (99.02%) aligned 0 times 197436 (0.32%) aligned exactly 1 time 401127 (0.65%) aligned >1 times 2.13% overall alignment rate Time searching: 00:05:30 Overall time: 00:05:30 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] 11037 / 362006 = 0.0305 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 16:46:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.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 16:46:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:46:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:46:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.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 16:46:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:46:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:46:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.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 16:46:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:46:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:46:31: 1000000 INFO @ Mon, 03 Jun 2019 16:46:32: 1000000 INFO @ Mon, 03 Jun 2019 16:46:33: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 16:46:33: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 16:46:33: #1 total tags in treatment: 350944 INFO @ Mon, 03 Jun 2019 16:46:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:46:33: #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 16:46:33: #1 tags after filtering in treatment: 346336 INFO @ Mon, 03 Jun 2019 16:46:33: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 03 Jun 2019 16:46:33: #1 finished! INFO @ Mon, 03 Jun 2019 16:46:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:46:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:46:33: #2 number of paired peaks: 2340 INFO @ Mon, 03 Jun 2019 16:46:33: start model_add_line... INFO @ Mon, 03 Jun 2019 16:46:33: start X-correlation... INFO @ Mon, 03 Jun 2019 16:46:33: end of X-cor INFO @ Mon, 03 Jun 2019 16:46:33: #2 finished! INFO @ Mon, 03 Jun 2019 16:46:33: #2 predicted fragment length is 128 bps INFO @ Mon, 03 Jun 2019 16:46:33: #2 alternative fragment length(s) may be 128,175,189,211,258 bps INFO @ Mon, 03 Jun 2019 16:46:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.05_model.r INFO @ Mon, 03 Jun 2019 16:46:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:46:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:46:34: 1000000 INFO @ Mon, 03 Jun 2019 16:46:34: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 16:46:34: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 16:46:34: #1 total tags in treatment: 350944 INFO @ Mon, 03 Jun 2019 16:46:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:46:34: #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 16:46:34: #1 tags after filtering in treatment: 346336 INFO @ Mon, 03 Jun 2019 16:46:34: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 03 Jun 2019 16:46:34: #1 finished! INFO @ Mon, 03 Jun 2019 16:46:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:46:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:46:34: #2 number of paired peaks: 2340 INFO @ Mon, 03 Jun 2019 16:46:34: start model_add_line... INFO @ Mon, 03 Jun 2019 16:46:34: start X-correlation... INFO @ Mon, 03 Jun 2019 16:46:34: end of X-cor INFO @ Mon, 03 Jun 2019 16:46:34: #2 finished! INFO @ Mon, 03 Jun 2019 16:46:34: #2 predicted fragment length is 128 bps INFO @ Mon, 03 Jun 2019 16:46:34: #2 alternative fragment length(s) may be 128,175,189,211,258 bps INFO @ Mon, 03 Jun 2019 16:46:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.10_model.r INFO @ Mon, 03 Jun 2019 16:46:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:46:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:46:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:46:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:46:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.05_peaks.xls INFO @ Mon, 03 Jun 2019 16:46:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:46:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.05_summits.bed INFO @ Mon, 03 Jun 2019 16:46:35: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (137 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:46:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.10_peaks.xls INFO @ Mon, 03 Jun 2019 16:46:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:46:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.10_summits.bed INFO @ Mon, 03 Jun 2019 16:46:35: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (50 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:46:36: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 16:46:36: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 16:46:36: #1 total tags in treatment: 350944 INFO @ Mon, 03 Jun 2019 16:46:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:46:36: #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 16:46:36: #1 tags after filtering in treatment: 346336 INFO @ Mon, 03 Jun 2019 16:46:36: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 03 Jun 2019 16:46:36: #1 finished! INFO @ Mon, 03 Jun 2019 16:46:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:46:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:46:36: #2 number of paired peaks: 2340 INFO @ Mon, 03 Jun 2019 16:46:36: start model_add_line... INFO @ Mon, 03 Jun 2019 16:46:36: start X-correlation... INFO @ Mon, 03 Jun 2019 16:46:36: end of X-cor INFO @ Mon, 03 Jun 2019 16:46:36: #2 finished! INFO @ Mon, 03 Jun 2019 16:46:36: #2 predicted fragment length is 128 bps INFO @ Mon, 03 Jun 2019 16:46:36: #2 alternative fragment length(s) may be 128,175,189,211,258 bps INFO @ Mon, 03 Jun 2019 16:46:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.20_model.r INFO @ Mon, 03 Jun 2019 16:46:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:46:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:46:37: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 16:46:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.20_peaks.xls INFO @ Mon, 03 Jun 2019 16:46:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:46:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650797/SRX4650797.20_summits.bed INFO @ Mon, 03 Jun 2019 16:46:38: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。