Job ID = 1293171 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T13:05:22 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' 2019-06-02T13:05:22 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/SRR8602969' 2019-06-02T13:05:22 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_db_type().VDBManagerOpenDBRead( 'SRR8602969' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T13:05:22 fasterq-dump.2.9.6 err: invalid accession 'SRR8602969' spots read : 3,488,323 reads read : 6,976,646 reads written : 3,488,323 reads 0-length : 3,488,323 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: 00:00:56 3488323 reads; of these: 3488323 (100.00%) were unpaired; of these: 32598 (0.93%) aligned 0 times 3147287 (90.22%) aligned exactly 1 time 308438 (8.84%) aligned >1 times 99.07% overall alignment rate Time searching: 00:00:56 Overall time: 00:00:56 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] 1050432 / 3455725 = 0.3040 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 22:09:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.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 22:09:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:09:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:09:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.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 22:09:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:09:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:09:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.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 22:09:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:09:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:09:11: 1000000 INFO @ Sun, 02 Jun 2019 22:09:12: 1000000 INFO @ Sun, 02 Jun 2019 22:09:13: 1000000 INFO @ Sun, 02 Jun 2019 22:09:18: 2000000 INFO @ Sun, 02 Jun 2019 22:09:21: 2000000 INFO @ Sun, 02 Jun 2019 22:09:21: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:09:21: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:09:21: #1 total tags in treatment: 2405293 INFO @ Sun, 02 Jun 2019 22:09:21: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:09:21: #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 22:09:22: #1 tags after filtering in treatment: 2405293 INFO @ Sun, 02 Jun 2019 22:09:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:09:22: #1 finished! INFO @ Sun, 02 Jun 2019 22:09:22: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:09:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:09:22: #2 number of paired peaks: 5045 INFO @ Sun, 02 Jun 2019 22:09:22: start model_add_line... INFO @ Sun, 02 Jun 2019 22:09:22: start X-correlation... INFO @ Sun, 02 Jun 2019 22:09:22: end of X-cor INFO @ Sun, 02 Jun 2019 22:09:22: #2 finished! INFO @ Sun, 02 Jun 2019 22:09:22: #2 predicted fragment length is 192 bps INFO @ Sun, 02 Jun 2019 22:09:22: #2 alternative fragment length(s) may be 192 bps INFO @ Sun, 02 Jun 2019 22:09:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.05_model.r INFO @ Sun, 02 Jun 2019 22:09:22: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:09:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:09:23: 2000000 INFO @ Sun, 02 Jun 2019 22:09:25: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:09:25: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:09:25: #1 total tags in treatment: 2405293 INFO @ Sun, 02 Jun 2019 22:09:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:09:25: #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 22:09:25: #1 tags after filtering in treatment: 2405293 INFO @ Sun, 02 Jun 2019 22:09:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:09:25: #1 finished! INFO @ Sun, 02 Jun 2019 22:09:25: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:09:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:09:26: #2 number of paired peaks: 5045 INFO @ Sun, 02 Jun 2019 22:09:26: start model_add_line... INFO @ Sun, 02 Jun 2019 22:09:26: start X-correlation... INFO @ Sun, 02 Jun 2019 22:09:26: end of X-cor INFO @ Sun, 02 Jun 2019 22:09:26: #2 finished! INFO @ Sun, 02 Jun 2019 22:09:26: #2 predicted fragment length is 192 bps INFO @ Sun, 02 Jun 2019 22:09:26: #2 alternative fragment length(s) may be 192 bps INFO @ Sun, 02 Jun 2019 22:09:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.20_model.r INFO @ Sun, 02 Jun 2019 22:09:26: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:09:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:09:27: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:09:27: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:09:27: #1 total tags in treatment: 2405293 INFO @ Sun, 02 Jun 2019 22:09:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:09:27: #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 22:09:27: #1 tags after filtering in treatment: 2405293 INFO @ Sun, 02 Jun 2019 22:09:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:09:27: #1 finished! INFO @ Sun, 02 Jun 2019 22:09:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:09:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:09:28: #2 number of paired peaks: 5045 INFO @ Sun, 02 Jun 2019 22:09:28: start model_add_line... INFO @ Sun, 02 Jun 2019 22:09:28: start X-correlation... INFO @ Sun, 02 Jun 2019 22:09:28: end of X-cor INFO @ Sun, 02 Jun 2019 22:09:28: #2 finished! INFO @ Sun, 02 Jun 2019 22:09:28: #2 predicted fragment length is 192 bps INFO @ Sun, 02 Jun 2019 22:09:28: #2 alternative fragment length(s) may be 192 bps INFO @ Sun, 02 Jun 2019 22:09:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.10_model.r INFO @ Sun, 02 Jun 2019 22:09:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:09:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:09:31: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:09:34: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:09:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:09:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:09:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.05_summits.bed INFO @ Sun, 02 Jun 2019 22:09:35: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4515 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:09:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:09:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:09:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:09:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.20_summits.bed INFO @ Sun, 02 Jun 2019 22:09:38: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2801 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:09:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:09:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:09:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402735/SRX5402735.10_summits.bed INFO @ Sun, 02 Jun 2019 22:09:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3602 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。