Job ID = 2009679 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T10:26:19 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 : 3,681,062 reads read : 3,681,062 reads written : 3,681,062 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR364339.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: 00:00:24 3681062 reads; of these: 3681062 (100.00%) were unpaired; of these: 2396513 (65.10%) aligned 0 times 1069309 (29.05%) aligned exactly 1 time 215240 (5.85%) aligned >1 times 34.90% overall alignment rate Time searching: 00:00:24 Overall time: 00:00:24 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_rmdupse_core] 482384 / 1284549 = 0.3755 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 19:28:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.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 19:28:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:28:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:28:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.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 19:28:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:28:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:28:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.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 19:28:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:28:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:29:01: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 19:29:01: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 19:29:01: #1 total tags in treatment: 802165 INFO @ Fri, 05 Jul 2019 19:29:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:29:01: #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 19:29:01: #1 tags after filtering in treatment: 802165 INFO @ Fri, 05 Jul 2019 19:29:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:29:01: #1 finished! INFO @ Fri, 05 Jul 2019 19:29:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:29:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:29:01: #2 number of paired peaks: 815 WARNING @ Fri, 05 Jul 2019 19:29:01: Fewer paired peaks (815) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 815 pairs to build model! INFO @ Fri, 05 Jul 2019 19:29:01: start model_add_line... INFO @ Fri, 05 Jul 2019 19:29:01: start X-correlation... INFO @ Fri, 05 Jul 2019 19:29:01: end of X-cor INFO @ Fri, 05 Jul 2019 19:29:01: #2 finished! INFO @ Fri, 05 Jul 2019 19:29:01: #2 predicted fragment length is 222 bps INFO @ Fri, 05 Jul 2019 19:29:01: #2 alternative fragment length(s) may be 3,16,199,222,256 bps INFO @ Fri, 05 Jul 2019 19:29:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.05_model.r INFO @ Fri, 05 Jul 2019 19:29:01: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 19:29:01: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 19:29:01: #1 total tags in treatment: 802165 INFO @ Fri, 05 Jul 2019 19:29:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:29:01: #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 19:29:01: #1 tags after filtering in treatment: 802165 INFO @ Fri, 05 Jul 2019 19:29:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:29:01: #1 finished! INFO @ Fri, 05 Jul 2019 19:29:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:29:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:29:01: #2 number of paired peaks: 815 WARNING @ Fri, 05 Jul 2019 19:29:01: Fewer paired peaks (815) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 815 pairs to build model! INFO @ Fri, 05 Jul 2019 19:29:01: start model_add_line... INFO @ Fri, 05 Jul 2019 19:29:01: start X-correlation... INFO @ Fri, 05 Jul 2019 19:29:01: end of X-cor INFO @ Fri, 05 Jul 2019 19:29:01: #2 finished! INFO @ Fri, 05 Jul 2019 19:29:01: #2 predicted fragment length is 222 bps INFO @ Fri, 05 Jul 2019 19:29:01: #2 alternative fragment length(s) may be 3,16,199,222,256 bps INFO @ Fri, 05 Jul 2019 19:29:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.10_model.r INFO @ Fri, 05 Jul 2019 19:29:03: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 19:29:03: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 19:29:03: #1 total tags in treatment: 802165 INFO @ Fri, 05 Jul 2019 19:29:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:29:03: #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 19:29:03: #1 tags after filtering in treatment: 802165 INFO @ Fri, 05 Jul 2019 19:29:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:29:03: #1 finished! INFO @ Fri, 05 Jul 2019 19:29:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:29:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:29:03: #2 number of paired peaks: 815 WARNING @ Fri, 05 Jul 2019 19:29:03: Fewer paired peaks (815) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 815 pairs to build model! INFO @ Fri, 05 Jul 2019 19:29:03: start model_add_line... INFO @ Fri, 05 Jul 2019 19:29:03: start X-correlation... INFO @ Fri, 05 Jul 2019 19:29:03: end of X-cor INFO @ Fri, 05 Jul 2019 19:29:03: #2 finished! INFO @ Fri, 05 Jul 2019 19:29:03: #2 predicted fragment length is 222 bps INFO @ Fri, 05 Jul 2019 19:29:03: #2 alternative fragment length(s) may be 3,16,199,222,256 bps INFO @ Fri, 05 Jul 2019 19:29:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.20_model.r INFO @ Fri, 05 Jul 2019 19:29:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:29:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:29:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:29:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:29:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:29:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:29:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:29:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:29:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:29:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:29:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:29:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.20_summits.bed INFO @ Fri, 05 Jul 2019 19:29:19: Done! INFO @ Fri, 05 Jul 2019 19:29:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:29:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:29:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.10_summits.bed INFO @ Fri, 05 Jul 2019 19:29:19: Done! INFO @ Fri, 05 Jul 2019 19:29:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.05_peaks.xls pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (155 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 19:29:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:29:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX105553/SRX105553.05_summits.bed INFO @ Fri, 05 Jul 2019 19:29:19: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (410 records, 4 fields): 5 millis pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (626 records, 4 fields): 4 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。