Job ID = 2006924 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,299,600 reads read : 2,299,600 reads written : 2,299,600 2019-07-05T06:38:41 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' 2019-07-05T06:38:41 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/ERR2529585/ERR2529585.1' 2019-07-05T06:38:41 fasterq-dump.2.9.6 err: invalid accession 'ERR2529585' 2019-07-05T06:38:56 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' 2019-07-05T06:38:56 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/ERR2529585/ERR2529585.1' 2019-07-05T06:38:56 fasterq-dump.2.9.6 err: invalid accession 'ERR2529585' 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/ERR2529585/ERR2529585.1' 2019-07-05T06:39:21 fasterq-dump.2.9.6 err: invalid accession 'ERR2529585' 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/ERR2529585/ERR2529585.1' 2019-07-05T06:39:36 fasterq-dump.2.9.6 err: invalid accession 'ERR2529585' 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/ERR2529585/ERR2529585.1' 2019-07-05T06:39:51 fasterq-dump.2.9.6 err: invalid accession 'ERR2529585' 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/ERR2529585/ERR2529585.1' 2019-07-05T06:40:06 fasterq-dump.2.9.6 err: invalid accession 'ERR2529585' spots read : 2,253,372 reads read : 2,253,372 reads written : 2,253,372 spots read : 2,318,528 reads read : 2,318,528 reads written : 2,318,528 spots read : 2,164,745 reads read : 2,164,745 reads written : 2,164,745 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529584.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529585.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: 00:08:43 9036245 reads; of these: 9036245 (100.00%) were unpaired; of these: 443025 (4.90%) aligned 0 times 7242736 (80.15%) aligned exactly 1 time 1350484 (14.95%) aligned >1 times 95.10% overall alignment rate Time searching: 00:08:43 Overall time: 00:08:43 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] 8408155 / 8593220 = 0.9785 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 15:59:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.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 15:59:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:59:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:59:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.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 15:59:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:59:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:59:26: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:59:26: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:59:26: #1 total tags in treatment: 185065 INFO @ Fri, 05 Jul 2019 15:59:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:59:26: #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 15:59:26: #1 tags after filtering in treatment: 185065 INFO @ Fri, 05 Jul 2019 15:59:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:59:26: #1 finished! INFO @ Fri, 05 Jul 2019 15:59:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:59:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:59:26: #2 number of paired peaks: 417 WARNING @ Fri, 05 Jul 2019 15:59:26: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Fri, 05 Jul 2019 15:59:26: start model_add_line... INFO @ Fri, 05 Jul 2019 15:59:26: start X-correlation... INFO @ Fri, 05 Jul 2019 15:59:26: end of X-cor INFO @ Fri, 05 Jul 2019 15:59:26: #2 finished! INFO @ Fri, 05 Jul 2019 15:59:26: #2 predicted fragment length is 79 bps INFO @ Fri, 05 Jul 2019 15:59:26: #2 alternative fragment length(s) may be 16,52,79,104,143,179,210,243,275,302,328,397,467,501,523,552,589 bps INFO @ Fri, 05 Jul 2019 15:59:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.05_model.r WARNING @ Fri, 05 Jul 2019 15:59:26: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:59:26: #2 You may need to consider one of the other alternative d(s): 16,52,79,104,143,179,210,243,275,302,328,397,467,501,523,552,589 WARNING @ Fri, 05 Jul 2019 15:59:26: #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 15:59:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:59:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:59:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.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 15:59:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:59:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:59:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:59:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:59:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:59:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.05_summits.bed INFO @ Fri, 05 Jul 2019 15:59:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (58 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:59:28: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:59:28: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:59:28: #1 total tags in treatment: 185065 INFO @ Fri, 05 Jul 2019 15:59:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:59:28: #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 15:59:28: #1 tags after filtering in treatment: 185065 INFO @ Fri, 05 Jul 2019 15:59:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:59:28: #1 finished! INFO @ Fri, 05 Jul 2019 15:59:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:59:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:59:28: #2 number of paired peaks: 417 WARNING @ Fri, 05 Jul 2019 15:59:28: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Fri, 05 Jul 2019 15:59:28: start model_add_line... INFO @ Fri, 05 Jul 2019 15:59:28: start X-correlation... INFO @ Fri, 05 Jul 2019 15:59:28: end of X-cor INFO @ Fri, 05 Jul 2019 15:59:28: #2 finished! INFO @ Fri, 05 Jul 2019 15:59:28: #2 predicted fragment length is 79 bps INFO @ Fri, 05 Jul 2019 15:59:28: #2 alternative fragment length(s) may be 16,52,79,104,143,179,210,243,275,302,328,397,467,501,523,552,589 bps INFO @ Fri, 05 Jul 2019 15:59:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.10_model.r WARNING @ Fri, 05 Jul 2019 15:59:28: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:59:28: #2 You may need to consider one of the other alternative d(s): 16,52,79,104,143,179,210,243,275,302,328,397,467,501,523,552,589 WARNING @ Fri, 05 Jul 2019 15:59:28: #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 15:59:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:59:28: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:59:28: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:59:28: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:59:28: #1 total tags in treatment: 185065 INFO @ Fri, 05 Jul 2019 15:59:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:59:28: #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 15:59:28: #1 tags after filtering in treatment: 185065 INFO @ Fri, 05 Jul 2019 15:59:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:59:28: #1 finished! INFO @ Fri, 05 Jul 2019 15:59:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:59:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:59:28: #2 number of paired peaks: 417 WARNING @ Fri, 05 Jul 2019 15:59:28: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Fri, 05 Jul 2019 15:59:28: start model_add_line... INFO @ Fri, 05 Jul 2019 15:59:28: start X-correlation... INFO @ Fri, 05 Jul 2019 15:59:28: end of X-cor INFO @ Fri, 05 Jul 2019 15:59:28: #2 finished! INFO @ Fri, 05 Jul 2019 15:59:28: #2 predicted fragment length is 79 bps INFO @ Fri, 05 Jul 2019 15:59:28: #2 alternative fragment length(s) may be 16,52,79,104,143,179,210,243,275,302,328,397,467,501,523,552,589 bps INFO @ Fri, 05 Jul 2019 15:59:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.20_model.r WARNING @ Fri, 05 Jul 2019 15:59:28: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:59:28: #2 You may need to consider one of the other alternative d(s): 16,52,79,104,143,179,210,243,275,302,328,397,467,501,523,552,589 WARNING @ Fri, 05 Jul 2019 15:59:28: #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 15:59:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:59:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:59:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:59:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:59:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:59:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.10_summits.bed INFO @ Fri, 05 Jul 2019 15:59:29: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (18 records, 4 fields): 1 millis BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 15:59:29: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 15:59:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:59:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:59:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548181/ERX2548181.20_summits.bed INFO @ Fri, 05 Jul 2019 15:59:29: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling