Job ID = 2006633 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,806,897 reads read : 1,806,897 reads written : 1,806,897 spots read : 1,744,590 reads read : 1,744,590 reads written : 1,744,590 spots read : 1,765,362 reads read : 1,765,362 reads written : 1,765,362 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/ERR2529569/ERR2529569.1' 2019-07-05T06:38:45 fasterq-dump.2.9.6 err: invalid accession 'ERR2529569' 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/ERR2529569/ERR2529569.1' 2019-07-05T06:39:00 fasterq-dump.2.9.6 err: invalid accession 'ERR2529569' 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/ERR2529569/ERR2529569.1' 2019-07-05T06:39:22 fasterq-dump.2.9.6 err: invalid accession 'ERR2529569' 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/ERR2529569/ERR2529569.1' 2019-07-05T06:39:37 fasterq-dump.2.9.6 err: invalid accession 'ERR2529569' 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/ERR2529569/ERR2529569.1' 2019-07-05T06:39:52 fasterq-dump.2.9.6 err: invalid accession 'ERR2529569' 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/ERR2529569/ERR2529569.1' 2019-07-05T06:40:07 fasterq-dump.2.9.6 err: invalid accession 'ERR2529569' spots read : 1,743,555 reads read : 1,743,555 reads written : 1,743,555 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529566.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529569.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: 00:01:52 7060404 reads; of these: 7060404 (100.00%) were unpaired; of these: 264235 (3.74%) aligned 0 times 5853928 (82.91%) aligned exactly 1 time 942241 (13.35%) aligned >1 times 96.26% overall alignment rate Time searching: 00:01:52 Overall time: 00:01:52 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] 6454124 / 6796169 = 0.9497 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 15:46:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.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 15:46:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:46:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:46:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.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 15:46:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:46:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:46:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.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 15:46:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:46:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:46:07: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:46:07: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:46:07: #1 total tags in treatment: 342045 INFO @ Fri, 05 Jul 2019 15:46:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:46:07: #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 15:46:07: #1 tags after filtering in treatment: 342045 INFO @ Fri, 05 Jul 2019 15:46:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:46:07: #1 finished! INFO @ Fri, 05 Jul 2019 15:46:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:46:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:46:07: #2 number of paired peaks: 479 WARNING @ Fri, 05 Jul 2019 15:46:07: Fewer paired peaks (479) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 479 pairs to build model! INFO @ Fri, 05 Jul 2019 15:46:07: start model_add_line... INFO @ Fri, 05 Jul 2019 15:46:07: start X-correlation... INFO @ Fri, 05 Jul 2019 15:46:08: end of X-cor INFO @ Fri, 05 Jul 2019 15:46:08: #2 finished! INFO @ Fri, 05 Jul 2019 15:46:08: #2 predicted fragment length is 97 bps INFO @ Fri, 05 Jul 2019 15:46:08: #2 alternative fragment length(s) may be 97 bps INFO @ Fri, 05 Jul 2019 15:46:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.05_model.r WARNING @ Fri, 05 Jul 2019 15:46:08: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:46:08: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Fri, 05 Jul 2019 15:46:08: #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 15:46:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:46:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:46:08: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:46:08: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:46:08: #1 total tags in treatment: 342045 INFO @ Fri, 05 Jul 2019 15:46:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:46:08: #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 15:46:08: #1 tags after filtering in treatment: 342045 INFO @ Fri, 05 Jul 2019 15:46:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:46:08: #1 finished! INFO @ Fri, 05 Jul 2019 15:46:08: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:46:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:46:08: #2 number of paired peaks: 479 WARNING @ Fri, 05 Jul 2019 15:46:08: Fewer paired peaks (479) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 479 pairs to build model! INFO @ Fri, 05 Jul 2019 15:46:08: start model_add_line... INFO @ Fri, 05 Jul 2019 15:46:08: start X-correlation... INFO @ Fri, 05 Jul 2019 15:46:08: end of X-cor INFO @ Fri, 05 Jul 2019 15:46:08: #2 finished! INFO @ Fri, 05 Jul 2019 15:46:08: #2 predicted fragment length is 97 bps INFO @ Fri, 05 Jul 2019 15:46:08: #2 alternative fragment length(s) may be 97 bps INFO @ Fri, 05 Jul 2019 15:46:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.10_model.r WARNING @ Fri, 05 Jul 2019 15:46:08: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:46:08: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Fri, 05 Jul 2019 15:46:08: #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 15:46:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:46:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:46:09: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:46:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:46:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:46:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.05_summits.bed INFO @ Fri, 05 Jul 2019 15:46:09: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (188 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:46:10: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:46:10: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:46:10: #1 total tags in treatment: 342045 INFO @ Fri, 05 Jul 2019 15:46:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:46:10: #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 15:46:10: #1 tags after filtering in treatment: 342045 INFO @ Fri, 05 Jul 2019 15:46:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:46:10: #1 finished! INFO @ Fri, 05 Jul 2019 15:46:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:46:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:46:10: #2 number of paired peaks: 479 WARNING @ Fri, 05 Jul 2019 15:46:10: Fewer paired peaks (479) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 479 pairs to build model! INFO @ Fri, 05 Jul 2019 15:46:10: start model_add_line... INFO @ Fri, 05 Jul 2019 15:46:10: start X-correlation... INFO @ Fri, 05 Jul 2019 15:46:10: end of X-cor INFO @ Fri, 05 Jul 2019 15:46:10: #2 finished! INFO @ Fri, 05 Jul 2019 15:46:10: #2 predicted fragment length is 97 bps INFO @ Fri, 05 Jul 2019 15:46:10: #2 alternative fragment length(s) may be 97 bps INFO @ Fri, 05 Jul 2019 15:46:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.20_model.r WARNING @ Fri, 05 Jul 2019 15:46:10: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:46:10: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Fri, 05 Jul 2019 15:46:10: #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 15:46:10: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:46:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:46:10: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:46:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.10_peaks.xls BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:46:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:46:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:46:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:46:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.20_summits.bed INFO @ Fri, 05 Jul 2019 15:46:12: Done! INFO @ Fri, 05 Jul 2019 15:46:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:46:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548175/ERX2548175.10_summits.bed INFO @ Fri, 05 Jul 2019 15:46:12: Done! BigWig に変換しました。 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (72 records, 4 fields): 2 millis pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (115 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling