Job ID = 1307901 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:31:04 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' 2019-06-03T13:31:04 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/sra76/SRR/008340/SRR8540823' 2019-06-03T13:31:04 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_table_names( 'SRR8540823' ).VDBManagerOpenDBRead() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 5,871,137 reads read : 11,742,274 reads written : 5,871,137 reads 0-length : 5,871,137 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: 00:01:40 5871137 reads; of these: 5871137 (100.00%) were unpaired; of these: 2030546 (34.59%) aligned 0 times 3368317 (57.37%) aligned exactly 1 time 472274 (8.04%) aligned >1 times 65.41% overall alignment rate Time searching: 00:01:40 Overall time: 00:01:40 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 2023989 / 3840591 = 0.5270 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 @ Mon, 03 Jun 2019 22:37:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 22:37:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:37:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:37:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 22:37:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:37:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:37:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 22:37:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:37:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:37:13: 1000000 INFO @ Mon, 03 Jun 2019 22:37:14: 1000000 INFO @ Mon, 03 Jun 2019 22:37:14: 1000000 INFO @ Mon, 03 Jun 2019 22:37:20: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:37:20: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:37:20: #1 total tags in treatment: 1816602 INFO @ Mon, 03 Jun 2019 22:37:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:37:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 22:37:21: #1 tags after filtering in treatment: 1816602 INFO @ Mon, 03 Jun 2019 22:37:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:37:21: #1 finished! INFO @ Mon, 03 Jun 2019 22:37:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:37:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:37:21: #2 number of paired peaks: 8160 INFO @ Mon, 03 Jun 2019 22:37:21: start model_add_line... INFO @ Mon, 03 Jun 2019 22:37:21: start X-correlation... INFO @ Mon, 03 Jun 2019 22:37:21: end of X-cor INFO @ Mon, 03 Jun 2019 22:37:21: #2 finished! INFO @ Mon, 03 Jun 2019 22:37:21: #2 predicted fragment length is 169 bps INFO @ Mon, 03 Jun 2019 22:37:21: #2 alternative fragment length(s) may be 169 bps INFO @ Mon, 03 Jun 2019 22:37:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.10_model.r INFO @ Mon, 03 Jun 2019 22:37:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:37:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:37:23: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:37:23: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:37:23: #1 total tags in treatment: 1816602 INFO @ Mon, 03 Jun 2019 22:37:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:37:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 22:37:23: #1 tags after filtering in treatment: 1816602 INFO @ Mon, 03 Jun 2019 22:37:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:37:23: #1 finished! INFO @ Mon, 03 Jun 2019 22:37:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:37:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:37:23: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:37:23: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:37:23: #1 total tags in treatment: 1816602 INFO @ Mon, 03 Jun 2019 22:37:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:37:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 22:37:23: #1 tags after filtering in treatment: 1816602 INFO @ Mon, 03 Jun 2019 22:37:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:37:23: #1 finished! INFO @ Mon, 03 Jun 2019 22:37:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:37:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:37:23: #2 number of paired peaks: 8160 INFO @ Mon, 03 Jun 2019 22:37:23: start model_add_line... INFO @ Mon, 03 Jun 2019 22:37:23: start X-correlation... INFO @ Mon, 03 Jun 2019 22:37:23: end of X-cor INFO @ Mon, 03 Jun 2019 22:37:23: #2 finished! INFO @ Mon, 03 Jun 2019 22:37:23: #2 predicted fragment length is 169 bps INFO @ Mon, 03 Jun 2019 22:37:23: #2 alternative fragment length(s) may be 169 bps INFO @ Mon, 03 Jun 2019 22:37:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.20_model.r INFO @ Mon, 03 Jun 2019 22:37:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:37:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:37:23: #2 number of paired peaks: 8160 INFO @ Mon, 03 Jun 2019 22:37:23: start model_add_line... INFO @ Mon, 03 Jun 2019 22:37:23: start X-correlation... INFO @ Mon, 03 Jun 2019 22:37:23: end of X-cor INFO @ Mon, 03 Jun 2019 22:37:23: #2 finished! INFO @ Mon, 03 Jun 2019 22:37:23: #2 predicted fragment length is 169 bps INFO @ Mon, 03 Jun 2019 22:37:23: #2 alternative fragment length(s) may be 169 bps INFO @ Mon, 03 Jun 2019 22:37:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.05_model.r INFO @ Mon, 03 Jun 2019 22:37:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:37:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:37:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:37:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:37:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:37:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:37:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:37:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.10_summits.bed INFO @ Mon, 03 Jun 2019 22:37:30: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4276 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:37:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:37:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:37:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.20_summits.bed INFO @ Mon, 03 Jun 2019 22:37:32: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1518 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:37:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:37:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:37:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343123/SRX5343123.05_summits.bed INFO @ Mon, 03 Jun 2019 22:37:32: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6308 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。