Job ID = 2640743 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T09:49:50 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 ) 2019-08-24T09:49:50 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-08-24T10:04:29 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 25,367,509 reads read : 25,367,509 reads written : 25,367,509 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: 00:03:38 25367509 reads; of these: 25367509 (100.00%) were unpaired; of these: 21856273 (86.16%) aligned 0 times 2788508 (10.99%) aligned exactly 1 time 722728 (2.85%) aligned >1 times 13.84% overall alignment rate Time searching: 00:03:38 Overall time: 00:03:38 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] 3118546 / 3511236 = 0.8882 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:10:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.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 @ Sat, 24 Aug 2019 19:10:12: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:10:12: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:10:16: #1 tag size is determined as 40 bps INFO @ Sat, 24 Aug 2019 19:10:16: #1 tag size = 40 INFO @ Sat, 24 Aug 2019 19:10:16: #1 total tags in treatment: 392690 INFO @ Sat, 24 Aug 2019 19:10:16: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:10:16: #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 19:10:16: #1 tags after filtering in treatment: 392690 INFO @ Sat, 24 Aug 2019 19:10:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:10:16: #1 finished! INFO @ Sat, 24 Aug 2019 19:10:16: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:10:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:10:16: #2 number of paired peaks: 203 WARNING @ Sat, 24 Aug 2019 19:10:16: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Sat, 24 Aug 2019 19:10:16: start model_add_line... INFO @ Sat, 24 Aug 2019 19:10:16: start X-correlation... INFO @ Sat, 24 Aug 2019 19:10:16: end of X-cor INFO @ Sat, 24 Aug 2019 19:10:16: #2 finished! INFO @ Sat, 24 Aug 2019 19:10:16: #2 predicted fragment length is 126 bps INFO @ Sat, 24 Aug 2019 19:10:16: #2 alternative fragment length(s) may be 123,126 bps INFO @ Sat, 24 Aug 2019 19:10:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.05_model.r INFO @ Sat, 24 Aug 2019 19:10:16: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:10:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:10:17: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:10:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.05_peaks.xls INFO @ Sat, 24 Aug 2019 19:10:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:10:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.05_summits.bed INFO @ Sat, 24 Aug 2019 19:10:18: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (369 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:10:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.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 @ Sat, 24 Aug 2019 19:10:41: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:10:41: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:10:45: #1 tag size is determined as 40 bps INFO @ Sat, 24 Aug 2019 19:10:45: #1 tag size = 40 INFO @ Sat, 24 Aug 2019 19:10:45: #1 total tags in treatment: 392690 INFO @ Sat, 24 Aug 2019 19:10:45: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:10:45: #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 19:10:45: #1 tags after filtering in treatment: 392690 INFO @ Sat, 24 Aug 2019 19:10:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:10:45: #1 finished! INFO @ Sat, 24 Aug 2019 19:10:45: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:10:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:10:45: #2 number of paired peaks: 203 WARNING @ Sat, 24 Aug 2019 19:10:45: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Sat, 24 Aug 2019 19:10:45: start model_add_line... INFO @ Sat, 24 Aug 2019 19:10:45: start X-correlation... INFO @ Sat, 24 Aug 2019 19:10:45: end of X-cor INFO @ Sat, 24 Aug 2019 19:10:45: #2 finished! INFO @ Sat, 24 Aug 2019 19:10:45: #2 predicted fragment length is 126 bps INFO @ Sat, 24 Aug 2019 19:10:45: #2 alternative fragment length(s) may be 123,126 bps INFO @ Sat, 24 Aug 2019 19:10:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.10_model.r INFO @ Sat, 24 Aug 2019 19:10:45: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:10:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:10:46: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:10:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.10_peaks.xls INFO @ Sat, 24 Aug 2019 19:10:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:10:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.10_summits.bed INFO @ Sat, 24 Aug 2019 19:10:47: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (174 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:11:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.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 @ Sat, 24 Aug 2019 19:11:11: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:11:11: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:11:14: #1 tag size is determined as 40 bps INFO @ Sat, 24 Aug 2019 19:11:14: #1 tag size = 40 INFO @ Sat, 24 Aug 2019 19:11:14: #1 total tags in treatment: 392690 INFO @ Sat, 24 Aug 2019 19:11:14: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:11:14: #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 19:11:14: #1 tags after filtering in treatment: 392690 INFO @ Sat, 24 Aug 2019 19:11:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:11:14: #1 finished! INFO @ Sat, 24 Aug 2019 19:11:14: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:11:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:11:14: #2 number of paired peaks: 203 WARNING @ Sat, 24 Aug 2019 19:11:14: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Sat, 24 Aug 2019 19:11:14: start model_add_line... INFO @ Sat, 24 Aug 2019 19:11:14: start X-correlation... INFO @ Sat, 24 Aug 2019 19:11:14: end of X-cor INFO @ Sat, 24 Aug 2019 19:11:14: #2 finished! INFO @ Sat, 24 Aug 2019 19:11:14: #2 predicted fragment length is 126 bps INFO @ Sat, 24 Aug 2019 19:11:14: #2 alternative fragment length(s) may be 123,126 bps INFO @ Sat, 24 Aug 2019 19:11:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.20_model.r INFO @ Sat, 24 Aug 2019 19:11:14: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:11:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:11:16: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:11:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.20_peaks.xls INFO @ Sat, 24 Aug 2019 19:11:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:11:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2732434/ERX2732434.20_summits.bed INFO @ Sat, 24 Aug 2019 19:11:16: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (67 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。