Job ID = 1292005 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 17,969,658 reads read : 35,939,316 reads written : 35,939,316 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: 00:37:32 17969658 reads; of these: 17969658 (100.00%) were paired; of these: 849987 (4.73%) aligned concordantly 0 times 9227198 (51.35%) aligned concordantly exactly 1 time 7892473 (43.92%) aligned concordantly >1 times ---- 849987 pairs aligned concordantly 0 times; of these: 98455 (11.58%) aligned discordantly 1 time ---- 751532 pairs aligned 0 times concordantly or discordantly; of these: 1503064 mates make up the pairs; of these: 1207237 (80.32%) aligned 0 times 117526 (7.82%) aligned exactly 1 time 178301 (11.86%) aligned >1 times 96.64% overall alignment rate Time searching: 00:37:32 Overall time: 00:37:32 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 16 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] 6216973 / 17194829 = 0.3616 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 18:06:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.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 18:06:14: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:06:14: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:06:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.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 18:06:15: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:06:15: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:06:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.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 18:06:15: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:06:15: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:06:22: 1000000 INFO @ Sun, 02 Jun 2019 18:06:22: 1000000 INFO @ Sun, 02 Jun 2019 18:06:23: 1000000 INFO @ Sun, 02 Jun 2019 18:06:28: 2000000 INFO @ Sun, 02 Jun 2019 18:06:30: 2000000 INFO @ Sun, 02 Jun 2019 18:06:32: 2000000 INFO @ Sun, 02 Jun 2019 18:06:35: 3000000 INFO @ Sun, 02 Jun 2019 18:06:37: 3000000 INFO @ Sun, 02 Jun 2019 18:06:40: 3000000 INFO @ Sun, 02 Jun 2019 18:06:42: 4000000 INFO @ Sun, 02 Jun 2019 18:06:45: 4000000 INFO @ Sun, 02 Jun 2019 18:06:49: 5000000 INFO @ Sun, 02 Jun 2019 18:06:49: 4000000 INFO @ Sun, 02 Jun 2019 18:06:52: 5000000 INFO @ Sun, 02 Jun 2019 18:06:56: 6000000 INFO @ Sun, 02 Jun 2019 18:06:57: 5000000 INFO @ Sun, 02 Jun 2019 18:07:00: 6000000 INFO @ Sun, 02 Jun 2019 18:07:03: 7000000 INFO @ Sun, 02 Jun 2019 18:07:06: 6000000 INFO @ Sun, 02 Jun 2019 18:07:07: 7000000 INFO @ Sun, 02 Jun 2019 18:07:09: 8000000 INFO @ Sun, 02 Jun 2019 18:07:14: 7000000 INFO @ Sun, 02 Jun 2019 18:07:15: 8000000 INFO @ Sun, 02 Jun 2019 18:07:16: 9000000 INFO @ Sun, 02 Jun 2019 18:07:22: 9000000 INFO @ Sun, 02 Jun 2019 18:07:22: 10000000 INFO @ Sun, 02 Jun 2019 18:07:23: 8000000 INFO @ Sun, 02 Jun 2019 18:07:29: 11000000 INFO @ Sun, 02 Jun 2019 18:07:29: 10000000 INFO @ Sun, 02 Jun 2019 18:07:31: 9000000 INFO @ Sun, 02 Jun 2019 18:07:35: 12000000 INFO @ Sun, 02 Jun 2019 18:07:37: 11000000 INFO @ Sun, 02 Jun 2019 18:07:40: 10000000 INFO @ Sun, 02 Jun 2019 18:07:42: 13000000 INFO @ Sun, 02 Jun 2019 18:07:44: 12000000 INFO @ Sun, 02 Jun 2019 18:07:48: 14000000 INFO @ Sun, 02 Jun 2019 18:07:48: 11000000 INFO @ Sun, 02 Jun 2019 18:07:51: 13000000 INFO @ Sun, 02 Jun 2019 18:07:55: 15000000 INFO @ Sun, 02 Jun 2019 18:07:57: 12000000 INFO @ Sun, 02 Jun 2019 18:07:59: 14000000 INFO @ Sun, 02 Jun 2019 18:08:01: 16000000 INFO @ Sun, 02 Jun 2019 18:08:06: 13000000 INFO @ Sun, 02 Jun 2019 18:08:06: 15000000 INFO @ Sun, 02 Jun 2019 18:08:08: 17000000 INFO @ Sun, 02 Jun 2019 18:08:13: 16000000 INFO @ Sun, 02 Jun 2019 18:08:14: 18000000 INFO @ Sun, 02 Jun 2019 18:08:14: 14000000 INFO @ Sun, 02 Jun 2019 18:08:20: 19000000 INFO @ Sun, 02 Jun 2019 18:08:20: 17000000 INFO @ Sun, 02 Jun 2019 18:08:22: 15000000 INFO @ Sun, 02 Jun 2019 18:08:27: 20000000 INFO @ Sun, 02 Jun 2019 18:08:27: 18000000 INFO @ Sun, 02 Jun 2019 18:08:30: 16000000 INFO @ Sun, 02 Jun 2019 18:08:33: 21000000 INFO @ Sun, 02 Jun 2019 18:08:34: 19000000 INFO @ Sun, 02 Jun 2019 18:08:39: 17000000 INFO @ Sun, 02 Jun 2019 18:08:40: 22000000 INFO @ Sun, 02 Jun 2019 18:08:42: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:08:42: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:08:42: #1 total tags in treatment: 10915544 INFO @ Sun, 02 Jun 2019 18:08:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:08:42: #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 18:08:42: 20000000 INFO @ Sun, 02 Jun 2019 18:08:42: #1 tags after filtering in treatment: 6705095 INFO @ Sun, 02 Jun 2019 18:08:42: #1 Redundant rate of treatment: 0.39 INFO @ Sun, 02 Jun 2019 18:08:42: #1 finished! INFO @ Sun, 02 Jun 2019 18:08:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:08:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:08:43: #2 number of paired peaks: 5180 INFO @ Sun, 02 Jun 2019 18:08:43: start model_add_line... INFO @ Sun, 02 Jun 2019 18:08:43: start X-correlation... INFO @ Sun, 02 Jun 2019 18:08:43: end of X-cor INFO @ Sun, 02 Jun 2019 18:08:43: #2 finished! INFO @ Sun, 02 Jun 2019 18:08:43: #2 predicted fragment length is 185 bps INFO @ Sun, 02 Jun 2019 18:08:43: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 02 Jun 2019 18:08:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.10_model.r INFO @ Sun, 02 Jun 2019 18:08:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:08:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:08:47: 18000000 INFO @ Sun, 02 Jun 2019 18:08:49: 21000000 INFO @ Sun, 02 Jun 2019 18:08:55: 19000000 INFO @ Sun, 02 Jun 2019 18:08:56: 22000000 INFO @ Sun, 02 Jun 2019 18:08:59: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:08:59: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:08:59: #1 total tags in treatment: 10915544 INFO @ Sun, 02 Jun 2019 18:08:59: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:08:59: #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 18:08:59: #1 tags after filtering in treatment: 6705095 INFO @ Sun, 02 Jun 2019 18:08:59: #1 Redundant rate of treatment: 0.39 INFO @ Sun, 02 Jun 2019 18:08:59: #1 finished! INFO @ Sun, 02 Jun 2019 18:08:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:08:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:09:00: #2 number of paired peaks: 5180 INFO @ Sun, 02 Jun 2019 18:09:00: start model_add_line... INFO @ Sun, 02 Jun 2019 18:09:00: start X-correlation... INFO @ Sun, 02 Jun 2019 18:09:00: end of X-cor INFO @ Sun, 02 Jun 2019 18:09:00: #2 finished! INFO @ Sun, 02 Jun 2019 18:09:00: #2 predicted fragment length is 185 bps INFO @ Sun, 02 Jun 2019 18:09:00: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 02 Jun 2019 18:09:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.20_model.r INFO @ Sun, 02 Jun 2019 18:09:00: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:09:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:09:03: 20000000 INFO @ Sun, 02 Jun 2019 18:09:11: 21000000 INFO @ Sun, 02 Jun 2019 18:09:12: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:09:19: 22000000 INFO @ Sun, 02 Jun 2019 18:09:21: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:09:21: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:09:21: #1 total tags in treatment: 10915544 INFO @ Sun, 02 Jun 2019 18:09:21: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:09:21: #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 18:09:21: #1 tags after filtering in treatment: 6705095 INFO @ Sun, 02 Jun 2019 18:09:21: #1 Redundant rate of treatment: 0.39 INFO @ Sun, 02 Jun 2019 18:09:21: #1 finished! INFO @ Sun, 02 Jun 2019 18:09:21: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:09:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:09:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:09:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:09:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.10_summits.bed INFO @ Sun, 02 Jun 2019 18:09:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4142 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:09:22: #2 number of paired peaks: 5180 INFO @ Sun, 02 Jun 2019 18:09:22: start model_add_line... INFO @ Sun, 02 Jun 2019 18:09:23: start X-correlation... INFO @ Sun, 02 Jun 2019 18:09:23: end of X-cor INFO @ Sun, 02 Jun 2019 18:09:23: #2 finished! INFO @ Sun, 02 Jun 2019 18:09:23: #2 predicted fragment length is 185 bps INFO @ Sun, 02 Jun 2019 18:09:23: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 02 Jun 2019 18:09:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.05_model.r INFO @ Sun, 02 Jun 2019 18:09:23: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:09:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:09:29: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:09:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:09:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:09:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.20_summits.bed INFO @ Sun, 02 Jun 2019 18:09:39: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2358 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:09:52: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 02 Jun 2019 18:10:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:10:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:10:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978701/SRX2978701.05_summits.bed INFO @ Sun, 02 Jun 2019 18:10:02: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (6192 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。