Job ID = 1306646 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T12:45:28 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' 2019-06-03T12:45:28 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/sra18/SRR/001184/SRR1213166' 2019-06-03T12:45:37 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1213166' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 12,292,203 reads read : 12,292,203 reads written : 12,292,203 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: 00:04:16 12292203 reads; of these: 12292203 (100.00%) were unpaired; of these: 2384809 (19.40%) aligned 0 times 6790504 (55.24%) aligned exactly 1 time 3116890 (25.36%) aligned >1 times 80.60% overall alignment rate Time searching: 00:04:16 Overall time: 00:04:16 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] 3524873 / 9907394 = 0.3558 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 21:59:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.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 21:59:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:59:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:59:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.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 21:59:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:59:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:59:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.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 21:59:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:59:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:59:23: 1000000 INFO @ Mon, 03 Jun 2019 21:59:24: 1000000 INFO @ Mon, 03 Jun 2019 21:59:24: 1000000 INFO @ Mon, 03 Jun 2019 21:59:33: 2000000 INFO @ Mon, 03 Jun 2019 21:59:35: 2000000 INFO @ Mon, 03 Jun 2019 21:59:35: 2000000 INFO @ Mon, 03 Jun 2019 21:59:43: 3000000 INFO @ Mon, 03 Jun 2019 21:59:45: 3000000 INFO @ Mon, 03 Jun 2019 21:59:46: 3000000 INFO @ Mon, 03 Jun 2019 21:59:53: 4000000 INFO @ Mon, 03 Jun 2019 21:59:56: 4000000 INFO @ Mon, 03 Jun 2019 21:59:57: 4000000 INFO @ Mon, 03 Jun 2019 22:00:03: 5000000 INFO @ Mon, 03 Jun 2019 22:00:06: 5000000 INFO @ Mon, 03 Jun 2019 22:00:08: 5000000 INFO @ Mon, 03 Jun 2019 22:00:13: 6000000 INFO @ Mon, 03 Jun 2019 22:00:16: 6000000 INFO @ Mon, 03 Jun 2019 22:00:17: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 22:00:17: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 22:00:17: #1 total tags in treatment: 6382521 INFO @ Mon, 03 Jun 2019 22:00:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:00:17: #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 22:00:17: #1 tags after filtering in treatment: 6382521 INFO @ Mon, 03 Jun 2019 22:00:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:00:17: #1 finished! INFO @ Mon, 03 Jun 2019 22:00:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:00:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:00:18: #2 number of paired peaks: 322 WARNING @ Mon, 03 Jun 2019 22:00:18: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Mon, 03 Jun 2019 22:00:18: start model_add_line... INFO @ Mon, 03 Jun 2019 22:00:18: start X-correlation... INFO @ Mon, 03 Jun 2019 22:00:18: end of X-cor INFO @ Mon, 03 Jun 2019 22:00:18: #2 finished! INFO @ Mon, 03 Jun 2019 22:00:18: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 22:00:18: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 22:00:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.05_model.r WARNING @ Mon, 03 Jun 2019 22:00:18: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:00:18: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 22:00:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 22:00:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:00:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:00:19: 6000000 INFO @ Mon, 03 Jun 2019 22:00:20: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 22:00:20: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 22:00:20: #1 total tags in treatment: 6382521 INFO @ Mon, 03 Jun 2019 22:00:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:00:20: #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 22:00:20: #1 tags after filtering in treatment: 6382521 INFO @ Mon, 03 Jun 2019 22:00:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:00:20: #1 finished! INFO @ Mon, 03 Jun 2019 22:00:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:00:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:00:21: #2 number of paired peaks: 322 WARNING @ Mon, 03 Jun 2019 22:00:21: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Mon, 03 Jun 2019 22:00:21: start model_add_line... INFO @ Mon, 03 Jun 2019 22:00:21: start X-correlation... INFO @ Mon, 03 Jun 2019 22:00:21: end of X-cor INFO @ Mon, 03 Jun 2019 22:00:21: #2 finished! INFO @ Mon, 03 Jun 2019 22:00:21: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 22:00:21: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 22:00:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.20_model.r WARNING @ Mon, 03 Jun 2019 22:00:21: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:00:21: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 22:00:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 22:00:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:00:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:00:23: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 22:00:23: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 22:00:23: #1 total tags in treatment: 6382521 INFO @ Mon, 03 Jun 2019 22:00:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:00:23: #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 22:00:24: #1 tags after filtering in treatment: 6382521 INFO @ Mon, 03 Jun 2019 22:00:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:00:24: #1 finished! INFO @ Mon, 03 Jun 2019 22:00:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:00:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:00:24: #2 number of paired peaks: 322 WARNING @ Mon, 03 Jun 2019 22:00:24: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Mon, 03 Jun 2019 22:00:24: start model_add_line... INFO @ Mon, 03 Jun 2019 22:00:24: start X-correlation... INFO @ Mon, 03 Jun 2019 22:00:24: end of X-cor INFO @ Mon, 03 Jun 2019 22:00:24: #2 finished! INFO @ Mon, 03 Jun 2019 22:00:24: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 22:00:24: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 22:00:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.10_model.r WARNING @ Mon, 03 Jun 2019 22:00:24: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:00:24: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 22:00:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 22:00:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:00:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:00:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:00:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:00:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:00:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:00:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:00:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.05_summits.bed INFO @ Mon, 03 Jun 2019 22:00:49: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1384 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:00:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:00:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:00:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.20_summits.bed INFO @ Mon, 03 Jun 2019 22:00:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (554 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:00:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:00:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:00:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507379/SRX507379.10_summits.bed INFO @ Mon, 03 Jun 2019 22:00:53: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (973 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。