Job ID = 2010587 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:25:45 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 ) 2019-07-05T14:25:45 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 : 4,150,780 reads read : 8,301,560 reads written : 8,301,560 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: 00:00:45 4150780 reads; of these: 4150780 (100.00%) were paired; of these: 3886679 (93.64%) aligned concordantly 0 times 211111 (5.09%) aligned concordantly exactly 1 time 52990 (1.28%) aligned concordantly >1 times ---- 3886679 pairs aligned concordantly 0 times; of these: 9116 (0.23%) aligned discordantly 1 time ---- 3877563 pairs aligned 0 times concordantly or discordantly; of these: 7755126 mates make up the pairs; of these: 7724359 (99.60%) aligned 0 times 13005 (0.17%) aligned exactly 1 time 17762 (0.23%) aligned >1 times 6.95% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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] 13619 / 273028 = 0.0499 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 23:28:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.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 23:28:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:28:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:28:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.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 23:28:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:28:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:28:15: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:28:15: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:28:15: #1 total tags in treatment: 251029 INFO @ Fri, 05 Jul 2019 23:28:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:28:15: #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 23:28:15: #1 tags after filtering in treatment: 224065 INFO @ Fri, 05 Jul 2019 23:28:15: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 05 Jul 2019 23:28:15: #1 finished! INFO @ Fri, 05 Jul 2019 23:28:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:28:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:28:15: #2 number of paired peaks: 300 WARNING @ Fri, 05 Jul 2019 23:28:15: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Fri, 05 Jul 2019 23:28:15: start model_add_line... INFO @ Fri, 05 Jul 2019 23:28:15: start X-correlation... INFO @ Fri, 05 Jul 2019 23:28:15: end of X-cor INFO @ Fri, 05 Jul 2019 23:28:15: #2 finished! INFO @ Fri, 05 Jul 2019 23:28:15: #2 predicted fragment length is 267 bps INFO @ Fri, 05 Jul 2019 23:28:15: #2 alternative fragment length(s) may be 4,267,287,310,451,483 bps INFO @ Fri, 05 Jul 2019 23:28:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.10_model.r INFO @ Fri, 05 Jul 2019 23:28:16: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:28:16: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:28:16: #1 total tags in treatment: 251029 INFO @ Fri, 05 Jul 2019 23:28:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:28:16: #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 23:28:16: #1 tags after filtering in treatment: 224065 INFO @ Fri, 05 Jul 2019 23:28:16: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 05 Jul 2019 23:28:16: #1 finished! INFO @ Fri, 05 Jul 2019 23:28:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:28:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:28:16: #2 number of paired peaks: 300 WARNING @ Fri, 05 Jul 2019 23:28:16: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Fri, 05 Jul 2019 23:28:16: start model_add_line... INFO @ Fri, 05 Jul 2019 23:28:16: start X-correlation... INFO @ Fri, 05 Jul 2019 23:28:16: end of X-cor INFO @ Fri, 05 Jul 2019 23:28:16: #2 finished! INFO @ Fri, 05 Jul 2019 23:28:16: #2 predicted fragment length is 267 bps INFO @ Fri, 05 Jul 2019 23:28:16: #2 alternative fragment length(s) may be 4,267,287,310,451,483 bps INFO @ Fri, 05 Jul 2019 23:28:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.05_model.r INFO @ Fri, 05 Jul 2019 23:28:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:28:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:28:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:28:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:28:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:28:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:28:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:28:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:28:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.10_summits.bed INFO @ Fri, 05 Jul 2019 23:28:29: Done! INFO @ Fri, 05 Jul 2019 23:28:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:28:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:28:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.05_summits.bed INFO @ Fri, 05 Jul 2019 23:28:29: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (58 records, 4 fields): 2 millis pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (131 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:28:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.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 23:28:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:28:30: #1 read treatment tags... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:28:35: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:28:35: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:28:35: #1 total tags in treatment: 251029 INFO @ Fri, 05 Jul 2019 23:28:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:28:35: #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 23:28:35: #1 tags after filtering in treatment: 224065 INFO @ Fri, 05 Jul 2019 23:28:35: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 05 Jul 2019 23:28:35: #1 finished! INFO @ Fri, 05 Jul 2019 23:28:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:28:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:28:35: #2 number of paired peaks: 300 WARNING @ Fri, 05 Jul 2019 23:28:35: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Fri, 05 Jul 2019 23:28:35: start model_add_line... INFO @ Fri, 05 Jul 2019 23:28:35: start X-correlation... INFO @ Fri, 05 Jul 2019 23:28:35: end of X-cor INFO @ Fri, 05 Jul 2019 23:28:35: #2 finished! INFO @ Fri, 05 Jul 2019 23:28:35: #2 predicted fragment length is 267 bps INFO @ Fri, 05 Jul 2019 23:28:35: #2 alternative fragment length(s) may be 4,267,287,310,451,483 bps INFO @ Fri, 05 Jul 2019 23:28:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.20_model.r INFO @ Fri, 05 Jul 2019 23:28:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:28:35: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:28:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:28:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:28:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:28:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381288/SRX381288.20_summits.bed INFO @ Fri, 05 Jul 2019 23:28:37: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (24 records, 4 fields): 2 millis BigWig に変換しました。 CompletedMACS2peakCalling