Job ID = 2010025 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T11:57:25 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 : 5,690,099 reads read : 11,380,198 reads written : 5,690,099 reads 0-length : 5,690,099 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: 00:01:11 5690099 reads; of these: 5690099 (100.00%) were unpaired; of these: 1138464 (20.01%) aligned 0 times 3010694 (52.91%) aligned exactly 1 time 1540941 (27.08%) aligned >1 times 79.99% overall alignment rate Time searching: 00:01:11 Overall time: 00:01:11 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] 2234856 / 4551635 = 0.4910 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 21:02:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.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 21:02:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:02:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:02:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.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 21:02:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:02:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:02:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.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 21:02:07: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:02:07: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:02:13: 1000000 INFO @ Fri, 05 Jul 2019 21:02:17: 1000000 INFO @ Fri, 05 Jul 2019 21:02:18: 1000000 INFO @ Fri, 05 Jul 2019 21:02:22: 2000000 INFO @ Fri, 05 Jul 2019 21:02:25: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:02:25: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:02:25: #1 total tags in treatment: 2316779 INFO @ Fri, 05 Jul 2019 21:02:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:02:25: #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 21:02:25: #1 tags after filtering in treatment: 2316779 INFO @ Fri, 05 Jul 2019 21:02:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:02:25: #1 finished! INFO @ Fri, 05 Jul 2019 21:02:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:02:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:02:25: #2 number of paired peaks: 205 WARNING @ Fri, 05 Jul 2019 21:02:25: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Fri, 05 Jul 2019 21:02:25: start model_add_line... INFO @ Fri, 05 Jul 2019 21:02:25: start X-correlation... INFO @ Fri, 05 Jul 2019 21:02:26: end of X-cor INFO @ Fri, 05 Jul 2019 21:02:26: #2 finished! INFO @ Fri, 05 Jul 2019 21:02:26: #2 predicted fragment length is 98 bps INFO @ Fri, 05 Jul 2019 21:02:26: #2 alternative fragment length(s) may be 3,98 bps INFO @ Fri, 05 Jul 2019 21:02:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.05_model.r WARNING @ Fri, 05 Jul 2019 21:02:26: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 21:02:26: #2 You may need to consider one of the other alternative d(s): 3,98 WARNING @ Fri, 05 Jul 2019 21:02:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 21:02:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:02:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:02:28: 2000000 INFO @ Fri, 05 Jul 2019 21:02:30: 2000000 INFO @ Fri, 05 Jul 2019 21:02:31: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:02:31: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:02:31: #1 total tags in treatment: 2316779 INFO @ Fri, 05 Jul 2019 21:02:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:02:31: #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 21:02:31: #1 tags after filtering in treatment: 2316779 INFO @ Fri, 05 Jul 2019 21:02:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:02:31: #1 finished! INFO @ Fri, 05 Jul 2019 21:02:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:02:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:02:31: #2 number of paired peaks: 205 WARNING @ Fri, 05 Jul 2019 21:02:31: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Fri, 05 Jul 2019 21:02:31: start model_add_line... INFO @ Fri, 05 Jul 2019 21:02:31: start X-correlation... INFO @ Fri, 05 Jul 2019 21:02:31: end of X-cor INFO @ Fri, 05 Jul 2019 21:02:31: #2 finished! INFO @ Fri, 05 Jul 2019 21:02:31: #2 predicted fragment length is 98 bps INFO @ Fri, 05 Jul 2019 21:02:31: #2 alternative fragment length(s) may be 3,98 bps INFO @ Fri, 05 Jul 2019 21:02:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.10_model.r WARNING @ Fri, 05 Jul 2019 21:02:31: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 21:02:31: #2 You may need to consider one of the other alternative d(s): 3,98 WARNING @ Fri, 05 Jul 2019 21:02:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 21:02:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:02:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:02:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:02:33: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:02:33: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:02:33: #1 total tags in treatment: 2316779 INFO @ Fri, 05 Jul 2019 21:02:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:02:33: #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 21:02:33: #1 tags after filtering in treatment: 2316779 INFO @ Fri, 05 Jul 2019 21:02:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:02:33: #1 finished! INFO @ Fri, 05 Jul 2019 21:02:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:02:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:02:34: #2 number of paired peaks: 205 WARNING @ Fri, 05 Jul 2019 21:02:34: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Fri, 05 Jul 2019 21:02:34: start model_add_line... INFO @ Fri, 05 Jul 2019 21:02:34: start X-correlation... INFO @ Fri, 05 Jul 2019 21:02:34: end of X-cor INFO @ Fri, 05 Jul 2019 21:02:34: #2 finished! INFO @ Fri, 05 Jul 2019 21:02:34: #2 predicted fragment length is 98 bps INFO @ Fri, 05 Jul 2019 21:02:34: #2 alternative fragment length(s) may be 3,98 bps INFO @ Fri, 05 Jul 2019 21:02:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.20_model.r WARNING @ Fri, 05 Jul 2019 21:02:34: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 21:02:34: #2 You may need to consider one of the other alternative d(s): 3,98 WARNING @ Fri, 05 Jul 2019 21:02:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 21:02:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:02:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:02:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.05_peaks.xls INFO @ Fri, 05 Jul 2019 21:02:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:02:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.05_summits.bed INFO @ Fri, 05 Jul 2019 21:02:35: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (363 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:02:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:02:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.10_peaks.xls INFO @ Fri, 05 Jul 2019 21:02:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:02:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.10_summits.bed INFO @ Fri, 05 Jul 2019 21:02:41: Done! INFO @ Fri, 05 Jul 2019 21:02:41: #3 Call peaks for each chromosome... pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (215 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:02:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.20_peaks.xls INFO @ Fri, 05 Jul 2019 21:02:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:02:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX249057/SRX249057.20_summits.bed INFO @ Fri, 05 Jul 2019 21:02:44: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (119 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。