Job ID = 1293014 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T12:20:38 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' 2019-06-02T12:20:38 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/sos/sra-pub-run-1/SRR8201409/SRR8201409.1' 2019-06-02T12:20:38 fasterq-dump.2.9.6 err: invalid accession 'SRR8201409' spots read : 7,467,832 reads read : 7,467,832 reads written : 7,467,832 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: 00:01:16 7467832 reads; of these: 7467832 (100.00%) were unpaired; of these: 4762946 (63.78%) aligned 0 times 2228314 (29.84%) aligned exactly 1 time 476572 (6.38%) aligned >1 times 36.22% overall alignment rate Time searching: 00:01:16 Overall time: 00:01:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 797379 / 2704886 = 0.2948 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 @ Sun, 02 Jun 2019 21:24:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 21:24:19: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:24:19: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:24:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 21:24:19: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:24:19: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:24:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 21:24:19: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:24:19: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:24:26: 1000000 INFO @ Sun, 02 Jun 2019 21:24:27: 1000000 INFO @ Sun, 02 Jun 2019 21:24:27: 1000000 INFO @ Sun, 02 Jun 2019 21:24:32: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:24:32: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:24:32: #1 total tags in treatment: 1907507 INFO @ Sun, 02 Jun 2019 21:24:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:24:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:24:32: #1 tags after filtering in treatment: 1907507 INFO @ Sun, 02 Jun 2019 21:24:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:24:32: #1 finished! INFO @ Sun, 02 Jun 2019 21:24:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:24:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:24:33: #2 number of paired peaks: 558 WARNING @ Sun, 02 Jun 2019 21:24:33: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Sun, 02 Jun 2019 21:24:33: start model_add_line... INFO @ Sun, 02 Jun 2019 21:24:33: start X-correlation... INFO @ Sun, 02 Jun 2019 21:24:33: end of X-cor INFO @ Sun, 02 Jun 2019 21:24:33: #2 finished! INFO @ Sun, 02 Jun 2019 21:24:33: #2 predicted fragment length is 54 bps INFO @ Sun, 02 Jun 2019 21:24:33: #2 alternative fragment length(s) may be 54 bps INFO @ Sun, 02 Jun 2019 21:24:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.10_model.r WARNING @ Sun, 02 Jun 2019 21:24:33: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:24:33: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sun, 02 Jun 2019 21:24:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 21:24:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:24:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:24:34: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:24:34: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:24:34: #1 total tags in treatment: 1907507 INFO @ Sun, 02 Jun 2019 21:24:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:24:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:24:34: #1 tags after filtering in treatment: 1907507 INFO @ Sun, 02 Jun 2019 21:24:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:24:34: #1 finished! INFO @ Sun, 02 Jun 2019 21:24:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:24:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:24:34: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:24:34: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:24:34: #1 total tags in treatment: 1907507 INFO @ Sun, 02 Jun 2019 21:24:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:24:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:24:35: #1 tags after filtering in treatment: 1907507 INFO @ Sun, 02 Jun 2019 21:24:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:24:35: #1 finished! INFO @ Sun, 02 Jun 2019 21:24:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:24:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:24:35: #2 number of paired peaks: 558 WARNING @ Sun, 02 Jun 2019 21:24:35: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Sun, 02 Jun 2019 21:24:35: start model_add_line... INFO @ Sun, 02 Jun 2019 21:24:35: start X-correlation... INFO @ Sun, 02 Jun 2019 21:24:35: end of X-cor INFO @ Sun, 02 Jun 2019 21:24:35: #2 finished! INFO @ Sun, 02 Jun 2019 21:24:35: #2 predicted fragment length is 54 bps INFO @ Sun, 02 Jun 2019 21:24:35: #2 alternative fragment length(s) may be 54 bps INFO @ Sun, 02 Jun 2019 21:24:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.05_model.r WARNING @ Sun, 02 Jun 2019 21:24:35: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:24:35: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sun, 02 Jun 2019 21:24:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 21:24:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:24:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:24:35: #2 number of paired peaks: 558 WARNING @ Sun, 02 Jun 2019 21:24:35: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Sun, 02 Jun 2019 21:24:35: start model_add_line... INFO @ Sun, 02 Jun 2019 21:24:35: start X-correlation... INFO @ Sun, 02 Jun 2019 21:24:35: end of X-cor INFO @ Sun, 02 Jun 2019 21:24:35: #2 finished! INFO @ Sun, 02 Jun 2019 21:24:35: #2 predicted fragment length is 54 bps INFO @ Sun, 02 Jun 2019 21:24:35: #2 alternative fragment length(s) may be 54 bps INFO @ Sun, 02 Jun 2019 21:24:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.20_model.r WARNING @ Sun, 02 Jun 2019 21:24:35: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:24:35: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sun, 02 Jun 2019 21:24:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 21:24:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:24:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:24:39: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:24:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:24:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:24:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:24:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:24:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.10_summits.bed INFO @ Sun, 02 Jun 2019 21:24:42: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (230 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:24:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:24:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:24:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.05_summits.bed INFO @ Sun, 02 Jun 2019 21:24:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (453 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:24:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:24:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:24:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020786/SRX5020786.20_summits.bed INFO @ Sun, 02 Jun 2019 21:24:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (108 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。