Job ID = 2010600 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:32:27 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 : 2,099,375 reads read : 4,198,750 reads written : 4,198,750 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:24 2099375 reads; of these: 2099375 (100.00%) were paired; of these: 782938 (37.29%) aligned concordantly 0 times 1067638 (50.86%) aligned concordantly exactly 1 time 248799 (11.85%) aligned concordantly >1 times ---- 782938 pairs aligned concordantly 0 times; of these: 2692 (0.34%) aligned discordantly 1 time ---- 780246 pairs aligned 0 times concordantly or discordantly; of these: 1560492 mates make up the pairs; of these: 1499500 (96.09%) aligned 0 times 45550 (2.92%) aligned exactly 1 time 15442 (0.99%) aligned >1 times 64.29% overall alignment rate Time searching: 00:01:24 Overall time: 00:01:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 377375 / 1318538 = 0.2862 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 @ Fri, 05 Jul 2019 23:36:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 23:36:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:36:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:36:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 23:36:03: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:36:03: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:36:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 23:36:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:36:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:36:11: 1000000 INFO @ Fri, 05 Jul 2019 23:36:11: 1000000 INFO @ Fri, 05 Jul 2019 23:36:18: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:36:18: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:36:18: #1 total tags in treatment: 939465 INFO @ Fri, 05 Jul 2019 23:36:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:36:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:36:18: #1 tags after filtering in treatment: 759648 INFO @ Fri, 05 Jul 2019 23:36:18: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 05 Jul 2019 23:36:18: #1 finished! INFO @ Fri, 05 Jul 2019 23:36:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:36:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:36:18: #2 number of paired peaks: 156 WARNING @ Fri, 05 Jul 2019 23:36:18: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Fri, 05 Jul 2019 23:36:18: start model_add_line... INFO @ Fri, 05 Jul 2019 23:36:18: start X-correlation... INFO @ Fri, 05 Jul 2019 23:36:18: end of X-cor INFO @ Fri, 05 Jul 2019 23:36:18: #2 finished! INFO @ Fri, 05 Jul 2019 23:36:18: #2 predicted fragment length is 333 bps INFO @ Fri, 05 Jul 2019 23:36:18: #2 alternative fragment length(s) may be 3,125,193,237,249,278,310,333,416,454,488,588 bps INFO @ Fri, 05 Jul 2019 23:36:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.10_model.r INFO @ Fri, 05 Jul 2019 23:36:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:36:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:36:18: 1000000 INFO @ Fri, 05 Jul 2019 23:36:19: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:36:19: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:36:19: #1 total tags in treatment: 939465 INFO @ Fri, 05 Jul 2019 23:36:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:36:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:36:19: #1 tags after filtering in treatment: 759648 INFO @ Fri, 05 Jul 2019 23:36:19: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 05 Jul 2019 23:36:19: #1 finished! INFO @ Fri, 05 Jul 2019 23:36:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:36:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:36:20: #2 number of paired peaks: 156 WARNING @ Fri, 05 Jul 2019 23:36:20: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Fri, 05 Jul 2019 23:36:20: start model_add_line... INFO @ Fri, 05 Jul 2019 23:36:20: start X-correlation... INFO @ Fri, 05 Jul 2019 23:36:20: end of X-cor INFO @ Fri, 05 Jul 2019 23:36:20: #2 finished! INFO @ Fri, 05 Jul 2019 23:36:20: #2 predicted fragment length is 333 bps INFO @ Fri, 05 Jul 2019 23:36:20: #2 alternative fragment length(s) may be 3,125,193,237,249,278,310,333,416,454,488,588 bps INFO @ Fri, 05 Jul 2019 23:36:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.05_model.r INFO @ Fri, 05 Jul 2019 23:36:20: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:36:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:36:21: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:36:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:36:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:36:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.10_summits.bed INFO @ Fri, 05 Jul 2019 23:36:23: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (37 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:36:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:36:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:36:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:36:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.05_summits.bed INFO @ Fri, 05 Jul 2019 23:36:24: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (140 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:36:27: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:36:27: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:36:27: #1 total tags in treatment: 939465 INFO @ Fri, 05 Jul 2019 23:36:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:36:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:36:27: #1 tags after filtering in treatment: 759648 INFO @ Fri, 05 Jul 2019 23:36:27: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 05 Jul 2019 23:36:27: #1 finished! INFO @ Fri, 05 Jul 2019 23:36:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:36:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:36:27: #2 number of paired peaks: 156 WARNING @ Fri, 05 Jul 2019 23:36:27: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Fri, 05 Jul 2019 23:36:27: start model_add_line... INFO @ Fri, 05 Jul 2019 23:36:27: start X-correlation... INFO @ Fri, 05 Jul 2019 23:36:27: end of X-cor INFO @ Fri, 05 Jul 2019 23:36:27: #2 finished! INFO @ Fri, 05 Jul 2019 23:36:27: #2 predicted fragment length is 333 bps INFO @ Fri, 05 Jul 2019 23:36:27: #2 alternative fragment length(s) may be 3,125,193,237,249,278,310,333,416,454,488,588 bps INFO @ Fri, 05 Jul 2019 23:36:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.20_model.r INFO @ Fri, 05 Jul 2019 23:36:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:36:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:36:30: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:36:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:36:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:36:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381300/SRX381300.20_summits.bed INFO @ Fri, 05 Jul 2019 23:36:31: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (13 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。