Job ID = 1290641 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,264,029 reads read : 10,264,029 reads written : 10,264,029 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:33 10264029 reads; of these: 10264029 (100.00%) were unpaired; of these: 486097 (4.74%) aligned 0 times 8280282 (80.67%) aligned exactly 1 time 1497650 (14.59%) aligned >1 times 95.26% overall alignment rate Time searching: 00:02:33 Overall time: 00:02:33 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] 1317721 / 9777932 = 0.1348 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 @ Sat, 01 Jun 2019 21:50:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.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 @ Sat, 01 Jun 2019 21:50:43: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:50:43: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:50:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.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 @ Sat, 01 Jun 2019 21:50:43: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:50:43: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:50:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.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 @ Sat, 01 Jun 2019 21:50:43: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:50:43: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:50:51: 1000000 INFO @ Sat, 01 Jun 2019 21:50:53: 1000000 INFO @ Sat, 01 Jun 2019 21:50:54: 1000000 INFO @ Sat, 01 Jun 2019 21:50:58: 2000000 INFO @ Sat, 01 Jun 2019 21:51:03: 2000000 INFO @ Sat, 01 Jun 2019 21:51:06: 3000000 INFO @ Sat, 01 Jun 2019 21:51:06: 2000000 INFO @ Sat, 01 Jun 2019 21:51:13: 4000000 INFO @ Sat, 01 Jun 2019 21:51:13: 3000000 INFO @ Sat, 01 Jun 2019 21:51:17: 3000000 INFO @ Sat, 01 Jun 2019 21:51:21: 5000000 INFO @ Sat, 01 Jun 2019 21:51:25: 4000000 INFO @ Sat, 01 Jun 2019 21:51:28: 4000000 INFO @ Sat, 01 Jun 2019 21:51:29: 6000000 INFO @ Sat, 01 Jun 2019 21:51:36: 5000000 INFO @ Sat, 01 Jun 2019 21:51:37: 7000000 INFO @ Sat, 01 Jun 2019 21:51:39: 5000000 INFO @ Sat, 01 Jun 2019 21:51:45: 8000000 INFO @ Sat, 01 Jun 2019 21:51:46: 6000000 INFO @ Sat, 01 Jun 2019 21:51:49: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:51:49: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:51:49: #1 total tags in treatment: 8460211 INFO @ Sat, 01 Jun 2019 21:51:49: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:51:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:51:50: #1 tags after filtering in treatment: 8460211 INFO @ Sat, 01 Jun 2019 21:51:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:51:50: #1 finished! INFO @ Sat, 01 Jun 2019 21:51:50: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:51:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:51:50: 6000000 INFO @ Sat, 01 Jun 2019 21:51:51: #2 number of paired peaks: 1010 INFO @ Sat, 01 Jun 2019 21:51:51: start model_add_line... INFO @ Sat, 01 Jun 2019 21:51:51: start X-correlation... INFO @ Sat, 01 Jun 2019 21:51:51: end of X-cor INFO @ Sat, 01 Jun 2019 21:51:51: #2 finished! INFO @ Sat, 01 Jun 2019 21:51:51: #2 predicted fragment length is 148 bps INFO @ Sat, 01 Jun 2019 21:51:51: #2 alternative fragment length(s) may be 4,148 bps INFO @ Sat, 01 Jun 2019 21:51:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.10_model.r INFO @ Sat, 01 Jun 2019 21:51:51: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:51:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:51:58: 7000000 INFO @ Sat, 01 Jun 2019 21:52:02: 7000000 INFO @ Sat, 01 Jun 2019 21:52:10: 8000000 INFO @ Sat, 01 Jun 2019 21:52:13: 8000000 INFO @ Sat, 01 Jun 2019 21:52:14: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:52:14: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:52:14: #1 total tags in treatment: 8460211 INFO @ Sat, 01 Jun 2019 21:52:14: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:52:14: #1 tags after filtering in treatment: 8460211 INFO @ Sat, 01 Jun 2019 21:52:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:14: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:14: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:15: #2 number of paired peaks: 1010 INFO @ Sat, 01 Jun 2019 21:52:15: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:15: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:15: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:15: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:15: #2 predicted fragment length is 148 bps INFO @ Sat, 01 Jun 2019 21:52:15: #2 alternative fragment length(s) may be 4,148 bps INFO @ Sat, 01 Jun 2019 21:52:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.20_model.r INFO @ Sat, 01 Jun 2019 21:52:15: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:17: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:52:17: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:52:17: #1 total tags in treatment: 8460211 INFO @ Sat, 01 Jun 2019 21:52:17: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:52:17: #1 tags after filtering in treatment: 8460211 INFO @ Sat, 01 Jun 2019 21:52:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:17: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:17: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:18: #2 number of paired peaks: 1010 INFO @ Sat, 01 Jun 2019 21:52:18: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:18: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:18: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:18: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:18: #2 predicted fragment length is 148 bps INFO @ Sat, 01 Jun 2019 21:52:18: #2 alternative fragment length(s) may be 4,148 bps INFO @ Sat, 01 Jun 2019 21:52:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.05_model.r INFO @ Sat, 01 Jun 2019 21:52:18: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:19: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:52:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.10_peaks.xls INFO @ Sat, 01 Jun 2019 21:52:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:52:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.10_summits.bed INFO @ Sat, 01 Jun 2019 21:52:33: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1089 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:52:43: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:52:46: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:52:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.20_peaks.xls INFO @ Sat, 01 Jun 2019 21:52:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:52:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.20_summits.bed INFO @ Sat, 01 Jun 2019 21:52:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (477 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:52:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.05_peaks.xls INFO @ Sat, 01 Jun 2019 21:52:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:52:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1099841/SRX1099841.05_summits.bed INFO @ Sat, 01 Jun 2019 21:52:59: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2291 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。