Job ID = 2006933 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T06:39:40 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' 2019-07-05T06:39:40 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/ERR2529596/ERR2529596.1' 2019-07-05T06:39:40 fasterq-dump.2.9.6 err: invalid accession 'ERR2529596' 2019-07-05T06:39:55 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' 2019-07-05T06:39:55 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/ERR2529596/ERR2529596.1' 2019-07-05T06:39:55 fasterq-dump.2.9.6 err: invalid accession 'ERR2529596' 2019-07-05T06:40:10 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' 2019-07-05T06:40:10 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/ERR2529596/ERR2529596.1' 2019-07-05T06:40:10 fasterq-dump.2.9.6 err: invalid accession 'ERR2529596' spots read : 1,438,726 reads read : 1,438,726 reads written : 1,438,726 spots read : 1,377,353 reads read : 1,377,353 reads written : 1,377,353 spots read : 1,518,789 reads read : 1,518,789 reads written : 1,518,789 spots read : 1,375,936 reads read : 1,375,936 reads written : 1,375,936 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529596.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529597.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529598.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529599.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: 00:03:30 5710804 reads; of these: 5710804 (100.00%) were unpaired; of these: 310404 (5.44%) aligned 0 times 4606544 (80.66%) aligned exactly 1 time 793856 (13.90%) aligned >1 times 94.56% overall alignment rate Time searching: 00:03:30 Overall time: 00:03:30 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] 5277293 / 5400400 = 0.9772 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 15:51:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.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 15:51:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:51:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:51:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.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 15:51:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:51:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:51:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.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 15:51:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:51:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:51:56: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:51:56: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:51:56: #1 total tags in treatment: 123107 INFO @ Fri, 05 Jul 2019 15:51:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:51:56: #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 15:51:56: #1 tags after filtering in treatment: 123107 INFO @ Fri, 05 Jul 2019 15:51:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:51:56: #1 finished! INFO @ Fri, 05 Jul 2019 15:51:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:51:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:51:56: #2 number of paired peaks: 418 WARNING @ Fri, 05 Jul 2019 15:51:56: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Fri, 05 Jul 2019 15:51:56: start model_add_line... INFO @ Fri, 05 Jul 2019 15:51:56: start X-correlation... INFO @ Fri, 05 Jul 2019 15:51:56: end of X-cor INFO @ Fri, 05 Jul 2019 15:51:56: #2 finished! INFO @ Fri, 05 Jul 2019 15:51:56: #2 predicted fragment length is 53 bps INFO @ Fri, 05 Jul 2019 15:51:56: #2 alternative fragment length(s) may be 4,53,106,129,186,231,271,295,309,366,401,460,464,476,503,566 bps INFO @ Fri, 05 Jul 2019 15:51:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.05_model.r WARNING @ Fri, 05 Jul 2019 15:51:56: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:51:56: #2 You may need to consider one of the other alternative d(s): 4,53,106,129,186,231,271,295,309,366,401,460,464,476,503,566 WARNING @ Fri, 05 Jul 2019 15:51:56: #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 15:51:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:51:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:51:56: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:51:56: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:51:56: #1 total tags in treatment: 123107 INFO @ Fri, 05 Jul 2019 15:51:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:51:56: #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 15:51:56: #1 tags after filtering in treatment: 123107 INFO @ Fri, 05 Jul 2019 15:51:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:51:56: #1 finished! INFO @ Fri, 05 Jul 2019 15:51:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:51:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:51:56: #2 number of paired peaks: 418 WARNING @ Fri, 05 Jul 2019 15:51:56: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Fri, 05 Jul 2019 15:51:56: start model_add_line... INFO @ Fri, 05 Jul 2019 15:51:56: start X-correlation... INFO @ Fri, 05 Jul 2019 15:51:56: end of X-cor INFO @ Fri, 05 Jul 2019 15:51:56: #2 finished! INFO @ Fri, 05 Jul 2019 15:51:56: #2 predicted fragment length is 53 bps INFO @ Fri, 05 Jul 2019 15:51:56: #2 alternative fragment length(s) may be 4,53,106,129,186,231,271,295,309,366,401,460,464,476,503,566 bps INFO @ Fri, 05 Jul 2019 15:51:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.10_model.r WARNING @ Fri, 05 Jul 2019 15:51:56: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:51:56: #2 You may need to consider one of the other alternative d(s): 4,53,106,129,186,231,271,295,309,366,401,460,464,476,503,566 WARNING @ Fri, 05 Jul 2019 15:51:56: #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 15:51:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:51:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:51:56: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:51:57: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:51:57: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:51:58: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:51:58: #1 total tags in treatment: 123107 INFO @ Fri, 05 Jul 2019 15:51:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:51:58: #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 15:51:58: #1 tags after filtering in treatment: 123107 INFO @ Fri, 05 Jul 2019 15:51:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:51:58: #1 finished! INFO @ Fri, 05 Jul 2019 15:51:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:51:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:51:58: #2 number of paired peaks: 418 WARNING @ Fri, 05 Jul 2019 15:51:58: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Fri, 05 Jul 2019 15:51:58: start model_add_line... INFO @ Fri, 05 Jul 2019 15:51:58: start X-correlation... INFO @ Fri, 05 Jul 2019 15:51:58: end of X-cor INFO @ Fri, 05 Jul 2019 15:51:58: #2 finished! INFO @ Fri, 05 Jul 2019 15:51:58: #2 predicted fragment length is 53 bps INFO @ Fri, 05 Jul 2019 15:51:58: #2 alternative fragment length(s) may be 4,53,106,129,186,231,271,295,309,366,401,460,464,476,503,566 bps INFO @ Fri, 05 Jul 2019 15:51:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.20_model.r WARNING @ Fri, 05 Jul 2019 15:51:58: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:51:58: #2 You may need to consider one of the other alternative d(s): 4,53,106,129,186,231,271,295,309,366,401,460,464,476,503,566 WARNING @ Fri, 05 Jul 2019 15:51:58: #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 15:51:58: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:51:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:51:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:51:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:51:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.05_summits.bed INFO @ Fri, 05 Jul 2019 15:51:58: Done! INFO @ Fri, 05 Jul 2019 15:51:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:51:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:51:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.10_summits.bed INFO @ Fri, 05 Jul 2019 15:51:58: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:51:58: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:51:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:51:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:51:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548187/ERX2548187.20_summits.bed INFO @ Fri, 05 Jul 2019 15:51:58: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (17 records, 4 fields): 2 millis pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling