Job ID = 2640726 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T09:33:05 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 : 7,567,759 reads read : 7,567,759 reads written : 7,567,759 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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:02:21 7567759 reads; of these: 7567759 (100.00%) were unpaired; of these: 967427 (12.78%) aligned 0 times 5464204 (72.20%) aligned exactly 1 time 1136128 (15.01%) aligned >1 times 87.22% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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] 808951 / 6600332 = 0.1226 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:40:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.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 18:40:43: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:40:43: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:40:50: 1000000 INFO @ Sat, 24 Aug 2019 18:40:57: 2000000 INFO @ Sat, 24 Aug 2019 18:41:03: 3000000 INFO @ Sat, 24 Aug 2019 18:41:10: 4000000 INFO @ Sat, 24 Aug 2019 18:41:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.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 18:41:12: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:41:12: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:41:17: 5000000 INFO @ Sat, 24 Aug 2019 18:41:20: 1000000 INFO @ Sat, 24 Aug 2019 18:41:22: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 18:41:22: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 18:41:22: #1 total tags in treatment: 5791381 INFO @ Sat, 24 Aug 2019 18:41:22: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:41:22: #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 18:41:22: #1 tags after filtering in treatment: 5791085 INFO @ Sat, 24 Aug 2019 18:41:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:41:22: #1 finished! INFO @ Sat, 24 Aug 2019 18:41:22: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:41:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:41:27: #2 number of paired peaks: 137600 INFO @ Sat, 24 Aug 2019 18:41:27: start model_add_line... INFO @ Sat, 24 Aug 2019 18:41:28: start X-correlation... INFO @ Sat, 24 Aug 2019 18:41:28: end of X-cor INFO @ Sat, 24 Aug 2019 18:41:28: #2 finished! INFO @ Sat, 24 Aug 2019 18:41:28: #2 predicted fragment length is 296 bps INFO @ Sat, 24 Aug 2019 18:41:28: #2 alternative fragment length(s) may be 296 bps INFO @ Sat, 24 Aug 2019 18:41:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.05_model.r INFO @ Sat, 24 Aug 2019 18:41:28: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:41:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:41:28: 2000000 INFO @ Sat, 24 Aug 2019 18:41:35: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:41:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.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 18:41:42: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:41:42: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:41:43: 4000000 INFO @ Sat, 24 Aug 2019 18:41:46: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:41:49: 1000000 INFO @ Sat, 24 Aug 2019 18:41:50: 5000000 INFO @ Sat, 24 Aug 2019 18:41:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:41:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:41:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.05_summits.bed INFO @ Sat, 24 Aug 2019 18:41:55: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (340 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:41:56: 2000000 INFO @ Sat, 24 Aug 2019 18:41:56: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 18:41:57: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 18:41:57: #1 total tags in treatment: 5791381 INFO @ Sat, 24 Aug 2019 18:41:57: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:41:57: #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 18:41:57: #1 tags after filtering in treatment: 5791085 INFO @ Sat, 24 Aug 2019 18:41:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:41:57: #1 finished! INFO @ Sat, 24 Aug 2019 18:41:57: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:41:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:42:02: #2 number of paired peaks: 137600 INFO @ Sat, 24 Aug 2019 18:42:02: start model_add_line... INFO @ Sat, 24 Aug 2019 18:42:02: start X-correlation... INFO @ Sat, 24 Aug 2019 18:42:02: end of X-cor INFO @ Sat, 24 Aug 2019 18:42:02: #2 finished! INFO @ Sat, 24 Aug 2019 18:42:02: #2 predicted fragment length is 296 bps INFO @ Sat, 24 Aug 2019 18:42:02: #2 alternative fragment length(s) may be 296 bps INFO @ Sat, 24 Aug 2019 18:42:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.10_model.r INFO @ Sat, 24 Aug 2019 18:42:02: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:42:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:42:03: 3000000 INFO @ Sat, 24 Aug 2019 18:42:09: 4000000 INFO @ Sat, 24 Aug 2019 18:42:16: 5000000 INFO @ Sat, 24 Aug 2019 18:42:21: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:42:21: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 18:42:21: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 18:42:21: #1 total tags in treatment: 5791381 INFO @ Sat, 24 Aug 2019 18:42:21: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:42:21: #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 18:42:22: #1 tags after filtering in treatment: 5791085 INFO @ Sat, 24 Aug 2019 18:42:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:42:22: #1 finished! INFO @ Sat, 24 Aug 2019 18:42:22: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:42:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:42:27: #2 number of paired peaks: 137600 INFO @ Sat, 24 Aug 2019 18:42:27: start model_add_line... INFO @ Sat, 24 Aug 2019 18:42:27: start X-correlation... INFO @ Sat, 24 Aug 2019 18:42:27: end of X-cor INFO @ Sat, 24 Aug 2019 18:42:27: #2 finished! INFO @ Sat, 24 Aug 2019 18:42:27: #2 predicted fragment length is 296 bps INFO @ Sat, 24 Aug 2019 18:42:27: #2 alternative fragment length(s) may be 296 bps INFO @ Sat, 24 Aug 2019 18:42:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.20_model.r INFO @ Sat, 24 Aug 2019 18:42:27: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:42:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:42:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:42:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:42:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.10_summits.bed INFO @ Sat, 24 Aug 2019 18:42:31: Done! pass1 - making usageList (18 chroms): 2 millis pass2 - checking and writing primary data (67 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:42:45: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:42:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:42:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:42:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX555170/SRX555170.20_summits.bed INFO @ Sat, 24 Aug 2019 18:42:54: Done! pass1 - making usageList (5 chroms): 2 millis pass2 - checking and writing primary data (15 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。