Job ID = 2589516 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T08:50:50 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 : 6,560,280 reads read : 6,560,280 reads written : 6,560,280 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR701492.sra.cache’: 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: 00:00:53 6560280 reads; of these: 6560280 (100.00%) were unpaired; of these: 3617446 (55.14%) aligned 0 times 2503499 (38.16%) aligned exactly 1 time 439335 (6.70%) aligned >1 times 44.86% overall alignment rate Time searching: 00:00:53 Overall time: 00:00:53 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] 557773 / 2942834 = 0.1895 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, 12 Aug 2019 17:53:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.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 @ Mon, 12 Aug 2019 17:53:09: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:53:09: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:53:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.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 @ Mon, 12 Aug 2019 17:53:10: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:53:10: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:53:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.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 @ Mon, 12 Aug 2019 17:53:11: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:53:11: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:53:16: 1000000 INFO @ Mon, 12 Aug 2019 17:53:17: 1000000 INFO @ Mon, 12 Aug 2019 17:53:19: 1000000 INFO @ Mon, 12 Aug 2019 17:53:23: 2000000 INFO @ Mon, 12 Aug 2019 17:53:24: 2000000 INFO @ Mon, 12 Aug 2019 17:53:26: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:53:26: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:53:26: #1 total tags in treatment: 2385061 INFO @ Mon, 12 Aug 2019 17:53:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:53:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:53:26: #1 tags after filtering in treatment: 2385061 INFO @ Mon, 12 Aug 2019 17:53:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:53:26: #1 finished! INFO @ Mon, 12 Aug 2019 17:53:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:53:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:53:27: #2 number of paired peaks: 1534 INFO @ Mon, 12 Aug 2019 17:53:27: start model_add_line... INFO @ Mon, 12 Aug 2019 17:53:27: start X-correlation... INFO @ Mon, 12 Aug 2019 17:53:27: end of X-cor INFO @ Mon, 12 Aug 2019 17:53:27: #2 finished! INFO @ Mon, 12 Aug 2019 17:53:27: #2 predicted fragment length is 149 bps INFO @ Mon, 12 Aug 2019 17:53:27: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 12 Aug 2019 17:53:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.05_model.r INFO @ Mon, 12 Aug 2019 17:53:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:53:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:53:27: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:53:27: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:53:27: #1 total tags in treatment: 2385061 INFO @ Mon, 12 Aug 2019 17:53:27: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:53:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:53:27: #1 tags after filtering in treatment: 2385061 INFO @ Mon, 12 Aug 2019 17:53:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:53:27: #1 finished! INFO @ Mon, 12 Aug 2019 17:53:27: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:53:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:53:28: #2 number of paired peaks: 1534 INFO @ Mon, 12 Aug 2019 17:53:28: start model_add_line... INFO @ Mon, 12 Aug 2019 17:53:28: 2000000 INFO @ Mon, 12 Aug 2019 17:53:28: start X-correlation... INFO @ Mon, 12 Aug 2019 17:53:28: end of X-cor INFO @ Mon, 12 Aug 2019 17:53:28: #2 finished! INFO @ Mon, 12 Aug 2019 17:53:28: #2 predicted fragment length is 149 bps INFO @ Mon, 12 Aug 2019 17:53:28: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 12 Aug 2019 17:53:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.10_model.r INFO @ Mon, 12 Aug 2019 17:53:28: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:53:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:53:31: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:53:31: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:53:31: #1 total tags in treatment: 2385061 INFO @ Mon, 12 Aug 2019 17:53:31: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:53:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:53:31: #1 tags after filtering in treatment: 2385061 INFO @ Mon, 12 Aug 2019 17:53:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:53:31: #1 finished! INFO @ Mon, 12 Aug 2019 17:53:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:53:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:53:31: #2 number of paired peaks: 1534 INFO @ Mon, 12 Aug 2019 17:53:31: start model_add_line... INFO @ Mon, 12 Aug 2019 17:53:31: start X-correlation... INFO @ Mon, 12 Aug 2019 17:53:31: end of X-cor INFO @ Mon, 12 Aug 2019 17:53:31: #2 finished! INFO @ Mon, 12 Aug 2019 17:53:31: #2 predicted fragment length is 149 bps INFO @ Mon, 12 Aug 2019 17:53:31: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 12 Aug 2019 17:53:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.20_model.r INFO @ Mon, 12 Aug 2019 17:53:31: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:53:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:53:34: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:53:35: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:53:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:53:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:53:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.05_summits.bed INFO @ Mon, 12 Aug 2019 17:53:38: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2697 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:53:39: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:53:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:53:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:53:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.10_summits.bed INFO @ Mon, 12 Aug 2019 17:53:39: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1772 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:53:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:53:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:53:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233417/SRX233417.20_summits.bed INFO @ Mon, 12 Aug 2019 17:53:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1040 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。