Job ID = 2006636 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 799,237 reads read : 799,237 reads written : 799,237 spots read : 769,963 reads read : 769,963 reads written : 769,963 spots read : 786,424 reads read : 786,424 reads written : 786,424 2019-07-05T06:38:27 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' 2019-07-05T06:38:27 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/ERR2529577/ERR2529577.1' 2019-07-05T06:38:27 fasterq-dump.2.9.6 err: invalid accession 'ERR2529577' 2019-07-05T06:38:42 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' 2019-07-05T06:38:42 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/ERR2529577/ERR2529577.1' 2019-07-05T06:38:42 fasterq-dump.2.9.6 err: invalid accession 'ERR2529577' 2019-07-05T06:38:57 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' 2019-07-05T06:38:57 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/ERR2529577/ERR2529577.1' 2019-07-05T06:38:57 fasterq-dump.2.9.6 err: invalid accession 'ERR2529577' 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/ERR2529577/ERR2529577.1' 2019-07-05T06:39:22 fasterq-dump.2.9.6 err: invalid accession 'ERR2529577' 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/ERR2529577/ERR2529577.1' 2019-07-05T06:39:36 fasterq-dump.2.9.6 err: invalid accession 'ERR2529577' 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/ERR2529577/ERR2529577.1' 2019-07-05T06:39:51 fasterq-dump.2.9.6 err: invalid accession 'ERR2529577' 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/ERR2529577/ERR2529577.1' 2019-07-05T06:40:06 fasterq-dump.2.9.6 err: invalid accession 'ERR2529577' spots read : 808,213 reads read : 808,213 reads written : 808,213 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529574.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529575.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529576.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529577.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: 00:01:36 3163837 reads; of these: 3163837 (100.00%) were unpaired; of these: 108677 (3.43%) aligned 0 times 2657113 (83.98%) aligned exactly 1 time 398047 (12.58%) aligned >1 times 96.57% overall alignment rate Time searching: 00:01:36 Overall time: 00:01:36 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] 3019942 / 3055160 = 0.9885 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 15:45:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.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 15:45:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:45:18: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:45:19: #1 tag size is determined as 142 bps INFO @ Fri, 05 Jul 2019 15:45:19: #1 tag size = 142 INFO @ Fri, 05 Jul 2019 15:45:19: #1 total tags in treatment: 35218 INFO @ Fri, 05 Jul 2019 15:45:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:45:19: #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 15:45:19: #1 tags after filtering in treatment: 35218 INFO @ Fri, 05 Jul 2019 15:45:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:45:19: #1 finished! INFO @ Fri, 05 Jul 2019 15:45:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:45:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:45:19: #2 number of paired peaks: 256 WARNING @ Fri, 05 Jul 2019 15:45:19: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Fri, 05 Jul 2019 15:45:19: start model_add_line... INFO @ Fri, 05 Jul 2019 15:45:19: start X-correlation... INFO @ Fri, 05 Jul 2019 15:45:19: end of X-cor INFO @ Fri, 05 Jul 2019 15:45:19: #2 finished! INFO @ Fri, 05 Jul 2019 15:45:19: #2 predicted fragment length is 236 bps INFO @ Fri, 05 Jul 2019 15:45:19: #2 alternative fragment length(s) may be 21,54,82,109,146,185,206,236,271,303,331,361,393,494,524,562 bps INFO @ Fri, 05 Jul 2019 15:45:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.05_model.r WARNING @ Fri, 05 Jul 2019 15:45:19: #2 Since the d (236) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:45:19: #2 You may need to consider one of the other alternative d(s): 21,54,82,109,146,185,206,236,271,303,331,361,393,494,524,562 WARNING @ Fri, 05 Jul 2019 15:45:19: #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 15:45:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:45:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:45:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:45:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:45:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:45:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.05_summits.bed INFO @ Fri, 05 Jul 2019 15:45:19: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:45:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.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 15:45:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:45:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:45:20: #1 tag size is determined as 142 bps INFO @ Fri, 05 Jul 2019 15:45:20: #1 tag size = 142 INFO @ Fri, 05 Jul 2019 15:45:20: #1 total tags in treatment: 35218 INFO @ Fri, 05 Jul 2019 15:45:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:45:20: #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 15:45:20: #1 tags after filtering in treatment: 35218 INFO @ Fri, 05 Jul 2019 15:45:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:45:20: #1 finished! INFO @ Fri, 05 Jul 2019 15:45:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:45:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:45:20: #2 number of paired peaks: 256 WARNING @ Fri, 05 Jul 2019 15:45:20: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Fri, 05 Jul 2019 15:45:20: start model_add_line... INFO @ Fri, 05 Jul 2019 15:45:20: start X-correlation... INFO @ Fri, 05 Jul 2019 15:45:20: end of X-cor INFO @ Fri, 05 Jul 2019 15:45:20: #2 finished! INFO @ Fri, 05 Jul 2019 15:45:20: #2 predicted fragment length is 236 bps INFO @ Fri, 05 Jul 2019 15:45:20: #2 alternative fragment length(s) may be 21,54,82,109,146,185,206,236,271,303,331,361,393,494,524,562 bps INFO @ Fri, 05 Jul 2019 15:45:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.10_model.r WARNING @ Fri, 05 Jul 2019 15:45:20: #2 Since the d (236) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:45:20: #2 You may need to consider one of the other alternative d(s): 21,54,82,109,146,185,206,236,271,303,331,361,393,494,524,562 WARNING @ Fri, 05 Jul 2019 15:45:20: #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 15:45:20: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:45:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:45:20: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:45:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:45:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:45:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.10_summits.bed INFO @ Fri, 05 Jul 2019 15:45:20: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 15:45:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.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 15:45:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:45:20: #1 read treatment tags... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 15:45:21: #1 tag size is determined as 142 bps INFO @ Fri, 05 Jul 2019 15:45:21: #1 tag size = 142 INFO @ Fri, 05 Jul 2019 15:45:21: #1 total tags in treatment: 35218 INFO @ Fri, 05 Jul 2019 15:45:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:45:21: #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 15:45:21: #1 tags after filtering in treatment: 35218 INFO @ Fri, 05 Jul 2019 15:45:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:45:21: #1 finished! INFO @ Fri, 05 Jul 2019 15:45:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:45:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:45:21: #2 number of paired peaks: 256 WARNING @ Fri, 05 Jul 2019 15:45:21: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Fri, 05 Jul 2019 15:45:21: start model_add_line... INFO @ Fri, 05 Jul 2019 15:45:21: start X-correlation... INFO @ Fri, 05 Jul 2019 15:45:21: end of X-cor INFO @ Fri, 05 Jul 2019 15:45:21: #2 finished! INFO @ Fri, 05 Jul 2019 15:45:21: #2 predicted fragment length is 236 bps INFO @ Fri, 05 Jul 2019 15:45:21: #2 alternative fragment length(s) may be 21,54,82,109,146,185,206,236,271,303,331,361,393,494,524,562 bps INFO @ Fri, 05 Jul 2019 15:45:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.20_model.r WARNING @ Fri, 05 Jul 2019 15:45:21: #2 Since the d (236) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:45:21: #2 You may need to consider one of the other alternative d(s): 21,54,82,109,146,185,206,236,271,303,331,361,393,494,524,562 WARNING @ Fri, 05 Jul 2019 15:45:21: #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 15:45:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:45:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:45:21: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:45:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:45:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:45:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548177/ERX2548177.20_summits.bed INFO @ Fri, 05 Jul 2019 15:45:21: Done! pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling