Job ID = 2589360 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,816,727 reads read : 24,816,727 reads written : 24,816,727 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: 00:07:03 24816727 reads; of these: 24816727 (100.00%) were unpaired; of these: 2480813 (10.00%) aligned 0 times 18574392 (74.85%) aligned exactly 1 time 3761522 (15.16%) aligned >1 times 90.00% overall alignment rate Time searching: 00:07:03 Overall time: 00:07:03 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_sort_core] merging from 12 files... [bam_rmdupse_core] 12111298 / 22335914 = 0.5422 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 17:55:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.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 17:55:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:55:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:56:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.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 17:56:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:56:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:56:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.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 17:56:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:56:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:56:06: 1000000 INFO @ Mon, 12 Aug 2019 17:56:08: 1000000 INFO @ Mon, 12 Aug 2019 17:56:10: 1000000 INFO @ Mon, 12 Aug 2019 17:56:13: 2000000 INFO @ Mon, 12 Aug 2019 17:56:15: 2000000 INFO @ Mon, 12 Aug 2019 17:56:18: 2000000 INFO @ Mon, 12 Aug 2019 17:56:19: 3000000 INFO @ Mon, 12 Aug 2019 17:56:22: 3000000 INFO @ Mon, 12 Aug 2019 17:56:26: 3000000 INFO @ Mon, 12 Aug 2019 17:56:26: 4000000 INFO @ Mon, 12 Aug 2019 17:56:29: 4000000 INFO @ Mon, 12 Aug 2019 17:56:33: 5000000 INFO @ Mon, 12 Aug 2019 17:56:34: 4000000 INFO @ Mon, 12 Aug 2019 17:56:36: 5000000 INFO @ Mon, 12 Aug 2019 17:56:40: 6000000 INFO @ Mon, 12 Aug 2019 17:56:42: 5000000 INFO @ Mon, 12 Aug 2019 17:56:44: 6000000 INFO @ Mon, 12 Aug 2019 17:56:46: 7000000 INFO @ Mon, 12 Aug 2019 17:56:50: 6000000 INFO @ Mon, 12 Aug 2019 17:56:51: 7000000 INFO @ Mon, 12 Aug 2019 17:56:53: 8000000 INFO @ Mon, 12 Aug 2019 17:56:58: 8000000 INFO @ Mon, 12 Aug 2019 17:56:58: 7000000 INFO @ Mon, 12 Aug 2019 17:57:00: 9000000 INFO @ Mon, 12 Aug 2019 17:57:05: 9000000 INFO @ Mon, 12 Aug 2019 17:57:06: 8000000 INFO @ Mon, 12 Aug 2019 17:57:06: 10000000 INFO @ Mon, 12 Aug 2019 17:57:08: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:57:08: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:57:08: #1 total tags in treatment: 10224616 INFO @ Mon, 12 Aug 2019 17:57:08: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:57:08: #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 17:57:08: #1 tags after filtering in treatment: 10224616 INFO @ Mon, 12 Aug 2019 17:57:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:57:08: #1 finished! INFO @ Mon, 12 Aug 2019 17:57:08: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:57:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:57:09: #2 number of paired peaks: 705 WARNING @ Mon, 12 Aug 2019 17:57:09: Fewer paired peaks (705) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 705 pairs to build model! INFO @ Mon, 12 Aug 2019 17:57:09: start model_add_line... INFO @ Mon, 12 Aug 2019 17:57:09: start X-correlation... INFO @ Mon, 12 Aug 2019 17:57:09: end of X-cor INFO @ Mon, 12 Aug 2019 17:57:09: #2 finished! INFO @ Mon, 12 Aug 2019 17:57:09: #2 predicted fragment length is 122 bps INFO @ Mon, 12 Aug 2019 17:57:09: #2 alternative fragment length(s) may be 122 bps INFO @ Mon, 12 Aug 2019 17:57:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.05_model.r INFO @ Mon, 12 Aug 2019 17:57:09: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:57:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:57:12: 10000000 INFO @ Mon, 12 Aug 2019 17:57:13: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:57:13: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:57:13: #1 total tags in treatment: 10224616 INFO @ Mon, 12 Aug 2019 17:57:13: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:57:13: #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 17:57:14: #1 tags after filtering in treatment: 10224616 INFO @ Mon, 12 Aug 2019 17:57:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:57:14: #1 finished! INFO @ Mon, 12 Aug 2019 17:57:14: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:57:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:57:14: 9000000 INFO @ Mon, 12 Aug 2019 17:57:15: #2 number of paired peaks: 705 WARNING @ Mon, 12 Aug 2019 17:57:15: Fewer paired peaks (705) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 705 pairs to build model! INFO @ Mon, 12 Aug 2019 17:57:15: start model_add_line... INFO @ Mon, 12 Aug 2019 17:57:15: start X-correlation... INFO @ Mon, 12 Aug 2019 17:57:15: end of X-cor INFO @ Mon, 12 Aug 2019 17:57:15: #2 finished! INFO @ Mon, 12 Aug 2019 17:57:15: #2 predicted fragment length is 122 bps INFO @ Mon, 12 Aug 2019 17:57:15: #2 alternative fragment length(s) may be 122 bps INFO @ Mon, 12 Aug 2019 17:57:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.10_model.r INFO @ Mon, 12 Aug 2019 17:57:15: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:57:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:57:22: 10000000 INFO @ Mon, 12 Aug 2019 17:57:24: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:57:24: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:57:24: #1 total tags in treatment: 10224616 INFO @ Mon, 12 Aug 2019 17:57:24: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:57:24: #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 17:57:24: #1 tags after filtering in treatment: 10224616 INFO @ Mon, 12 Aug 2019 17:57:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:57:24: #1 finished! INFO @ Mon, 12 Aug 2019 17:57:24: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:57:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:57:25: #2 number of paired peaks: 705 WARNING @ Mon, 12 Aug 2019 17:57:25: Fewer paired peaks (705) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 705 pairs to build model! INFO @ Mon, 12 Aug 2019 17:57:25: start model_add_line... INFO @ Mon, 12 Aug 2019 17:57:25: start X-correlation... INFO @ Mon, 12 Aug 2019 17:57:25: end of X-cor INFO @ Mon, 12 Aug 2019 17:57:25: #2 finished! INFO @ Mon, 12 Aug 2019 17:57:25: #2 predicted fragment length is 122 bps INFO @ Mon, 12 Aug 2019 17:57:25: #2 alternative fragment length(s) may be 122 bps INFO @ Mon, 12 Aug 2019 17:57:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.20_model.r INFO @ Mon, 12 Aug 2019 17:57:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:57:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:57:40: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:57:46: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:57:55: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:57:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:57:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:57:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.05_summits.bed INFO @ Mon, 12 Aug 2019 17:57:56: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5378 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:58:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:58:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:58:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.10_summits.bed INFO @ Mon, 12 Aug 2019 17:58:00: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2836 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:58:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:58:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:58:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078713/SRX1078713.20_summits.bed INFO @ Mon, 12 Aug 2019 17:58:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1101 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。