Job ID = 1292006 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 17,929,000 reads read : 35,858,000 reads written : 35,858,000 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: 00:37:41 17929000 reads; of these: 17929000 (100.00%) were paired; of these: 854242 (4.76%) aligned concordantly 0 times 9193348 (51.28%) aligned concordantly exactly 1 time 7881410 (43.96%) aligned concordantly >1 times ---- 854242 pairs aligned concordantly 0 times; of these: 97320 (11.39%) aligned discordantly 1 time ---- 756922 pairs aligned 0 times concordantly or discordantly; of these: 1513844 mates make up the pairs; of these: 1214919 (80.25%) aligned 0 times 118768 (7.85%) aligned exactly 1 time 180157 (11.90%) aligned >1 times 96.61% overall alignment rate Time searching: 00:37:41 Overall time: 00:37:41 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] 6187054 / 17148943 = 0.3608 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 18:07:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.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 18:07:22: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:07:22: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:07:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.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 18:07:22: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:07:22: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:07:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.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 18:07:22: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:07:22: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:07:30: 1000000 INFO @ Sun, 02 Jun 2019 18:07:30: 1000000 INFO @ Sun, 02 Jun 2019 18:07:32: 1000000 INFO @ Sun, 02 Jun 2019 18:07:37: 2000000 INFO @ Sun, 02 Jun 2019 18:07:37: 2000000 INFO @ Sun, 02 Jun 2019 18:07:42: 2000000 INFO @ Sun, 02 Jun 2019 18:07:44: 3000000 INFO @ Sun, 02 Jun 2019 18:07:44: 3000000 INFO @ Sun, 02 Jun 2019 18:07:51: 4000000 INFO @ Sun, 02 Jun 2019 18:07:52: 3000000 INFO @ Sun, 02 Jun 2019 18:07:52: 4000000 INFO @ Sun, 02 Jun 2019 18:07:58: 5000000 INFO @ Sun, 02 Jun 2019 18:07:59: 5000000 INFO @ Sun, 02 Jun 2019 18:08:02: 4000000 INFO @ Sun, 02 Jun 2019 18:08:05: 6000000 INFO @ Sun, 02 Jun 2019 18:08:06: 6000000 INFO @ Sun, 02 Jun 2019 18:08:11: 5000000 INFO @ Sun, 02 Jun 2019 18:08:13: 7000000 INFO @ Sun, 02 Jun 2019 18:08:13: 7000000 INFO @ Sun, 02 Jun 2019 18:08:20: 8000000 INFO @ Sun, 02 Jun 2019 18:08:20: 8000000 INFO @ Sun, 02 Jun 2019 18:08:21: 6000000 INFO @ Sun, 02 Jun 2019 18:08:27: 9000000 INFO @ Sun, 02 Jun 2019 18:08:27: 9000000 INFO @ Sun, 02 Jun 2019 18:08:31: 7000000 INFO @ Sun, 02 Jun 2019 18:08:34: 10000000 INFO @ Sun, 02 Jun 2019 18:08:34: 10000000 INFO @ Sun, 02 Jun 2019 18:08:40: 8000000 INFO @ Sun, 02 Jun 2019 18:08:41: 11000000 INFO @ Sun, 02 Jun 2019 18:08:41: 11000000 INFO @ Sun, 02 Jun 2019 18:08:48: 12000000 INFO @ Sun, 02 Jun 2019 18:08:48: 12000000 INFO @ Sun, 02 Jun 2019 18:08:50: 9000000 INFO @ Sun, 02 Jun 2019 18:08:55: 13000000 INFO @ Sun, 02 Jun 2019 18:08:55: 13000000 INFO @ Sun, 02 Jun 2019 18:08:59: 10000000 INFO @ Sun, 02 Jun 2019 18:09:02: 14000000 INFO @ Sun, 02 Jun 2019 18:09:02: 14000000 INFO @ Sun, 02 Jun 2019 18:09:09: 11000000 INFO @ Sun, 02 Jun 2019 18:09:09: 15000000 INFO @ Sun, 02 Jun 2019 18:09:09: 15000000 INFO @ Sun, 02 Jun 2019 18:09:16: 16000000 INFO @ Sun, 02 Jun 2019 18:09:16: 16000000 INFO @ Sun, 02 Jun 2019 18:09:18: 12000000 INFO @ Sun, 02 Jun 2019 18:09:23: 17000000 INFO @ Sun, 02 Jun 2019 18:09:23: 17000000 INFO @ Sun, 02 Jun 2019 18:09:27: 13000000 INFO @ Sun, 02 Jun 2019 18:09:30: 18000000 INFO @ Sun, 02 Jun 2019 18:09:30: 18000000 INFO @ Sun, 02 Jun 2019 18:09:37: 19000000 INFO @ Sun, 02 Jun 2019 18:09:37: 14000000 INFO @ Sun, 02 Jun 2019 18:09:37: 19000000 INFO @ Sun, 02 Jun 2019 18:09:44: 20000000 INFO @ Sun, 02 Jun 2019 18:09:44: 20000000 INFO @ Sun, 02 Jun 2019 18:09:46: 15000000 INFO @ Sun, 02 Jun 2019 18:09:50: 21000000 INFO @ Sun, 02 Jun 2019 18:09:52: 21000000 INFO @ Sun, 02 Jun 2019 18:09:55: 16000000 INFO @ Sun, 02 Jun 2019 18:09:59: 22000000 INFO @ Sun, 02 Jun 2019 18:10:00: 22000000 INFO @ Sun, 02 Jun 2019 18:10:01: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:10:01: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:10:01: #1 total tags in treatment: 10900245 INFO @ Sun, 02 Jun 2019 18:10:01: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:10:01: #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 18:10:02: #1 tags after filtering in treatment: 6690579 INFO @ Sun, 02 Jun 2019 18:10:02: #1 Redundant rate of treatment: 0.39 INFO @ Sun, 02 Jun 2019 18:10:02: #1 finished! INFO @ Sun, 02 Jun 2019 18:10:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:10:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:10:02: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:10:02: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:10:02: #1 total tags in treatment: 10900245 INFO @ Sun, 02 Jun 2019 18:10:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:10:02: #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 18:10:02: #1 tags after filtering in treatment: 6690579 INFO @ Sun, 02 Jun 2019 18:10:02: #1 Redundant rate of treatment: 0.39 INFO @ Sun, 02 Jun 2019 18:10:02: #1 finished! INFO @ Sun, 02 Jun 2019 18:10:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:10:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:10:03: #2 number of paired peaks: 5142 INFO @ Sun, 02 Jun 2019 18:10:03: start model_add_line... INFO @ Sun, 02 Jun 2019 18:10:03: start X-correlation... INFO @ Sun, 02 Jun 2019 18:10:03: end of X-cor INFO @ Sun, 02 Jun 2019 18:10:03: #2 finished! INFO @ Sun, 02 Jun 2019 18:10:03: #2 predicted fragment length is 183 bps INFO @ Sun, 02 Jun 2019 18:10:03: #2 alternative fragment length(s) may be 183 bps INFO @ Sun, 02 Jun 2019 18:10:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.05_model.r INFO @ Sun, 02 Jun 2019 18:10:03: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:10:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:10:03: #2 number of paired peaks: 5142 INFO @ Sun, 02 Jun 2019 18:10:03: start model_add_line... INFO @ Sun, 02 Jun 2019 18:10:04: start X-correlation... INFO @ Sun, 02 Jun 2019 18:10:04: end of X-cor INFO @ Sun, 02 Jun 2019 18:10:04: #2 finished! INFO @ Sun, 02 Jun 2019 18:10:04: #2 predicted fragment length is 183 bps INFO @ Sun, 02 Jun 2019 18:10:04: #2 alternative fragment length(s) may be 183 bps INFO @ Sun, 02 Jun 2019 18:10:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.10_model.r INFO @ Sun, 02 Jun 2019 18:10:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:10:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:10:04: 17000000 INFO @ Sun, 02 Jun 2019 18:10:13: 18000000 INFO @ Sun, 02 Jun 2019 18:10:22: 19000000 INFO @ Sun, 02 Jun 2019 18:10:31: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:10:32: 20000000 INFO @ Sun, 02 Jun 2019 18:10:33: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:10:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:10:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:10:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.05_summits.bed INFO @ Sun, 02 Jun 2019 18:10:41: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (6325 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:10:42: 21000000 INFO @ Sun, 02 Jun 2019 18:10:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:10:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:10:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.10_summits.bed INFO @ Sun, 02 Jun 2019 18:10:42: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4123 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:10:51: 22000000 INFO @ Sun, 02 Jun 2019 18:10:54: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:10:54: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:10:54: #1 total tags in treatment: 10900245 INFO @ Sun, 02 Jun 2019 18:10:54: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:10:54: #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 18:10:54: #1 tags after filtering in treatment: 6690579 INFO @ Sun, 02 Jun 2019 18:10:54: #1 Redundant rate of treatment: 0.39 INFO @ Sun, 02 Jun 2019 18:10:54: #1 finished! INFO @ Sun, 02 Jun 2019 18:10:54: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:10:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:10:55: #2 number of paired peaks: 5142 INFO @ Sun, 02 Jun 2019 18:10:55: start model_add_line... INFO @ Sun, 02 Jun 2019 18:10:55: start X-correlation... INFO @ Sun, 02 Jun 2019 18:10:55: end of X-cor INFO @ Sun, 02 Jun 2019 18:10:55: #2 finished! INFO @ Sun, 02 Jun 2019 18:10:55: #2 predicted fragment length is 183 bps INFO @ Sun, 02 Jun 2019 18:10:55: #2 alternative fragment length(s) may be 183 bps INFO @ Sun, 02 Jun 2019 18:10:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.20_model.r INFO @ Sun, 02 Jun 2019 18:10:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:10:55: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 02 Jun 2019 18:11:24: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:11:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:11:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:11:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978702/SRX2978702.20_summits.bed INFO @ Sun, 02 Jun 2019 18:11:34: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2325 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。