Job ID = 2007639 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,186,561 reads read : 3,186,561 reads written : 3,186,561 spots read : 3,056,537 reads read : 3,056,537 reads written : 3,056,537 spots read : 3,110,627 reads read : 3,110,627 reads written : 3,110,627 2019-07-05T07:11:35 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 ) 2019-07-05T07:11:35 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 ) 2019-07-05T07:11:35 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 : 3,038,443 reads read : 3,038,443 reads written : 3,038,443 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529770.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529772.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529773.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: 00:06:04 12392168 reads; of these: 12392168 (100.00%) were unpaired; of these: 445776 (3.60%) aligned 0 times 9827114 (79.30%) aligned exactly 1 time 2119278 (17.10%) aligned >1 times 96.40% overall alignment rate Time searching: 00:06:04 Overall time: 00:06:04 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_sort_core] merging from 8 files... [bam_rmdupse_core] 11464970 / 11946392 = 0.9597 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 05 Jul 2019 16:21:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.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 BedGraph に変換中... INFO @ Fri, 05 Jul 2019 16:21:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.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 16:21:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:21:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:21:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:21:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:21:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.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 16:21:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:21:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:21:41: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:21:42: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:21:42: #1 total tags in treatment: 481422 INFO @ Fri, 05 Jul 2019 16:21:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:21:42: #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 16:21:42: #1 tags after filtering in treatment: 481422 INFO @ Fri, 05 Jul 2019 16:21:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:21:42: #1 finished! INFO @ Fri, 05 Jul 2019 16:21:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:21:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:21:43: #2 number of paired peaks: 487 WARNING @ Fri, 05 Jul 2019 16:21:43: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Fri, 05 Jul 2019 16:21:43: start model_add_line... INFO @ Fri, 05 Jul 2019 16:21:43: start X-correlation... INFO @ Fri, 05 Jul 2019 16:21:43: end of X-cor INFO @ Fri, 05 Jul 2019 16:21:43: #2 finished! INFO @ Fri, 05 Jul 2019 16:21:43: #2 predicted fragment length is 160 bps INFO @ Fri, 05 Jul 2019 16:21:43: #2 alternative fragment length(s) may be 160,191 bps INFO @ Fri, 05 Jul 2019 16:21:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.10_model.r INFO @ Fri, 05 Jul 2019 16:21:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:21:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:21:43: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:21:43: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:21:43: #1 total tags in treatment: 481422 INFO @ Fri, 05 Jul 2019 16:21:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:21:43: #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 16:21:43: #1 tags after filtering in treatment: 481422 INFO @ Fri, 05 Jul 2019 16:21:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:21:43: #1 finished! INFO @ Fri, 05 Jul 2019 16:21:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:21:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:21:43: #2 number of paired peaks: 487 WARNING @ Fri, 05 Jul 2019 16:21:43: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Fri, 05 Jul 2019 16:21:43: start model_add_line... INFO @ Fri, 05 Jul 2019 16:21:43: start X-correlation... INFO @ Fri, 05 Jul 2019 16:21:43: end of X-cor INFO @ Fri, 05 Jul 2019 16:21:43: #2 finished! INFO @ Fri, 05 Jul 2019 16:21:43: #2 predicted fragment length is 160 bps INFO @ Fri, 05 Jul 2019 16:21:43: #2 alternative fragment length(s) may be 160,191 bps INFO @ Fri, 05 Jul 2019 16:21:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.20_model.r INFO @ Fri, 05 Jul 2019 16:21:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:21:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:21:43: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:21:43: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:21:43: #1 total tags in treatment: 481422 INFO @ Fri, 05 Jul 2019 16:21:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:21:43: #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 16:21:43: #1 tags after filtering in treatment: 481422 INFO @ Fri, 05 Jul 2019 16:21:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:21:43: #1 finished! INFO @ Fri, 05 Jul 2019 16:21:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:21:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:21:43: #2 number of paired peaks: 487 WARNING @ Fri, 05 Jul 2019 16:21:43: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Fri, 05 Jul 2019 16:21:43: start model_add_line... INFO @ Fri, 05 Jul 2019 16:21:43: start X-correlation... INFO @ Fri, 05 Jul 2019 16:21:43: end of X-cor INFO @ Fri, 05 Jul 2019 16:21:43: #2 finished! INFO @ Fri, 05 Jul 2019 16:21:43: #2 predicted fragment length is 160 bps INFO @ Fri, 05 Jul 2019 16:21:43: #2 alternative fragment length(s) may be 160,191 bps INFO @ Fri, 05 Jul 2019 16:21:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.05_model.r INFO @ Fri, 05 Jul 2019 16:21:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:21:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:21:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:21:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:21:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:21:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:21:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.10_summits.bed INFO @ Fri, 05 Jul 2019 16:21:45: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (108 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 16:21:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:21:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:21:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:21:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.20_summits.bed INFO @ Fri, 05 Jul 2019 16:21:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (59 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:21:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:21:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:21:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548238/ERX2548238.05_summits.bed INFO @ Fri, 05 Jul 2019 16:21:46: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (229 records, 4 fields): 6 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling