Job ID = 1292394 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,889,143 reads read : 4,889,143 reads written : 4,889,143 spots read : 5,689,358 reads read : 5,689,358 reads written : 5,689,358 rm: cannot remove ‘fastqDump_tmp*’: 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:14 10578501 reads; of these: 10578501 (100.00%) were unpaired; of these: 5603834 (52.97%) aligned 0 times 4047271 (38.26%) aligned exactly 1 time 927396 (8.77%) aligned >1 times 47.03% overall alignment rate Time searching: 00:01:15 Overall time: 00:01:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 2131694 / 4974667 = 0.4285 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 @ Sun, 02 Jun 2019 18:19:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 18:19:35: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:19:35: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:19:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 18:19:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 18:19:35: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:19:35: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:19:35: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:19:35: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:19:42: 1000000 INFO @ Sun, 02 Jun 2019 18:19:42: 1000000 INFO @ Sun, 02 Jun 2019 18:19:43: 1000000 INFO @ Sun, 02 Jun 2019 18:19:50: 2000000 INFO @ Sun, 02 Jun 2019 18:19:50: 2000000 INFO @ Sun, 02 Jun 2019 18:19:50: 2000000 INFO @ Sun, 02 Jun 2019 18:19:56: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 18:19:56: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 18:19:56: #1 total tags in treatment: 2842973 INFO @ Sun, 02 Jun 2019 18:19:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:19:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:19:56: #1 tags after filtering in treatment: 2842973 INFO @ Sun, 02 Jun 2019 18:19:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:19:56: #1 finished! INFO @ Sun, 02 Jun 2019 18:19:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:19:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:19:56: #2 number of paired peaks: 950 WARNING @ Sun, 02 Jun 2019 18:19:56: Fewer paired peaks (950) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 950 pairs to build model! INFO @ Sun, 02 Jun 2019 18:19:56: start model_add_line... INFO @ Sun, 02 Jun 2019 18:19:56: start X-correlation... INFO @ Sun, 02 Jun 2019 18:19:56: end of X-cor INFO @ Sun, 02 Jun 2019 18:19:56: #2 finished! INFO @ Sun, 02 Jun 2019 18:19:56: #2 predicted fragment length is 155 bps INFO @ Sun, 02 Jun 2019 18:19:56: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 02 Jun 2019 18:19:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.05_model.r INFO @ Sun, 02 Jun 2019 18:19:56: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:19:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:19:57: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 18:19:57: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 18:19:57: #1 total tags in treatment: 2842973 INFO @ Sun, 02 Jun 2019 18:19:57: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:19:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:19:57: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 18:19:57: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 18:19:57: #1 total tags in treatment: 2842973 INFO @ Sun, 02 Jun 2019 18:19:57: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:19:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:19:57: #1 tags after filtering in treatment: 2842973 INFO @ Sun, 02 Jun 2019 18:19:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:19:57: #1 finished! INFO @ Sun, 02 Jun 2019 18:19:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:19:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:19:57: #1 tags after filtering in treatment: 2842973 INFO @ Sun, 02 Jun 2019 18:19:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:19:57: #1 finished! INFO @ Sun, 02 Jun 2019 18:19:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:19:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:19:57: #2 number of paired peaks: 950 WARNING @ Sun, 02 Jun 2019 18:19:57: Fewer paired peaks (950) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 950 pairs to build model! INFO @ Sun, 02 Jun 2019 18:19:57: start model_add_line... INFO @ Sun, 02 Jun 2019 18:19:57: start X-correlation... INFO @ Sun, 02 Jun 2019 18:19:57: end of X-cor INFO @ Sun, 02 Jun 2019 18:19:57: #2 finished! INFO @ Sun, 02 Jun 2019 18:19:57: #2 predicted fragment length is 155 bps INFO @ Sun, 02 Jun 2019 18:19:57: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 02 Jun 2019 18:19:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.10_model.r INFO @ Sun, 02 Jun 2019 18:19:57: #2 number of paired peaks: 950 WARNING @ Sun, 02 Jun 2019 18:19:57: Fewer paired peaks (950) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 950 pairs to build model! INFO @ Sun, 02 Jun 2019 18:19:57: start model_add_line... INFO @ Sun, 02 Jun 2019 18:19:57: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:19:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:19:57: start X-correlation... INFO @ Sun, 02 Jun 2019 18:19:57: end of X-cor INFO @ Sun, 02 Jun 2019 18:19:57: #2 finished! INFO @ Sun, 02 Jun 2019 18:19:57: #2 predicted fragment length is 155 bps INFO @ Sun, 02 Jun 2019 18:19:57: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 02 Jun 2019 18:19:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.20_model.r INFO @ Sun, 02 Jun 2019 18:19:57: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:19:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:20:05: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:20:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:20:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:20:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:20:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:20:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.05_summits.bed INFO @ Sun, 02 Jun 2019 18:20:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1998 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:20:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:20:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:20:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.20_summits.bed INFO @ Sun, 02 Jun 2019 18:20:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (479 records, 4 fields): 4 millis INFO @ Sun, 02 Jun 2019 18:20:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.10_peaks.xls CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:20:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:20:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX395527/SRX395527.10_summits.bed INFO @ Sun, 02 Jun 2019 18:20:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1103 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。