Job ID = 2006929 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T06:39:00 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T06:39:00 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-2/ERR2529594/ERR2529594.1' 2019-07-05T06:39:00 fasterq-dump.2.9.6 err: invalid accession 'ERR2529594' 2019-07-05T06:39:22 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T06:39:22 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-2/ERR2529594/ERR2529594.1' 2019-07-05T06:39:22 fasterq-dump.2.9.6 err: invalid accession 'ERR2529594' 2019-07-05T06:39:36 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T06:39:36 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-2/ERR2529594/ERR2529594.1' 2019-07-05T06:39:36 fasterq-dump.2.9.6 err: invalid accession 'ERR2529594' 2019-07-05T06:39:51 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T06:39:51 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-2/ERR2529594/ERR2529594.1' 2019-07-05T06:39:51 fasterq-dump.2.9.6 err: invalid accession 'ERR2529594' 2019-07-05T06:40:06 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T06:40:06 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-2/ERR2529594/ERR2529594.1' 2019-07-05T06:40:06 fasterq-dump.2.9.6 err: invalid accession 'ERR2529594' spots read : 12,714,870 reads read : 12,714,870 reads written : 12,714,870 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529594.sra.cache’: 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: 00:03:01 12714870 reads; of these: 12714870 (100.00%) were unpaired; of these: 446771 (3.51%) aligned 0 times 10085078 (79.32%) aligned exactly 1 time 2183021 (17.17%) aligned >1 times 96.49% overall alignment rate Time searching: 00:03:01 Overall time: 00:03:01 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 12015373 / 12268099 = 0.9794 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 @ Fri, 05 Jul 2019 15:59:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 15:59:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:59:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:59:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 15:59:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:59:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:59:21: #1 tag size is determined as 58 bps INFO @ Fri, 05 Jul 2019 15:59:21: #1 tag size = 58 INFO @ Fri, 05 Jul 2019 15:59:21: #1 total tags in treatment: 252726 INFO @ Fri, 05 Jul 2019 15:59:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:59:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 15:59:21: #1 tags after filtering in treatment: 252726 INFO @ Fri, 05 Jul 2019 15:59:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:59:21: #1 finished! INFO @ Fri, 05 Jul 2019 15:59:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:59:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:59:21: #2 number of paired peaks: 477 WARNING @ Fri, 05 Jul 2019 15:59:21: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Fri, 05 Jul 2019 15:59:21: start model_add_line... INFO @ Fri, 05 Jul 2019 15:59:21: start X-correlation... INFO @ Fri, 05 Jul 2019 15:59:21: end of X-cor INFO @ Fri, 05 Jul 2019 15:59:21: #2 finished! INFO @ Fri, 05 Jul 2019 15:59:21: #2 predicted fragment length is 80 bps INFO @ Fri, 05 Jul 2019 15:59:21: #2 alternative fragment length(s) may be 42,80,110,164,482,508,546,580 bps INFO @ Fri, 05 Jul 2019 15:59:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.05_model.r WARNING @ Fri, 05 Jul 2019 15:59:21: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:59:21: #2 You may need to consider one of the other alternative d(s): 42,80,110,164,482,508,546,580 WARNING @ Fri, 05 Jul 2019 15:59:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 15:59:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:59:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:59:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 15:59:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:59:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:59:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:59:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:59:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:59:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.05_summits.bed INFO @ Fri, 05 Jul 2019 15:59:23: Done! INFO @ Fri, 05 Jul 2019 15:59:23: #1 tag size is determined as 58 bps INFO @ Fri, 05 Jul 2019 15:59:23: #1 tag size = 58 INFO @ Fri, 05 Jul 2019 15:59:23: #1 total tags in treatment: 252726 INFO @ Fri, 05 Jul 2019 15:59:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:59:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 15:59:23: #1 tags after filtering in treatment: 252726 INFO @ Fri, 05 Jul 2019 15:59:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:59:23: #1 finished! INFO @ Fri, 05 Jul 2019 15:59:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:59:23: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (268 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:59:23: #2 number of paired peaks: 477 WARNING @ Fri, 05 Jul 2019 15:59:23: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Fri, 05 Jul 2019 15:59:23: start model_add_line... INFO @ Fri, 05 Jul 2019 15:59:23: start X-correlation... INFO @ Fri, 05 Jul 2019 15:59:23: end of X-cor INFO @ Fri, 05 Jul 2019 15:59:23: #2 finished! INFO @ Fri, 05 Jul 2019 15:59:23: #2 predicted fragment length is 80 bps INFO @ Fri, 05 Jul 2019 15:59:23: #2 alternative fragment length(s) may be 42,80,110,164,482,508,546,580 bps INFO @ Fri, 05 Jul 2019 15:59:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.10_model.r WARNING @ Fri, 05 Jul 2019 15:59:23: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:59:23: #2 You may need to consider one of the other alternative d(s): 42,80,110,164,482,508,546,580 WARNING @ Fri, 05 Jul 2019 15:59:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 15:59:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:59:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:59:24: #1 tag size is determined as 58 bps INFO @ Fri, 05 Jul 2019 15:59:24: #1 tag size = 58 INFO @ Fri, 05 Jul 2019 15:59:24: #1 total tags in treatment: 252726 INFO @ Fri, 05 Jul 2019 15:59:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:59:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 15:59:24: #1 tags after filtering in treatment: 252726 INFO @ Fri, 05 Jul 2019 15:59:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:59:24: #1 finished! INFO @ Fri, 05 Jul 2019 15:59:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:59:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:59:24: #2 number of paired peaks: 477 WARNING @ Fri, 05 Jul 2019 15:59:24: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Fri, 05 Jul 2019 15:59:24: start model_add_line... INFO @ Fri, 05 Jul 2019 15:59:24: start X-correlation... INFO @ Fri, 05 Jul 2019 15:59:24: end of X-cor INFO @ Fri, 05 Jul 2019 15:59:24: #2 finished! INFO @ Fri, 05 Jul 2019 15:59:24: #2 predicted fragment length is 80 bps INFO @ Fri, 05 Jul 2019 15:59:24: #2 alternative fragment length(s) may be 42,80,110,164,482,508,546,580 bps INFO @ Fri, 05 Jul 2019 15:59:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.20_model.r WARNING @ Fri, 05 Jul 2019 15:59:24: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:59:24: #2 You may need to consider one of the other alternative d(s): 42,80,110,164,482,508,546,580 WARNING @ Fri, 05 Jul 2019 15:59:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 15:59:24: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:59:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:59:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:59:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:59:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:59:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.10_summits.bed INFO @ Fri, 05 Jul 2019 15:59:24: Done! INFO @ Fri, 05 Jul 2019 15:59:25: #3 Call peaks for each chromosome... pass1 - making usageList (16 chroms)CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 15:59:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.20_peaks.xls : 0 millis pass2 - checking and writing primary data (101 records, 4 fields)INFO @ Fri, 05 Jul 2019 15:59:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.20_peaks.narrowPeak : 1500 millis INFO @ Fri, 05 Jul 2019 15:59:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548185/ERX2548185.20_summits.bed INFO @ Fri, 05 Jul 2019 15:59:27: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (28 records, 4 fields): 2 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling