Job ID = 2590234 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,010,084 reads read : 20,010,084 reads written : 20,010,084 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: 00:03:58 20010084 reads; of these: 20010084 (100.00%) were unpaired; of these: 12992315 (64.93%) aligned 0 times 6055320 (30.26%) aligned exactly 1 time 962449 (4.81%) aligned >1 times 35.07% overall alignment rate Time searching: 00:03:58 Overall time: 00:03:58 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] 1376553 / 7017769 = 0.1962 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 @ Mon, 12 Aug 2019 20:35:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.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 @ Mon, 12 Aug 2019 20:35:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:35:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:35:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.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 @ Mon, 12 Aug 2019 20:35:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:35:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:35:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.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 @ Mon, 12 Aug 2019 20:35:38: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:35:38: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:35:45: 1000000 INFO @ Mon, 12 Aug 2019 20:35:48: 1000000 INFO @ Mon, 12 Aug 2019 20:35:48: 1000000 INFO @ Mon, 12 Aug 2019 20:35:54: 2000000 INFO @ Mon, 12 Aug 2019 20:35:58: 2000000 INFO @ Mon, 12 Aug 2019 20:35:58: 2000000 INFO @ Mon, 12 Aug 2019 20:36:03: 3000000 INFO @ Mon, 12 Aug 2019 20:36:07: 3000000 INFO @ Mon, 12 Aug 2019 20:36:08: 3000000 INFO @ Mon, 12 Aug 2019 20:36:12: 4000000 INFO @ Mon, 12 Aug 2019 20:36:17: 4000000 INFO @ Mon, 12 Aug 2019 20:36:19: 4000000 INFO @ Mon, 12 Aug 2019 20:36:21: 5000000 INFO @ Mon, 12 Aug 2019 20:36:26: 5000000 INFO @ Mon, 12 Aug 2019 20:36:26: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:36:26: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:36:26: #1 total tags in treatment: 5641216 INFO @ Mon, 12 Aug 2019 20:36:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:36:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:36:26: #1 tags after filtering in treatment: 5641216 INFO @ Mon, 12 Aug 2019 20:36:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:36:26: #1 finished! INFO @ Mon, 12 Aug 2019 20:36:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:36:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:36:27: #2 number of paired peaks: 636 WARNING @ Mon, 12 Aug 2019 20:36:27: Fewer paired peaks (636) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 636 pairs to build model! INFO @ Mon, 12 Aug 2019 20:36:27: start model_add_line... INFO @ Mon, 12 Aug 2019 20:36:27: start X-correlation... INFO @ Mon, 12 Aug 2019 20:36:27: end of X-cor INFO @ Mon, 12 Aug 2019 20:36:27: #2 finished! INFO @ Mon, 12 Aug 2019 20:36:27: #2 predicted fragment length is 160 bps INFO @ Mon, 12 Aug 2019 20:36:27: #2 alternative fragment length(s) may be 160 bps INFO @ Mon, 12 Aug 2019 20:36:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.05_model.r INFO @ Mon, 12 Aug 2019 20:36:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:36:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:36:30: 5000000 INFO @ Mon, 12 Aug 2019 20:36:32: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:36:32: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:36:32: #1 total tags in treatment: 5641216 INFO @ Mon, 12 Aug 2019 20:36:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:36:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:36:32: #1 tags after filtering in treatment: 5641216 INFO @ Mon, 12 Aug 2019 20:36:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:36:32: #1 finished! INFO @ Mon, 12 Aug 2019 20:36:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:36:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:36:33: #2 number of paired peaks: 636 WARNING @ Mon, 12 Aug 2019 20:36:33: Fewer paired peaks (636) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 636 pairs to build model! INFO @ Mon, 12 Aug 2019 20:36:33: start model_add_line... INFO @ Mon, 12 Aug 2019 20:36:33: start X-correlation... INFO @ Mon, 12 Aug 2019 20:36:33: end of X-cor INFO @ Mon, 12 Aug 2019 20:36:33: #2 finished! INFO @ Mon, 12 Aug 2019 20:36:33: #2 predicted fragment length is 160 bps INFO @ Mon, 12 Aug 2019 20:36:33: #2 alternative fragment length(s) may be 160 bps INFO @ Mon, 12 Aug 2019 20:36:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.20_model.r INFO @ Mon, 12 Aug 2019 20:36:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:36:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:36:36: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:36:36: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:36:36: #1 total tags in treatment: 5641216 INFO @ Mon, 12 Aug 2019 20:36:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:36:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:36:36: #1 tags after filtering in treatment: 5641216 INFO @ Mon, 12 Aug 2019 20:36:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:36:36: #1 finished! INFO @ Mon, 12 Aug 2019 20:36:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:36:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:36:37: #2 number of paired peaks: 636 WARNING @ Mon, 12 Aug 2019 20:36:37: Fewer paired peaks (636) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 636 pairs to build model! INFO @ Mon, 12 Aug 2019 20:36:37: start model_add_line... INFO @ Mon, 12 Aug 2019 20:36:37: start X-correlation... INFO @ Mon, 12 Aug 2019 20:36:37: end of X-cor INFO @ Mon, 12 Aug 2019 20:36:37: #2 finished! INFO @ Mon, 12 Aug 2019 20:36:37: #2 predicted fragment length is 160 bps INFO @ Mon, 12 Aug 2019 20:36:37: #2 alternative fragment length(s) may be 160 bps INFO @ Mon, 12 Aug 2019 20:36:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.10_model.r INFO @ Mon, 12 Aug 2019 20:36:37: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:36:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:36:45: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:36:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:36:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:36:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:36:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.05_summits.bed INFO @ Mon, 12 Aug 2019 20:36:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2834 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:36:55: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:37:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:37:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:37:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.20_summits.bed INFO @ Mon, 12 Aug 2019 20:37:00: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (339 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:37:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:37:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:37:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985668/SRX5985668.10_summits.bed INFO @ Mon, 12 Aug 2019 20:37:03: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1107 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。