Job ID = 2006928 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T06:38:47 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' 2019-07-05T06:38:47 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/ERR2529593/ERR2529593.1' 2019-07-05T06:38:47 fasterq-dump.2.9.6 err: invalid accession 'ERR2529593' 2019-07-05T06:39:02 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' 2019-07-05T06:39:02 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/ERR2529593/ERR2529593.1' 2019-07-05T06:39:02 fasterq-dump.2.9.6 err: invalid accession 'ERR2529593' 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/ERR2529593/ERR2529593.1' 2019-07-05T06:39:22 fasterq-dump.2.9.6 err: invalid accession 'ERR2529593' 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/ERR2529593/ERR2529593.1' 2019-07-05T06:39:36 fasterq-dump.2.9.6 err: invalid accession 'ERR2529593' 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/ERR2529593/ERR2529593.1' 2019-07-05T06:39:51 fasterq-dump.2.9.6 err: invalid accession 'ERR2529593' 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/ERR2529593/ERR2529593.1' 2019-07-05T06:40:06 fasterq-dump.2.9.6 err: invalid accession 'ERR2529593' spots read : 10,184,760 reads read : 10,184,760 reads written : 10,184,760 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529593.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: 00:05:37 10184760 reads; of these: 10184760 (100.00%) were unpaired; of these: 615036 (6.04%) aligned 0 times 7947088 (78.03%) aligned exactly 1 time 1622636 (15.93%) aligned >1 times 93.96% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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] 9292177 / 9569724 = 0.9710 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 15:55:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.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 15:55:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:55:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:55:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.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 15:55:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:55:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:55:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.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 15:55:51: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:55:51: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:55:52: #1 tag size is determined as 76 bps INFO @ Fri, 05 Jul 2019 15:55:52: #1 tag size = 76 INFO @ Fri, 05 Jul 2019 15:55:52: #1 total tags in treatment: 277547 INFO @ Fri, 05 Jul 2019 15:55:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:55:52: #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 15:55:52: #1 tags after filtering in treatment: 277547 INFO @ Fri, 05 Jul 2019 15:55:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:55:52: #1 finished! INFO @ Fri, 05 Jul 2019 15:55:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:55:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:55:52: #2 number of paired peaks: 459 WARNING @ Fri, 05 Jul 2019 15:55:52: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Fri, 05 Jul 2019 15:55:52: start model_add_line... INFO @ Fri, 05 Jul 2019 15:55:52: start X-correlation... INFO @ Fri, 05 Jul 2019 15:55:52: end of X-cor INFO @ Fri, 05 Jul 2019 15:55:52: #2 finished! INFO @ Fri, 05 Jul 2019 15:55:52: #2 predicted fragment length is 48 bps INFO @ Fri, 05 Jul 2019 15:55:52: #2 alternative fragment length(s) may be 48,90,136,171,210,263,281,369,414,431,466,502,538 bps INFO @ Fri, 05 Jul 2019 15:55:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.05_model.r WARNING @ Fri, 05 Jul 2019 15:55:52: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:55:52: #2 You may need to consider one of the other alternative d(s): 48,90,136,171,210,263,281,369,414,431,466,502,538 WARNING @ Fri, 05 Jul 2019 15:55:52: #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 15:55:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:55:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:55:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:55:53: #1 tag size is determined as 76 bps INFO @ Fri, 05 Jul 2019 15:55:53: #1 tag size = 76 INFO @ Fri, 05 Jul 2019 15:55:53: #1 total tags in treatment: 277547 INFO @ Fri, 05 Jul 2019 15:55:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:55:53: #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 15:55:53: #1 tags after filtering in treatment: 277547 INFO @ Fri, 05 Jul 2019 15:55:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:55:53: #1 finished! INFO @ Fri, 05 Jul 2019 15:55:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:55:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:55:53: #2 number of paired peaks: 459 WARNING @ Fri, 05 Jul 2019 15:55:53: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Fri, 05 Jul 2019 15:55:53: start model_add_line... INFO @ Fri, 05 Jul 2019 15:55:53: start X-correlation... INFO @ Fri, 05 Jul 2019 15:55:53: end of X-cor INFO @ Fri, 05 Jul 2019 15:55:53: #2 finished! INFO @ Fri, 05 Jul 2019 15:55:53: #2 predicted fragment length is 48 bps INFO @ Fri, 05 Jul 2019 15:55:53: #2 alternative fragment length(s) may be 48,90,136,171,210,263,281,369,414,431,466,502,538 bps INFO @ Fri, 05 Jul 2019 15:55:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.10_model.r WARNING @ Fri, 05 Jul 2019 15:55:53: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:55:53: #2 You may need to consider one of the other alternative d(s): 48,90,136,171,210,263,281,369,414,431,466,502,538 WARNING @ Fri, 05 Jul 2019 15:55:53: #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 15:55:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:55:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:55:53: #1 tag size is determined as 76 bps INFO @ Fri, 05 Jul 2019 15:55:53: #1 tag size = 76 INFO @ Fri, 05 Jul 2019 15:55:53: #1 total tags in treatment: 277547 INFO @ Fri, 05 Jul 2019 15:55:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:55:53: #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 15:55:53: #1 tags after filtering in treatment: 277547 INFO @ Fri, 05 Jul 2019 15:55:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:55:53: #1 finished! INFO @ Fri, 05 Jul 2019 15:55:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:55:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:55:53: #2 number of paired peaks: 459 WARNING @ Fri, 05 Jul 2019 15:55:53: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Fri, 05 Jul 2019 15:55:53: start model_add_line... INFO @ Fri, 05 Jul 2019 15:55:53: start X-correlation... INFO @ Fri, 05 Jul 2019 15:55:53: end of X-cor INFO @ Fri, 05 Jul 2019 15:55:53: #2 finished! INFO @ Fri, 05 Jul 2019 15:55:53: #2 predicted fragment length is 48 bps INFO @ Fri, 05 Jul 2019 15:55:53: #2 alternative fragment length(s) may be 48,90,136,171,210,263,281,369,414,431,466,502,538 bps INFO @ Fri, 05 Jul 2019 15:55:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.20_model.r WARNING @ Fri, 05 Jul 2019 15:55:53: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:55:53: #2 You may need to consider one of the other alternative d(s): 48,90,136,171,210,263,281,369,414,431,466,502,538 WARNING @ Fri, 05 Jul 2019 15:55:53: #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 15:55:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:55:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:55:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:55:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:55:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.05_summits.bed INFO @ Fri, 05 Jul 2019 15:55:53: Done! pass1 - making usageList (16 chroms): 1 millis BedGraph に変換しました。 pass2 - checking and writing primary data (115 records, 4 fields): 14 millis BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:55:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:55:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:55:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:55:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:55:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.10_summits.bed INFO @ Fri, 05 Jul 2019 15:55:55: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (29 records, 4 fields): 3 millis BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 15:55:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:55:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:55:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548184/ERX2548184.20_summits.bed INFO @ Fri, 05 Jul 2019 15:55:55: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 8 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling