Job ID = 2640686 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T09:12:16 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 6,405,750 reads read : 12,811,500 reads written : 6,405,750 reads 0-length : 6,405,750 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:10 6405750 reads; of these: 6405750 (100.00%) were unpaired; of these: 455461 (7.11%) aligned 0 times 5014062 (78.27%) aligned exactly 1 time 936227 (14.62%) aligned >1 times 92.89% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 257762 / 5950289 = 0.0433 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:21:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:21:21: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:21:21: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:21:32: 1000000 INFO @ Sat, 24 Aug 2019 18:21:43: 2000000 INFO @ Sat, 24 Aug 2019 18:21:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:21:50: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:21:50: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:21:53: 3000000 INFO @ Sat, 24 Aug 2019 18:22:02: 1000000 INFO @ Sat, 24 Aug 2019 18:22:04: 4000000 INFO @ Sat, 24 Aug 2019 18:22:13: 2000000 INFO @ Sat, 24 Aug 2019 18:22:15: 5000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:22:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:22:20: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:22:20: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:22:23: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:22:23: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:22:23: #1 total tags in treatment: 5692527 INFO @ Sat, 24 Aug 2019 18:22:23: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:22:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:22:23: #1 tags after filtering in treatment: 5692256 INFO @ Sat, 24 Aug 2019 18:22:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:22:23: #1 finished! INFO @ Sat, 24 Aug 2019 18:22:23: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:22:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:22:24: 3000000 INFO @ Sat, 24 Aug 2019 18:22:26: #2 number of paired peaks: 54896 INFO @ Sat, 24 Aug 2019 18:22:26: start model_add_line... INFO @ Sat, 24 Aug 2019 18:22:26: start X-correlation... INFO @ Sat, 24 Aug 2019 18:22:26: end of X-cor INFO @ Sat, 24 Aug 2019 18:22:26: #2 finished! INFO @ Sat, 24 Aug 2019 18:22:26: #2 predicted fragment length is 179 bps INFO @ Sat, 24 Aug 2019 18:22:26: #2 alternative fragment length(s) may be 179 bps INFO @ Sat, 24 Aug 2019 18:22:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.05_model.r INFO @ Sat, 24 Aug 2019 18:22:26: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:22:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:22:28: 1000000 INFO @ Sat, 24 Aug 2019 18:22:34: 4000000 INFO @ Sat, 24 Aug 2019 18:22:36: 2000000 INFO @ Sat, 24 Aug 2019 18:22:43: 3000000 INFO @ Sat, 24 Aug 2019 18:22:44: 5000000 INFO @ Sat, 24 Aug 2019 18:22:45: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:22:50: 4000000 INFO @ Sat, 24 Aug 2019 18:22:51: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:22:51: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:22:51: #1 total tags in treatment: 5692527 INFO @ Sat, 24 Aug 2019 18:22:51: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:22:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:22:51: #1 tags after filtering in treatment: 5692256 INFO @ Sat, 24 Aug 2019 18:22:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:22:51: #1 finished! INFO @ Sat, 24 Aug 2019 18:22:51: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:22:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:22:54: #2 number of paired peaks: 54896 INFO @ Sat, 24 Aug 2019 18:22:54: start model_add_line... INFO @ Sat, 24 Aug 2019 18:22:54: start X-correlation... INFO @ Sat, 24 Aug 2019 18:22:54: end of X-cor INFO @ Sat, 24 Aug 2019 18:22:54: #2 finished! INFO @ Sat, 24 Aug 2019 18:22:54: #2 predicted fragment length is 179 bps INFO @ Sat, 24 Aug 2019 18:22:54: #2 alternative fragment length(s) may be 179 bps INFO @ Sat, 24 Aug 2019 18:22:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.10_model.r INFO @ Sat, 24 Aug 2019 18:22:54: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:22:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:22:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:22:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:22:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.05_summits.bed INFO @ Sat, 24 Aug 2019 18:22:55: Done! pass1 - making usageList (85 chroms): 9 millis pass2 - checking and writing primary data (19817 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:22:57: 5000000 INFO @ Sat, 24 Aug 2019 18:23:02: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:23:02: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:23:02: #1 total tags in treatment: 5692527 INFO @ Sat, 24 Aug 2019 18:23:02: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:23:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:23:03: #1 tags after filtering in treatment: 5692256 INFO @ Sat, 24 Aug 2019 18:23:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:23:03: #1 finished! INFO @ Sat, 24 Aug 2019 18:23:03: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:23:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:23:05: #2 number of paired peaks: 54896 INFO @ Sat, 24 Aug 2019 18:23:05: start model_add_line... INFO @ Sat, 24 Aug 2019 18:23:05: start X-correlation... INFO @ Sat, 24 Aug 2019 18:23:05: end of X-cor INFO @ Sat, 24 Aug 2019 18:23:05: #2 finished! INFO @ Sat, 24 Aug 2019 18:23:05: #2 predicted fragment length is 179 bps INFO @ Sat, 24 Aug 2019 18:23:05: #2 alternative fragment length(s) may be 179 bps INFO @ Sat, 24 Aug 2019 18:23:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.20_model.r INFO @ Sat, 24 Aug 2019 18:23:05: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:23:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:23:12: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:23:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:23:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:23:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.10_summits.bed INFO @ Sat, 24 Aug 2019 18:23:22: Done! pass1 - making usageList (67 chroms): 5 millis pass2 - checking and writing primary data (11649 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:23:24: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:23:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:23:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:23:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375047/SRX5375047.20_summits.bed INFO @ Sat, 24 Aug 2019 18:23:34: Done! pass1 - making usageList (36 chroms): 2 millis pass2 - checking and writing primary data (4971 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。