Job ID = 1302448 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T11:05:41 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' 2019-06-03T11:05:41 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/sra72/SRR/007917/SRR8107276' 2019-06-03T11:05:41 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR8107276', 'SEQUENCE', 'NAME' ).VDBManagerOpenDBRead() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T11:05:45 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' 2019-06-03T11:05:45 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/sra72/SRR/007917/SRR8107276' 2019-06-03T11:05:45 fasterq-dump.2.9.6 err: invalid accession 'SRR8107276' 2019-06-03T11:05:50 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' 2019-06-03T11:05:50 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/sra72/SRR/007917/SRR8107276' 2019-06-03T11:05:50 fasterq-dump.2.9.6 err: invalid accession 'SRR8107276' spots read : 9,792,526 reads read : 19,585,052 reads written : 9,792,526 reads 0-length : 9,792,526 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: 00:03:41 9792526 reads; of these: 9792526 (100.00%) were unpaired; of these: 550861 (5.63%) aligned 0 times 6734238 (68.77%) aligned exactly 1 time 2507427 (25.61%) aligned >1 times 94.37% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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_rmdupse_core] 3667338 / 9241665 = 0.3968 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 20:18:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.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 20:18:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:18:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:18:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.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 20:18:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:18:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:18:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.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 20:18:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:18:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:18:58: 1000000 INFO @ Mon, 03 Jun 2019 20:18:59: 1000000 INFO @ Mon, 03 Jun 2019 20:18:59: 1000000 INFO @ Mon, 03 Jun 2019 20:19:06: 2000000 INFO @ Mon, 03 Jun 2019 20:19:08: 2000000 INFO @ Mon, 03 Jun 2019 20:19:10: 2000000 INFO @ Mon, 03 Jun 2019 20:19:14: 3000000 INFO @ Mon, 03 Jun 2019 20:19:19: 3000000 INFO @ Mon, 03 Jun 2019 20:19:20: 3000000 INFO @ Mon, 03 Jun 2019 20:19:22: 4000000 INFO @ Mon, 03 Jun 2019 20:19:28: 4000000 INFO @ Mon, 03 Jun 2019 20:19:29: 4000000 INFO @ Mon, 03 Jun 2019 20:19:30: 5000000 INFO @ Mon, 03 Jun 2019 20:19:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:19:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:19:34: #1 total tags in treatment: 5574327 INFO @ Mon, 03 Jun 2019 20:19:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:19:34: #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 20:19:35: #1 tags after filtering in treatment: 5574327 INFO @ Mon, 03 Jun 2019 20:19:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:19:35: #1 finished! INFO @ Mon, 03 Jun 2019 20:19:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:19:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:19:35: #2 number of paired peaks: 125 WARNING @ Mon, 03 Jun 2019 20:19:35: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Mon, 03 Jun 2019 20:19:35: start model_add_line... INFO @ Mon, 03 Jun 2019 20:19:35: start X-correlation... INFO @ Mon, 03 Jun 2019 20:19:35: end of X-cor INFO @ Mon, 03 Jun 2019 20:19:35: #2 finished! INFO @ Mon, 03 Jun 2019 20:19:35: #2 predicted fragment length is 322 bps INFO @ Mon, 03 Jun 2019 20:19:35: #2 alternative fragment length(s) may be 298,322 bps INFO @ Mon, 03 Jun 2019 20:19:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.10_model.r INFO @ Mon, 03 Jun 2019 20:19:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:19:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:19:37: 5000000 INFO @ Mon, 03 Jun 2019 20:19:37: 5000000 INFO @ Mon, 03 Jun 2019 20:19:42: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:19:42: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:19:42: #1 total tags in treatment: 5574327 INFO @ Mon, 03 Jun 2019 20:19:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:19:42: #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 20:19:42: #1 tags after filtering in treatment: 5574327 INFO @ Mon, 03 Jun 2019 20:19:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:19:42: #1 finished! INFO @ Mon, 03 Jun 2019 20:19:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:19:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:19:42: #2 number of paired peaks: 125 WARNING @ Mon, 03 Jun 2019 20:19:42: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Mon, 03 Jun 2019 20:19:42: start model_add_line... INFO @ Mon, 03 Jun 2019 20:19:42: start X-correlation... INFO @ Mon, 03 Jun 2019 20:19:42: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:19:42: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:19:42: #1 total tags in treatment: 5574327 INFO @ Mon, 03 Jun 2019 20:19:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:19:42: #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 20:19:42: end of X-cor INFO @ Mon, 03 Jun 2019 20:19:42: #2 finished! INFO @ Mon, 03 Jun 2019 20:19:42: #2 predicted fragment length is 322 bps INFO @ Mon, 03 Jun 2019 20:19:42: #2 alternative fragment length(s) may be 298,322 bps INFO @ Mon, 03 Jun 2019 20:19:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.05_model.r INFO @ Mon, 03 Jun 2019 20:19:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:19:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:19:42: #1 tags after filtering in treatment: 5574327 INFO @ Mon, 03 Jun 2019 20:19:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:19:42: #1 finished! INFO @ Mon, 03 Jun 2019 20:19:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:19:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:19:43: #2 number of paired peaks: 125 WARNING @ Mon, 03 Jun 2019 20:19:43: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Mon, 03 Jun 2019 20:19:43: start model_add_line... INFO @ Mon, 03 Jun 2019 20:19:43: start X-correlation... INFO @ Mon, 03 Jun 2019 20:19:43: end of X-cor INFO @ Mon, 03 Jun 2019 20:19:43: #2 finished! INFO @ Mon, 03 Jun 2019 20:19:43: #2 predicted fragment length is 322 bps INFO @ Mon, 03 Jun 2019 20:19:43: #2 alternative fragment length(s) may be 298,322 bps INFO @ Mon, 03 Jun 2019 20:19:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.20_model.r INFO @ Mon, 03 Jun 2019 20:19:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:19:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:19:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:20:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:20:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:20:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:20:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:20:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.10_summits.bed INFO @ Mon, 03 Jun 2019 20:20:01: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (580 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:20:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:20:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:20:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.05_summits.bed INFO @ Mon, 03 Jun 2019 20:20:08: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (981 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:20:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:20:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:20:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933886/SRX4933886.20_summits.bed INFO @ Mon, 03 Jun 2019 20:20:09: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (326 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。