Job ID = 2009839 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T11:10:16 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 : 15,327,890 reads read : 15,327,890 reads written : 15,327,890 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: 00:01:57 15327890 reads; of these: 15327890 (100.00%) were unpaired; of these: 2910953 (18.99%) aligned 0 times 10449221 (68.17%) aligned exactly 1 time 1967716 (12.84%) aligned >1 times 81.01% overall alignment rate Time searching: 00:01:57 Overall time: 00:01:57 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] 11034936 / 12416937 = 0.8887 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 20:14:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.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 20:14:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:14:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:14:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.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 20:14:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:14:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:14:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.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 20:14:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:14:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:14:46: 1000000 INFO @ Fri, 05 Jul 2019 20:14:46: 1000000 INFO @ Fri, 05 Jul 2019 20:14:47: 1000000 INFO @ Fri, 05 Jul 2019 20:14:49: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 20:14:49: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 20:14:49: #1 total tags in treatment: 1382001 INFO @ Fri, 05 Jul 2019 20:14:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:14:49: #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 20:14:49: #1 tags after filtering in treatment: 1382001 INFO @ Fri, 05 Jul 2019 20:14:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:14:49: #1 finished! INFO @ Fri, 05 Jul 2019 20:14:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:14:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:14:49: #2 number of paired peaks: 290 WARNING @ Fri, 05 Jul 2019 20:14:49: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Fri, 05 Jul 2019 20:14:49: start model_add_line... INFO @ Fri, 05 Jul 2019 20:14:49: start X-correlation... INFO @ Fri, 05 Jul 2019 20:14:49: end of X-cor INFO @ Fri, 05 Jul 2019 20:14:49: #2 finished! INFO @ Fri, 05 Jul 2019 20:14:49: #2 predicted fragment length is 1 bps INFO @ Fri, 05 Jul 2019 20:14:49: #2 alternative fragment length(s) may be 1,29,67,101,112,137,148,471,503,554 bps INFO @ Fri, 05 Jul 2019 20:14:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.05_model.r WARNING @ Fri, 05 Jul 2019 20:14:49: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 20:14:49: #2 You may need to consider one of the other alternative d(s): 1,29,67,101,112,137,148,471,503,554 WARNING @ Fri, 05 Jul 2019 20:14:49: #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 20:14:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:14:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:14:49: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 20:14:49: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 20:14:49: #1 total tags in treatment: 1382001 INFO @ Fri, 05 Jul 2019 20:14:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:14:49: #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 20:14:49: #1 tags after filtering in treatment: 1382001 INFO @ Fri, 05 Jul 2019 20:14:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:14:49: #1 finished! INFO @ Fri, 05 Jul 2019 20:14:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:14:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:14:50: #2 number of paired peaks: 290 WARNING @ Fri, 05 Jul 2019 20:14:50: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Fri, 05 Jul 2019 20:14:50: start model_add_line... INFO @ Fri, 05 Jul 2019 20:14:50: start X-correlation... INFO @ Fri, 05 Jul 2019 20:14:50: end of X-cor INFO @ Fri, 05 Jul 2019 20:14:50: #2 finished! INFO @ Fri, 05 Jul 2019 20:14:50: #2 predicted fragment length is 1 bps INFO @ Fri, 05 Jul 2019 20:14:50: #2 alternative fragment length(s) may be 1,29,67,101,112,137,148,471,503,554 bps INFO @ Fri, 05 Jul 2019 20:14:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.10_model.r WARNING @ Fri, 05 Jul 2019 20:14:50: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 20:14:50: #2 You may need to consider one of the other alternative d(s): 1,29,67,101,112,137,148,471,503,554 WARNING @ Fri, 05 Jul 2019 20:14:50: #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 20:14:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:14:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:14:50: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 20:14:50: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 20:14:50: #1 total tags in treatment: 1382001 INFO @ Fri, 05 Jul 2019 20:14:50: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:14:50: #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 20:14:50: #1 tags after filtering in treatment: 1382001 INFO @ Fri, 05 Jul 2019 20:14:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:14:50: #1 finished! INFO @ Fri, 05 Jul 2019 20:14:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:14:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:14:50: #2 number of paired peaks: 290 WARNING @ Fri, 05 Jul 2019 20:14:50: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Fri, 05 Jul 2019 20:14:50: start model_add_line... INFO @ Fri, 05 Jul 2019 20:14:50: start X-correlation... INFO @ Fri, 05 Jul 2019 20:14:50: end of X-cor INFO @ Fri, 05 Jul 2019 20:14:50: #2 finished! INFO @ Fri, 05 Jul 2019 20:14:50: #2 predicted fragment length is 1 bps INFO @ Fri, 05 Jul 2019 20:14:50: #2 alternative fragment length(s) may be 1,29,67,101,112,137,148,471,503,554 bps INFO @ Fri, 05 Jul 2019 20:14:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.20_model.r WARNING @ Fri, 05 Jul 2019 20:14:50: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 20:14:50: #2 You may need to consider one of the other alternative d(s): 1,29,67,101,112,137,148,471,503,554 WARNING @ Fri, 05 Jul 2019 20:14:50: #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 20:14:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:14:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:14:52: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:14:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:14:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:14:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.05_peaks.xls INFO @ Fri, 05 Jul 2019 20:14:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:14:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.05_summits.bed INFO @ Fri, 05 Jul 2019 20:14:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Fri, 05 Jul 2019 20:14:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.10_peaks.xls INFO @ Fri, 05 Jul 2019 20:14:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:14:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.10_summits.bed INFO @ Fri, 05 Jul 2019 20:14:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Fri, 05 Jul 2019 20:14:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.20_peaks.xls INFO @ Fri, 05 Jul 2019 20:14:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:14:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX185636/SRX185636.20_summits.bed INFO @ Fri, 05 Jul 2019 20:14:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。