Job ID = 2006637 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 812,912 reads read : 812,912 reads written : 812,912 spots read : 781,739 reads read : 781,739 reads written : 781,739 spots read : 800,546 reads read : 800,546 reads written : 800,546 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/ERR2529581/ERR2529581.1' 2019-07-05T06:38:30 fasterq-dump.2.9.6 err: invalid accession 'ERR2529581' 2019-07-05T06:38:44 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' 2019-07-05T06:38:44 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/ERR2529581/ERR2529581.1' 2019-07-05T06:38:44 fasterq-dump.2.9.6 err: invalid accession 'ERR2529581' 2019-07-05T06:38:59 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' 2019-07-05T06:38:59 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/ERR2529581/ERR2529581.1' 2019-07-05T06:38:59 fasterq-dump.2.9.6 err: invalid accession 'ERR2529581' 2019-07-05T06:39:21 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' 2019-07-05T06:39:21 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/ERR2529581/ERR2529581.1' 2019-07-05T06:39:21 fasterq-dump.2.9.6 err: invalid accession 'ERR2529581' 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/ERR2529581/ERR2529581.1' 2019-07-05T06:39:36 fasterq-dump.2.9.6 err: invalid accession 'ERR2529581' 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/ERR2529581/ERR2529581.1' 2019-07-05T06:39:51 fasterq-dump.2.9.6 err: invalid accession 'ERR2529581' 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/ERR2529581/ERR2529581.1' 2019-07-05T06:40:06 fasterq-dump.2.9.6 err: invalid accession 'ERR2529581' spots read : 815,616 reads read : 815,616 reads written : 815,616 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529578.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529579.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529581.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: 00:02:52 3210813 reads; of these: 3210813 (100.00%) were unpaired; of these: 103286 (3.22%) aligned 0 times 2694978 (83.93%) aligned exactly 1 time 412549 (12.85%) aligned >1 times 96.78% overall alignment rate Time searching: 00:02:52 Overall time: 00:02:52 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] 3073418 / 3107527 = 0.9890 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 15:47:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.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 15:47:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:47:11: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:47:11: #1 tag size is determined as 148 bps INFO @ Fri, 05 Jul 2019 15:47:11: #1 tag size = 148 INFO @ Fri, 05 Jul 2019 15:47:11: #1 total tags in treatment: 34109 INFO @ Fri, 05 Jul 2019 15:47:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:47:11: #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 15:47:11: #1 tags after filtering in treatment: 34109 INFO @ Fri, 05 Jul 2019 15:47:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:47:11: #1 finished! INFO @ Fri, 05 Jul 2019 15:47:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:47:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:47:11: #2 number of paired peaks: 261 WARNING @ Fri, 05 Jul 2019 15:47:11: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Fri, 05 Jul 2019 15:47:11: start model_add_line... INFO @ Fri, 05 Jul 2019 15:47:11: start X-correlation... INFO @ Fri, 05 Jul 2019 15:47:11: end of X-cor INFO @ Fri, 05 Jul 2019 15:47:11: #2 finished! INFO @ Fri, 05 Jul 2019 15:47:11: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 15:47:11: #2 alternative fragment length(s) may be 18,73,135,164,194,237,311,411,438,494,531,558,593 bps INFO @ Fri, 05 Jul 2019 15:47:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.05_model.r WARNING @ Fri, 05 Jul 2019 15:47:11: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:47:11: #2 You may need to consider one of the other alternative d(s): 18,73,135,164,194,237,311,411,438,494,531,558,593 WARNING @ Fri, 05 Jul 2019 15:47:11: #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 15:47:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:47:11: #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: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:47:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:47:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.05_summits.bed INFO @ Fri, 05 Jul 2019 15:47:11: Done! INFO @ Fri, 05 Jul 2019 15:47:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.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 15:47:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:47:12: #1 read treatment tags... pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (22 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:47:12: #1 tag size is determined as 148 bps INFO @ Fri, 05 Jul 2019 15:47:12: #1 tag size = 148 INFO @ Fri, 05 Jul 2019 15:47:12: #1 total tags in treatment: 34109 INFO @ Fri, 05 Jul 2019 15:47:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:47:12: #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 15:47:12: #1 tags after filtering in treatment: 34109 INFO @ Fri, 05 Jul 2019 15:47:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:47:12: #1 finished! INFO @ Fri, 05 Jul 2019 15:47:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:47:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:47:12: #2 number of paired peaks: 261 WARNING @ Fri, 05 Jul 2019 15:47:12: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Fri, 05 Jul 2019 15:47:12: start model_add_line... INFO @ Fri, 05 Jul 2019 15:47:12: start X-correlation... INFO @ Fri, 05 Jul 2019 15:47:12: end of X-cor INFO @ Fri, 05 Jul 2019 15:47:12: #2 finished! INFO @ Fri, 05 Jul 2019 15:47:12: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 15:47:12: #2 alternative fragment length(s) may be 18,73,135,164,194,237,311,411,438,494,531,558,593 bps INFO @ Fri, 05 Jul 2019 15:47:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.10_model.r WARNING @ Fri, 05 Jul 2019 15:47:12: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:47:12: #2 You may need to consider one of the other alternative d(s): 18,73,135,164,194,237,311,411,438,494,531,558,593 WARNING @ Fri, 05 Jul 2019 15:47:12: #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 15:47:12: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:47:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:47:12: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:47:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:47:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:47:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.10_summits.bed INFO @ Fri, 05 Jul 2019 15:47:12: 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 15:47:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.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 15:47:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:47:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:47:13: #1 tag size is determined as 148 bps INFO @ Fri, 05 Jul 2019 15:47:13: #1 tag size = 148 INFO @ Fri, 05 Jul 2019 15:47:13: #1 total tags in treatment: 34109 INFO @ Fri, 05 Jul 2019 15:47:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:47:13: #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 15:47:13: #1 tags after filtering in treatment: 34109 INFO @ Fri, 05 Jul 2019 15:47:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:47:13: #1 finished! INFO @ Fri, 05 Jul 2019 15:47:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:47:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:47:13: #2 number of paired peaks: 261 WARNING @ Fri, 05 Jul 2019 15:47:13: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Fri, 05 Jul 2019 15:47:13: start model_add_line... INFO @ Fri, 05 Jul 2019 15:47:13: start X-correlation... INFO @ Fri, 05 Jul 2019 15:47:13: end of X-cor INFO @ Fri, 05 Jul 2019 15:47:13: #2 finished! INFO @ Fri, 05 Jul 2019 15:47:13: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 15:47:13: #2 alternative fragment length(s) may be 18,73,135,164,194,237,311,411,438,494,531,558,593 bps INFO @ Fri, 05 Jul 2019 15:47:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.20_model.r WARNING @ Fri, 05 Jul 2019 15:47:13: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:47:13: #2 You may need to consider one of the other alternative d(s): 18,73,135,164,194,237,311,411,438,494,531,558,593 WARNING @ Fri, 05 Jul 2019 15:47:13: #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 15:47:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:47:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:47:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:47:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:47:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:47:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548178/ERX2548178.20_summits.bed INFO @ Fri, 05 Jul 2019 15:47:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling