Job ID = 1293806 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T17:25:37 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' 2019-06-02T17:25:37 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/sra33/SRR/002096/SRR2147087' 2019-06-02T17:25:37 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR2147087' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 12,237,483 reads read : 12,237,483 reads written : 12,237,483 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: 00:02:56 12237483 reads; of these: 12237483 (100.00%) were unpaired; of these: 1130295 (9.24%) aligned 0 times 10040948 (82.05%) aligned exactly 1 time 1066240 (8.71%) aligned >1 times 90.76% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 6974689 / 11107188 = 0.6279 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 02:39:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.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 02:39:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:39:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:39:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.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 02:39:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:39:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:39:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.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 02:39:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:39:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:39:36: 1000000 INFO @ Mon, 03 Jun 2019 02:39:36: 1000000 INFO @ Mon, 03 Jun 2019 02:39:37: 1000000 INFO @ Mon, 03 Jun 2019 02:39:47: 2000000 INFO @ Mon, 03 Jun 2019 02:39:47: 2000000 INFO @ Mon, 03 Jun 2019 02:39:47: 2000000 INFO @ Mon, 03 Jun 2019 02:39:57: 3000000 INFO @ Mon, 03 Jun 2019 02:39:57: 3000000 INFO @ Mon, 03 Jun 2019 02:39:57: 3000000 INFO @ Mon, 03 Jun 2019 02:40:07: 4000000 INFO @ Mon, 03 Jun 2019 02:40:07: 4000000 INFO @ Mon, 03 Jun 2019 02:40:08: 4000000 INFO @ Mon, 03 Jun 2019 02:40:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:40:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:40:08: #1 total tags in treatment: 4132499 INFO @ Mon, 03 Jun 2019 02:40:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:40:08: #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 02:40:08: #1 tags after filtering in treatment: 4132499 INFO @ Mon, 03 Jun 2019 02:40:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:40:08: #1 finished! INFO @ Mon, 03 Jun 2019 02:40:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:40:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:40:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:40:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:40:09: #1 total tags in treatment: 4132499 INFO @ Mon, 03 Jun 2019 02:40:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:40:09: #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 02:40:09: #2 number of paired peaks: 5799 INFO @ Mon, 03 Jun 2019 02:40:09: start model_add_line... INFO @ Mon, 03 Jun 2019 02:40:09: #1 tags after filtering in treatment: 4132499 INFO @ Mon, 03 Jun 2019 02:40:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:40:09: #1 finished! INFO @ Mon, 03 Jun 2019 02:40:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:40:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:40:09: start X-correlation... INFO @ Mon, 03 Jun 2019 02:40:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:40:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:40:09: #1 total tags in treatment: 4132499 INFO @ Mon, 03 Jun 2019 02:40:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:40:09: #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 02:40:09: end of X-cor INFO @ Mon, 03 Jun 2019 02:40:09: #2 finished! INFO @ Mon, 03 Jun 2019 02:40:09: #2 predicted fragment length is 185 bps INFO @ Mon, 03 Jun 2019 02:40:09: #2 alternative fragment length(s) may be 185 bps INFO @ Mon, 03 Jun 2019 02:40:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.05_model.r INFO @ Mon, 03 Jun 2019 02:40:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:40:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:40:09: #1 tags after filtering in treatment: 4132499 INFO @ Mon, 03 Jun 2019 02:40:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:40:09: #1 finished! INFO @ Mon, 03 Jun 2019 02:40:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:40:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:40:09: #2 number of paired peaks: 5799 INFO @ Mon, 03 Jun 2019 02:40:09: start model_add_line... INFO @ Mon, 03 Jun 2019 02:40:10: start X-correlation... INFO @ Mon, 03 Jun 2019 02:40:10: end of X-cor INFO @ Mon, 03 Jun 2019 02:40:10: #2 finished! INFO @ Mon, 03 Jun 2019 02:40:10: #2 predicted fragment length is 185 bps INFO @ Mon, 03 Jun 2019 02:40:10: #2 alternative fragment length(s) may be 185 bps INFO @ Mon, 03 Jun 2019 02:40:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.20_model.r INFO @ Mon, 03 Jun 2019 02:40:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:40:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:40:10: #2 number of paired peaks: 5799 INFO @ Mon, 03 Jun 2019 02:40:10: start model_add_line... INFO @ Mon, 03 Jun 2019 02:40:10: start X-correlation... INFO @ Mon, 03 Jun 2019 02:40:10: end of X-cor INFO @ Mon, 03 Jun 2019 02:40:10: #2 finished! INFO @ Mon, 03 Jun 2019 02:40:10: #2 predicted fragment length is 185 bps INFO @ Mon, 03 Jun 2019 02:40:10: #2 alternative fragment length(s) may be 185 bps INFO @ Mon, 03 Jun 2019 02:40:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.10_model.r INFO @ Mon, 03 Jun 2019 02:40:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:40:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:40:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:40:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:40:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:40:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:40:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:40:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.05_summits.bed INFO @ Mon, 03 Jun 2019 02:40:32: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5533 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 02:40:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:40:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:40:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.20_summits.bed INFO @ Mon, 03 Jun 2019 02:40:33: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2878 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:40:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:40:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:40:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134706/SRX1134706.10_summits.bed INFO @ Mon, 03 Jun 2019 02:40:34: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4186 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。