Job ID = 1291999 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 28,902,116 reads read : 57,804,232 reads written : 57,804,232 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: 00:31:28 28902116 reads; of these: 28902116 (100.00%) were paired; of these: 8360114 (28.93%) aligned concordantly 0 times 14968502 (51.79%) aligned concordantly exactly 1 time 5573500 (19.28%) aligned concordantly >1 times ---- 8360114 pairs aligned concordantly 0 times; of these: 2707522 (32.39%) aligned discordantly 1 time ---- 5652592 pairs aligned 0 times concordantly or discordantly; of these: 11305184 mates make up the pairs; of these: 8358675 (73.94%) aligned 0 times 1176310 (10.41%) aligned exactly 1 time 1770199 (15.66%) aligned >1 times 85.54% overall alignment rate Time searching: 00:31:28 Overall time: 00:31:28 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 24 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 14252986 / 23238696 = 0.6133 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 18:12:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.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 18:12:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:12:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:12:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.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 18:12:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:12:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:12:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.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 18:12:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:12:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:12:20: 1000000 INFO @ Sun, 02 Jun 2019 18:12:21: 1000000 INFO @ Sun, 02 Jun 2019 18:12:22: 1000000 INFO @ Sun, 02 Jun 2019 18:12:28: 2000000 INFO @ Sun, 02 Jun 2019 18:12:30: 2000000 INFO @ Sun, 02 Jun 2019 18:12:31: 2000000 INFO @ Sun, 02 Jun 2019 18:12:36: 3000000 INFO @ Sun, 02 Jun 2019 18:12:37: 3000000 INFO @ Sun, 02 Jun 2019 18:12:41: 3000000 INFO @ Sun, 02 Jun 2019 18:12:44: 4000000 INFO @ Sun, 02 Jun 2019 18:12:44: 4000000 INFO @ Sun, 02 Jun 2019 18:12:51: 4000000 INFO @ Sun, 02 Jun 2019 18:12:51: 5000000 INFO @ Sun, 02 Jun 2019 18:12:52: 5000000 INFO @ Sun, 02 Jun 2019 18:12:59: 6000000 INFO @ Sun, 02 Jun 2019 18:13:00: 6000000 INFO @ Sun, 02 Jun 2019 18:13:01: 5000000 INFO @ Sun, 02 Jun 2019 18:13:05: 7000000 INFO @ Sun, 02 Jun 2019 18:13:07: 7000000 INFO @ Sun, 02 Jun 2019 18:13:13: 6000000 INFO @ Sun, 02 Jun 2019 18:13:13: 8000000 INFO @ Sun, 02 Jun 2019 18:13:15: 8000000 INFO @ Sun, 02 Jun 2019 18:13:20: 9000000 INFO @ Sun, 02 Jun 2019 18:13:22: 7000000 INFO @ Sun, 02 Jun 2019 18:13:22: 9000000 INFO @ Sun, 02 Jun 2019 18:13:28: 10000000 INFO @ Sun, 02 Jun 2019 18:13:30: 10000000 INFO @ Sun, 02 Jun 2019 18:13:31: 8000000 INFO @ Sun, 02 Jun 2019 18:13:35: 11000000 INFO @ Sun, 02 Jun 2019 18:13:37: 11000000 INFO @ Sun, 02 Jun 2019 18:13:40: 9000000 INFO @ Sun, 02 Jun 2019 18:13:42: 12000000 INFO @ Sun, 02 Jun 2019 18:13:45: 12000000 INFO @ Sun, 02 Jun 2019 18:13:49: 13000000 INFO @ Sun, 02 Jun 2019 18:13:49: 10000000 INFO @ Sun, 02 Jun 2019 18:13:52: 13000000 INFO @ Sun, 02 Jun 2019 18:13:56: 14000000 INFO @ Sun, 02 Jun 2019 18:13:59: 11000000 INFO @ Sun, 02 Jun 2019 18:14:00: 14000000 INFO @ Sun, 02 Jun 2019 18:14:03: 15000000 INFO @ Sun, 02 Jun 2019 18:14:07: 15000000 INFO @ Sun, 02 Jun 2019 18:14:08: 12000000 INFO @ Sun, 02 Jun 2019 18:14:10: 16000000 INFO @ Sun, 02 Jun 2019 18:14:14: 16000000 INFO @ Sun, 02 Jun 2019 18:14:17: 13000000 INFO @ Sun, 02 Jun 2019 18:14:17: 17000000 INFO @ Sun, 02 Jun 2019 18:14:22: 17000000 INFO @ Sun, 02 Jun 2019 18:14:25: 18000000 INFO @ Sun, 02 Jun 2019 18:14:26: 14000000 INFO @ Sun, 02 Jun 2019 18:14:29: 18000000 INFO @ Sun, 02 Jun 2019 18:14:32: 19000000 INFO @ Sun, 02 Jun 2019 18:14:35: 15000000 INFO @ Sun, 02 Jun 2019 18:14:36: 19000000 INFO @ Sun, 02 Jun 2019 18:14:39: 20000000 INFO @ Sun, 02 Jun 2019 18:14:44: 20000000 INFO @ Sun, 02 Jun 2019 18:14:44: 16000000 INFO @ Sun, 02 Jun 2019 18:14:45: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:14:45: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:14:45: #1 total tags in treatment: 7707661 INFO @ Sun, 02 Jun 2019 18:14:45: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:14:45: #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 18:14:46: #1 tags after filtering in treatment: 5407314 INFO @ Sun, 02 Jun 2019 18:14:46: #1 Redundant rate of treatment: 0.30 INFO @ Sun, 02 Jun 2019 18:14:46: #1 finished! INFO @ Sun, 02 Jun 2019 18:14:46: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:14:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:14:47: #2 number of paired peaks: 5036 INFO @ Sun, 02 Jun 2019 18:14:47: start model_add_line... INFO @ Sun, 02 Jun 2019 18:14:47: start X-correlation... INFO @ Sun, 02 Jun 2019 18:14:47: end of X-cor INFO @ Sun, 02 Jun 2019 18:14:47: #2 finished! INFO @ Sun, 02 Jun 2019 18:14:47: #2 predicted fragment length is 245 bps INFO @ Sun, 02 Jun 2019 18:14:47: #2 alternative fragment length(s) may be 4,245 bps INFO @ Sun, 02 Jun 2019 18:14:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.20_model.r INFO @ Sun, 02 Jun 2019 18:14:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:14:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:14:51: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:14:51: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:14:51: #1 total tags in treatment: 7707661 INFO @ Sun, 02 Jun 2019 18:14:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:14:51: #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 18:14:51: #1 tags after filtering in treatment: 5407314 INFO @ Sun, 02 Jun 2019 18:14:51: #1 Redundant rate of treatment: 0.30 INFO @ Sun, 02 Jun 2019 18:14:51: #1 finished! INFO @ Sun, 02 Jun 2019 18:14:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:14:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:14:52: #2 number of paired peaks: 5036 INFO @ Sun, 02 Jun 2019 18:14:52: start model_add_line... INFO @ Sun, 02 Jun 2019 18:14:52: start X-correlation... INFO @ Sun, 02 Jun 2019 18:14:52: end of X-cor INFO @ Sun, 02 Jun 2019 18:14:52: #2 finished! INFO @ Sun, 02 Jun 2019 18:14:52: #2 predicted fragment length is 245 bps INFO @ Sun, 02 Jun 2019 18:14:52: #2 alternative fragment length(s) may be 4,245 bps INFO @ Sun, 02 Jun 2019 18:14:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.05_model.r INFO @ Sun, 02 Jun 2019 18:14:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:14:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:14:53: 17000000 INFO @ Sun, 02 Jun 2019 18:15:01: 18000000 INFO @ Sun, 02 Jun 2019 18:15:10: 19000000 INFO @ Sun, 02 Jun 2019 18:15:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:15:18: 20000000 INFO @ Sun, 02 Jun 2019 18:15:22: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:15:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:15:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:15:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.20_summits.bed INFO @ Sun, 02 Jun 2019 18:15:25: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1478 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:15:26: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:15:26: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:15:26: #1 total tags in treatment: 7707661 INFO @ Sun, 02 Jun 2019 18:15:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:15:26: #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 18:15:26: #1 tags after filtering in treatment: 5407314 INFO @ Sun, 02 Jun 2019 18:15:26: #1 Redundant rate of treatment: 0.30 INFO @ Sun, 02 Jun 2019 18:15:26: #1 finished! INFO @ Sun, 02 Jun 2019 18:15:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:15:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:15:27: #2 number of paired peaks: 5036 INFO @ Sun, 02 Jun 2019 18:15:27: start model_add_line... INFO @ Sun, 02 Jun 2019 18:15:28: start X-correlation... INFO @ Sun, 02 Jun 2019 18:15:28: end of X-cor INFO @ Sun, 02 Jun 2019 18:15:28: #2 finished! INFO @ Sun, 02 Jun 2019 18:15:28: #2 predicted fragment length is 245 bps INFO @ Sun, 02 Jun 2019 18:15:28: #2 alternative fragment length(s) may be 4,245 bps INFO @ Sun, 02 Jun 2019 18:15:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.10_model.r INFO @ Sun, 02 Jun 2019 18:15:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:15:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:15:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:15:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:15:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.05_summits.bed INFO @ Sun, 02 Jun 2019 18:15:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4025 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 02 Jun 2019 18:15:58: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:16:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:16:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:16:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978695/SRX2978695.10_summits.bed INFO @ Sun, 02 Jun 2019 18:16:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2594 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。