Job ID = 1292881 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 17,088,064 reads read : 34,176,128 reads written : 34,176,128 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: 00:16:58 17088064 reads; of these: 17088064 (100.00%) were paired; of these: 3945955 (23.09%) aligned concordantly 0 times 11063330 (64.74%) aligned concordantly exactly 1 time 2078779 (12.17%) aligned concordantly >1 times ---- 3945955 pairs aligned concordantly 0 times; of these: 910500 (23.07%) aligned discordantly 1 time ---- 3035455 pairs aligned 0 times concordantly or discordantly; of these: 6070910 mates make up the pairs; of these: 5514405 (90.83%) aligned 0 times 298962 (4.92%) aligned exactly 1 time 257543 (4.24%) aligned >1 times 83.86% overall alignment rate Time searching: 00:16:58 Overall time: 00:16:58 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_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] 4135006 / 14042669 = 0.2945 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 21:30:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.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 21:30:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:30:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:30:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.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 21:30:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:30:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:30:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.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 21:30:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:30:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:31:04: 1000000 INFO @ Sun, 02 Jun 2019 21:31:04: 1000000 INFO @ Sun, 02 Jun 2019 21:31:07: 1000000 INFO @ Sun, 02 Jun 2019 21:31:11: 2000000 INFO @ Sun, 02 Jun 2019 21:31:11: 2000000 INFO @ Sun, 02 Jun 2019 21:31:17: 2000000 INFO @ Sun, 02 Jun 2019 21:31:19: 3000000 INFO @ Sun, 02 Jun 2019 21:31:19: 3000000 INFO @ Sun, 02 Jun 2019 21:31:26: 4000000 INFO @ Sun, 02 Jun 2019 21:31:26: 4000000 INFO @ Sun, 02 Jun 2019 21:31:28: 3000000 INFO @ Sun, 02 Jun 2019 21:31:33: 5000000 INFO @ Sun, 02 Jun 2019 21:31:33: 5000000 INFO @ Sun, 02 Jun 2019 21:31:38: 4000000 INFO @ Sun, 02 Jun 2019 21:31:41: 6000000 INFO @ Sun, 02 Jun 2019 21:31:41: 6000000 INFO @ Sun, 02 Jun 2019 21:31:48: 7000000 INFO @ Sun, 02 Jun 2019 21:31:48: 7000000 INFO @ Sun, 02 Jun 2019 21:31:48: 5000000 INFO @ Sun, 02 Jun 2019 21:31:55: 8000000 INFO @ Sun, 02 Jun 2019 21:31:55: 8000000 INFO @ Sun, 02 Jun 2019 21:31:59: 6000000 INFO @ Sun, 02 Jun 2019 21:32:03: 9000000 INFO @ Sun, 02 Jun 2019 21:32:03: 9000000 INFO @ Sun, 02 Jun 2019 21:32:09: 7000000 INFO @ Sun, 02 Jun 2019 21:32:10: 10000000 INFO @ Sun, 02 Jun 2019 21:32:10: 10000000 INFO @ Sun, 02 Jun 2019 21:32:17: 11000000 INFO @ Sun, 02 Jun 2019 21:32:17: 11000000 INFO @ Sun, 02 Jun 2019 21:32:20: 8000000 INFO @ Sun, 02 Jun 2019 21:32:25: 12000000 INFO @ Sun, 02 Jun 2019 21:32:25: 12000000 INFO @ Sun, 02 Jun 2019 21:32:30: 9000000 INFO @ Sun, 02 Jun 2019 21:32:32: 13000000 INFO @ Sun, 02 Jun 2019 21:32:33: 13000000 INFO @ Sun, 02 Jun 2019 21:32:40: 14000000 INFO @ Sun, 02 Jun 2019 21:32:40: 10000000 INFO @ Sun, 02 Jun 2019 21:32:40: 14000000 INFO @ Sun, 02 Jun 2019 21:32:47: 15000000 INFO @ Sun, 02 Jun 2019 21:32:47: 15000000 INFO @ Sun, 02 Jun 2019 21:32:50: 11000000 INFO @ Sun, 02 Jun 2019 21:32:54: 16000000 INFO @ Sun, 02 Jun 2019 21:32:55: 16000000 INFO @ Sun, 02 Jun 2019 21:33:00: 12000000 INFO @ Sun, 02 Jun 2019 21:33:01: 17000000 INFO @ Sun, 02 Jun 2019 21:33:02: 17000000 INFO @ Sun, 02 Jun 2019 21:33:08: 18000000 INFO @ Sun, 02 Jun 2019 21:33:09: 18000000 INFO @ Sun, 02 Jun 2019 21:33:10: 13000000 INFO @ Sun, 02 Jun 2019 21:33:15: 19000000 INFO @ Sun, 02 Jun 2019 21:33:16: 19000000 INFO @ Sun, 02 Jun 2019 21:33:20: 14000000 INFO @ Sun, 02 Jun 2019 21:33:22: 20000000 INFO @ Sun, 02 Jun 2019 21:33:24: 20000000 INFO @ Sun, 02 Jun 2019 21:33:25: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:33:25: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:33:25: #1 total tags in treatment: 9128085 INFO @ Sun, 02 Jun 2019 21:33:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:33:25: #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 21:33:25: #1 tags after filtering in treatment: 8458683 INFO @ Sun, 02 Jun 2019 21:33:25: #1 Redundant rate of treatment: 0.07 INFO @ Sun, 02 Jun 2019 21:33:25: #1 finished! INFO @ Sun, 02 Jun 2019 21:33:25: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:33:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:33:26: #2 number of paired peaks: 561 WARNING @ Sun, 02 Jun 2019 21:33:26: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Sun, 02 Jun 2019 21:33:26: start model_add_line... INFO @ Sun, 02 Jun 2019 21:33:26: start X-correlation... INFO @ Sun, 02 Jun 2019 21:33:26: end of X-cor INFO @ Sun, 02 Jun 2019 21:33:26: #2 finished! INFO @ Sun, 02 Jun 2019 21:33:26: #2 predicted fragment length is 160 bps INFO @ Sun, 02 Jun 2019 21:33:26: #2 alternative fragment length(s) may be 4,160 bps INFO @ Sun, 02 Jun 2019 21:33:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.05_model.r INFO @ Sun, 02 Jun 2019 21:33:26: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:33:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:33:26: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:33:26: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:33:26: #1 total tags in treatment: 9128085 INFO @ Sun, 02 Jun 2019 21:33:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:33:26: #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 21:33:26: #1 tags after filtering in treatment: 8458683 INFO @ Sun, 02 Jun 2019 21:33:26: #1 Redundant rate of treatment: 0.07 INFO @ Sun, 02 Jun 2019 21:33:26: #1 finished! INFO @ Sun, 02 Jun 2019 21:33:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:33:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:33:27: #2 number of paired peaks: 561 WARNING @ Sun, 02 Jun 2019 21:33:27: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Sun, 02 Jun 2019 21:33:27: start model_add_line... INFO @ Sun, 02 Jun 2019 21:33:27: start X-correlation... INFO @ Sun, 02 Jun 2019 21:33:27: end of X-cor INFO @ Sun, 02 Jun 2019 21:33:27: #2 finished! INFO @ Sun, 02 Jun 2019 21:33:27: #2 predicted fragment length is 160 bps INFO @ Sun, 02 Jun 2019 21:33:27: #2 alternative fragment length(s) may be 4,160 bps INFO @ Sun, 02 Jun 2019 21:33:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.10_model.r INFO @ Sun, 02 Jun 2019 21:33:27: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:33:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:33:29: 15000000 INFO @ Sun, 02 Jun 2019 21:33:38: 16000000 INFO @ Sun, 02 Jun 2019 21:33:47: 17000000 INFO @ Sun, 02 Jun 2019 21:33:51: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:33:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:33:56: 18000000 INFO @ Sun, 02 Jun 2019 21:34:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:34:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:34:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.05_summits.bed INFO @ Sun, 02 Jun 2019 21:34:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (439 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:34:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:34:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:34:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.10_summits.bed INFO @ Sun, 02 Jun 2019 21:34:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (319 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:34:06: 19000000 INFO @ Sun, 02 Jun 2019 21:34:15: 20000000 INFO @ Sun, 02 Jun 2019 21:34:18: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:34:18: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:34:18: #1 total tags in treatment: 9128085 INFO @ Sun, 02 Jun 2019 21:34:18: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:34:18: #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 21:34:18: #1 tags after filtering in treatment: 8458683 INFO @ Sun, 02 Jun 2019 21:34:18: #1 Redundant rate of treatment: 0.07 INFO @ Sun, 02 Jun 2019 21:34:18: #1 finished! INFO @ Sun, 02 Jun 2019 21:34:18: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:34:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:34:19: #2 number of paired peaks: 561 WARNING @ Sun, 02 Jun 2019 21:34:19: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Sun, 02 Jun 2019 21:34:19: start model_add_line... INFO @ Sun, 02 Jun 2019 21:34:19: start X-correlation... INFO @ Sun, 02 Jun 2019 21:34:19: end of X-cor INFO @ Sun, 02 Jun 2019 21:34:19: #2 finished! INFO @ Sun, 02 Jun 2019 21:34:19: #2 predicted fragment length is 160 bps INFO @ Sun, 02 Jun 2019 21:34:19: #2 alternative fragment length(s) may be 4,160 bps INFO @ Sun, 02 Jun 2019 21:34:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.20_model.r INFO @ Sun, 02 Jun 2019 21:34:19: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:34:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:34:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:34:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:34:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:34:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996811/SRX4996811.20_summits.bed INFO @ Sun, 02 Jun 2019 21:34:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (210 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。