Job ID = 2006635 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,238,338 reads read : 2,238,338 reads written : 2,238,338 spots read : 2,157,595 reads read : 2,157,595 reads written : 2,157,595 spots read : 2,181,907 reads read : 2,181,907 reads written : 2,181,907 2019-07-05T06:38:14 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' 2019-07-05T06:38:14 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/ERR2529573/ERR2529573.1' 2019-07-05T06:38:14 fasterq-dump.2.9.6 err: invalid accession 'ERR2529573' 2019-07-05T06:38:30 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' 2019-07-05T06:38:30 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/ERR2529573/ERR2529573.1' 2019-07-05T06:38:30 fasterq-dump.2.9.6 err: invalid accession 'ERR2529573' 2019-07-05T06:38:45 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' 2019-07-05T06:38:45 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/ERR2529573/ERR2529573.1' 2019-07-05T06:38:45 fasterq-dump.2.9.6 err: invalid accession 'ERR2529573' 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/ERR2529573/ERR2529573.1' 2019-07-05T06:39:00 fasterq-dump.2.9.6 err: invalid accession 'ERR2529573' 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/ERR2529573/ERR2529573.1' 2019-07-05T06:39:22 fasterq-dump.2.9.6 err: invalid accession 'ERR2529573' 2019-07-05T06:39:37 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' 2019-07-05T06:39:37 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/ERR2529573/ERR2529573.1' 2019-07-05T06:39:37 fasterq-dump.2.9.6 err: invalid accession 'ERR2529573' 2019-07-05T06:39:52 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' 2019-07-05T06:39:52 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/ERR2529573/ERR2529573.1' 2019-07-05T06:39:52 fasterq-dump.2.9.6 err: invalid accession 'ERR2529573' 2019-07-05T06:40:07 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' 2019-07-05T06:40:07 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/ERR2529573/ERR2529573.1' 2019-07-05T06:40:07 fasterq-dump.2.9.6 err: invalid accession 'ERR2529573' spots read : 2,146,680 reads read : 2,146,680 reads written : 2,146,680 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529570.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529571.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529572.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529573.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: 00:02:56 8724520 reads; of these: 8724520 (100.00%) were unpaired; of these: 326104 (3.74%) aligned 0 times 7222430 (82.78%) aligned exactly 1 time 1175986 (13.48%) aligned >1 times 96.26% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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_rmdupse_core] 7998138 / 8398416 = 0.9523 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 15:47:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.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 15:47:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:47:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:47:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.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 15:47:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:47:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:47:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.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 15:47:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:47:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:47:07: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:47:07: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:47:07: #1 total tags in treatment: 400278 INFO @ Fri, 05 Jul 2019 15:47:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:47:07: #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 15:47:07: #1 tags after filtering in treatment: 400278 INFO @ Fri, 05 Jul 2019 15:47:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:47:07: #1 finished! INFO @ Fri, 05 Jul 2019 15:47:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:47:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:47:07: #2 number of paired peaks: 490 WARNING @ Fri, 05 Jul 2019 15:47:07: Fewer paired peaks (490) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 490 pairs to build model! INFO @ Fri, 05 Jul 2019 15:47:07: start model_add_line... INFO @ Fri, 05 Jul 2019 15:47:07: start X-correlation... INFO @ Fri, 05 Jul 2019 15:47:07: end of X-cor INFO @ Fri, 05 Jul 2019 15:47:07: #2 finished! INFO @ Fri, 05 Jul 2019 15:47:07: #2 predicted fragment length is 71 bps INFO @ Fri, 05 Jul 2019 15:47:07: #2 alternative fragment length(s) may be 71 bps INFO @ Fri, 05 Jul 2019 15:47:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.05_model.r WARNING @ Fri, 05 Jul 2019 15:47:07: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:47:07: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Fri, 05 Jul 2019 15:47:07: #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 15:47:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:47:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:47:09: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:47:09: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:47:09: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:47:09: #1 total tags in treatment: 400278 INFO @ Fri, 05 Jul 2019 15:47:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:47:09: #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 15:47:09: #1 tags after filtering in treatment: 400278 INFO @ Fri, 05 Jul 2019 15:47:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:47:09: #1 finished! INFO @ Fri, 05 Jul 2019 15:47:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:47:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:47:09: #2 number of paired peaks: 490 WARNING @ Fri, 05 Jul 2019 15:47:09: Fewer paired peaks (490) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 490 pairs to build model! INFO @ Fri, 05 Jul 2019 15:47:09: start model_add_line... INFO @ Fri, 05 Jul 2019 15:47:09: start X-correlation... INFO @ Fri, 05 Jul 2019 15:47:09: end of X-cor INFO @ Fri, 05 Jul 2019 15:47:09: #2 finished! INFO @ Fri, 05 Jul 2019 15:47:09: #2 predicted fragment length is 71 bps INFO @ Fri, 05 Jul 2019 15:47:09: #2 alternative fragment length(s) may be 71 bps INFO @ Fri, 05 Jul 2019 15:47:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.10_model.r WARNING @ Fri, 05 Jul 2019 15:47:09: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:47:09: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Fri, 05 Jul 2019 15:47:09: #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 15:47:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:47:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:47:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:47:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:47:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.05_summits.bed INFO @ Fri, 05 Jul 2019 15:47:09: Done! INFO @ Fri, 05 Jul 2019 15:47:10: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:47:10: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:47:10: #1 total tags in treatment: 400278 INFO @ Fri, 05 Jul 2019 15:47:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:47:10: #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 15:47:10: #1 tags after filtering in treatment: 400278 INFO @ Fri, 05 Jul 2019 15:47:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:47:10: #1 finished! INFO @ Fri, 05 Jul 2019 15:47:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:47:10: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (220 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 15:47:10: #2 number of paired peaks: 490 WARNING @ Fri, 05 Jul 2019 15:47:10: Fewer paired peaks (490) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 490 pairs to build model! INFO @ Fri, 05 Jul 2019 15:47:10: start model_add_line... INFO @ Fri, 05 Jul 2019 15:47:10: start X-correlation... INFO @ Fri, 05 Jul 2019 15:47:10: end of X-cor INFO @ Fri, 05 Jul 2019 15:47:10: #2 finished! INFO @ Fri, 05 Jul 2019 15:47:10: #2 predicted fragment length is 71 bps INFO @ Fri, 05 Jul 2019 15:47:10: #2 alternative fragment length(s) may be 71 bps INFO @ Fri, 05 Jul 2019 15:47:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.20_model.r WARNING @ Fri, 05 Jul 2019 15:47:10: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:47:10: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Fri, 05 Jul 2019 15:47:10: #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 15:47:10: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:47:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:47:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:47:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:47:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:47:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:47:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.10_summits.bed INFO @ Fri, 05 Jul 2019 15:47:11: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (131 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:47:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:47:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:47:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548176/ERX2548176.20_summits.bed INFO @ Fri, 05 Jul 2019 15:47:12: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (86 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 CompletedMACS2peakCalling