Job ID = 1293167 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T13:05:34 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T13:05:34 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra77/SRR/008401/SRR8602966' 2019-06-02T13:05:34 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR8602966' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T13:05:34 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 6,768,843 reads read : 13,537,686 reads written : 6,768,843 reads 0-length : 6,768,843 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:01:26 6768843 reads; of these: 6768843 (100.00%) were unpaired; of these: 543110 (8.02%) aligned 0 times 5725895 (84.59%) aligned exactly 1 time 499838 (7.38%) aligned >1 times 91.98% overall alignment rate Time searching: 00:01:26 Overall time: 00:01:26 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 4447283 / 6225733 = 0.7143 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 @ Sun, 02 Jun 2019 22:12:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 22:12:56: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:12:56: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:12:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 22:12:56: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:12:56: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:12:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 22:12:56: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:12:56: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:13:04: 1000000 INFO @ Sun, 02 Jun 2019 22:13:04: 1000000 INFO @ Sun, 02 Jun 2019 22:13:05: 1000000 INFO @ Sun, 02 Jun 2019 22:13:10: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:13:10: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:13:10: #1 total tags in treatment: 1778450 INFO @ Sun, 02 Jun 2019 22:13:10: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:13:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:13:10: #1 tags after filtering in treatment: 1778450 INFO @ Sun, 02 Jun 2019 22:13:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:13:10: #1 finished! INFO @ Sun, 02 Jun 2019 22:13:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:13:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:13:10: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:13:10: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:13:10: #1 total tags in treatment: 1778450 INFO @ Sun, 02 Jun 2019 22:13:10: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:13:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:13:10: #1 tags after filtering in treatment: 1778450 INFO @ Sun, 02 Jun 2019 22:13:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:13:10: #1 finished! INFO @ Sun, 02 Jun 2019 22:13:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:13:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:13:10: #2 number of paired peaks: 5256 INFO @ Sun, 02 Jun 2019 22:13:10: start model_add_line... INFO @ Sun, 02 Jun 2019 22:13:10: start X-correlation... INFO @ Sun, 02 Jun 2019 22:13:10: end of X-cor INFO @ Sun, 02 Jun 2019 22:13:10: #2 finished! INFO @ Sun, 02 Jun 2019 22:13:10: #2 predicted fragment length is 157 bps INFO @ Sun, 02 Jun 2019 22:13:10: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 02 Jun 2019 22:13:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.20_model.r INFO @ Sun, 02 Jun 2019 22:13:10: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:13:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:13:10: #2 number of paired peaks: 5256 INFO @ Sun, 02 Jun 2019 22:13:10: start model_add_line... INFO @ Sun, 02 Jun 2019 22:13:10: start X-correlation... INFO @ Sun, 02 Jun 2019 22:13:11: end of X-cor INFO @ Sun, 02 Jun 2019 22:13:11: #2 finished! INFO @ Sun, 02 Jun 2019 22:13:11: #2 predicted fragment length is 157 bps INFO @ Sun, 02 Jun 2019 22:13:11: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 02 Jun 2019 22:13:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.10_model.r INFO @ Sun, 02 Jun 2019 22:13:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:13:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:13:11: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:13:11: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:13:11: #1 total tags in treatment: 1778450 INFO @ Sun, 02 Jun 2019 22:13:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:13:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:13:11: #1 tags after filtering in treatment: 1778450 INFO @ Sun, 02 Jun 2019 22:13:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:13:11: #1 finished! INFO @ Sun, 02 Jun 2019 22:13:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:13:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:13:12: #2 number of paired peaks: 5256 INFO @ Sun, 02 Jun 2019 22:13:12: start model_add_line... INFO @ Sun, 02 Jun 2019 22:13:12: start X-correlation... INFO @ Sun, 02 Jun 2019 22:13:12: end of X-cor INFO @ Sun, 02 Jun 2019 22:13:12: #2 finished! INFO @ Sun, 02 Jun 2019 22:13:12: #2 predicted fragment length is 157 bps INFO @ Sun, 02 Jun 2019 22:13:12: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 02 Jun 2019 22:13:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.05_model.r INFO @ Sun, 02 Jun 2019 22:13:12: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:13:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:13:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:13:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:13:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:13:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:13:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:13:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.20_summits.bed INFO @ Sun, 02 Jun 2019 22:13:19: Done! INFO @ Sun, 02 Jun 2019 22:13:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:13:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:13:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.10_summits.bed INFO @ Sun, 02 Jun 2019 22:13:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2434 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (3104 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:13:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:13:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:13:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402732/SRX5402732.05_summits.bed INFO @ Sun, 02 Jun 2019 22:13:21: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3897 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。