Job ID = 2589967 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 34,080,196 reads read : 34,080,196 reads written : 34,080,196 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1163564.sra.cache’: 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: 00:11:42 34080196 reads; of these: 34080196 (100.00%) were unpaired; of these: 1432423 (4.20%) aligned 0 times 20949758 (61.47%) aligned exactly 1 time 11698015 (34.32%) aligned >1 times 95.80% overall alignment rate Time searching: 00:11:42 Overall time: 00:11:42 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_rmdupse_core] 13710283 / 32647773 = 0.4199 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 @ Mon, 12 Aug 2019 19:14:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.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 @ Mon, 12 Aug 2019 19:14:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:14:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:14:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.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 @ Mon, 12 Aug 2019 19:14:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:14:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:14:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.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 @ Mon, 12 Aug 2019 19:14:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:14:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:14:58: 1000000 INFO @ Mon, 12 Aug 2019 19:14:59: 1000000 INFO @ Mon, 12 Aug 2019 19:15:00: 1000000 INFO @ Mon, 12 Aug 2019 19:15:06: 2000000 INFO @ Mon, 12 Aug 2019 19:15:07: 2000000 INFO @ Mon, 12 Aug 2019 19:15:08: 2000000 INFO @ Mon, 12 Aug 2019 19:15:14: 3000000 INFO @ Mon, 12 Aug 2019 19:15:15: 3000000 INFO @ Mon, 12 Aug 2019 19:15:16: 3000000 INFO @ Mon, 12 Aug 2019 19:15:22: 4000000 INFO @ Mon, 12 Aug 2019 19:15:23: 4000000 INFO @ Mon, 12 Aug 2019 19:15:24: 4000000 INFO @ Mon, 12 Aug 2019 19:15:30: 5000000 INFO @ Mon, 12 Aug 2019 19:15:31: 5000000 INFO @ Mon, 12 Aug 2019 19:15:32: 5000000 INFO @ Mon, 12 Aug 2019 19:15:38: 6000000 INFO @ Mon, 12 Aug 2019 19:15:39: 6000000 INFO @ Mon, 12 Aug 2019 19:15:40: 6000000 INFO @ Mon, 12 Aug 2019 19:15:46: 7000000 INFO @ Mon, 12 Aug 2019 19:15:47: 7000000 INFO @ Mon, 12 Aug 2019 19:15:48: 7000000 INFO @ Mon, 12 Aug 2019 19:15:54: 8000000 INFO @ Mon, 12 Aug 2019 19:15:55: 8000000 INFO @ Mon, 12 Aug 2019 19:15:56: 8000000 INFO @ Mon, 12 Aug 2019 19:16:02: 9000000 INFO @ Mon, 12 Aug 2019 19:16:02: 9000000 INFO @ Mon, 12 Aug 2019 19:16:03: 9000000 INFO @ Mon, 12 Aug 2019 19:16:10: 10000000 INFO @ Mon, 12 Aug 2019 19:16:10: 10000000 INFO @ Mon, 12 Aug 2019 19:16:11: 10000000 INFO @ Mon, 12 Aug 2019 19:16:18: 11000000 INFO @ Mon, 12 Aug 2019 19:16:18: 11000000 INFO @ Mon, 12 Aug 2019 19:16:19: 11000000 INFO @ Mon, 12 Aug 2019 19:16:25: 12000000 INFO @ Mon, 12 Aug 2019 19:16:26: 12000000 INFO @ Mon, 12 Aug 2019 19:16:27: 12000000 INFO @ Mon, 12 Aug 2019 19:16:33: 13000000 INFO @ Mon, 12 Aug 2019 19:16:34: 13000000 INFO @ Mon, 12 Aug 2019 19:16:35: 13000000 INFO @ Mon, 12 Aug 2019 19:16:41: 14000000 INFO @ Mon, 12 Aug 2019 19:16:42: 14000000 INFO @ Mon, 12 Aug 2019 19:16:43: 14000000 INFO @ Mon, 12 Aug 2019 19:16:49: 15000000 INFO @ Mon, 12 Aug 2019 19:16:50: 15000000 INFO @ Mon, 12 Aug 2019 19:16:51: 15000000 INFO @ Mon, 12 Aug 2019 19:16:57: 16000000 INFO @ Mon, 12 Aug 2019 19:16:58: 16000000 INFO @ Mon, 12 Aug 2019 19:16:59: 16000000 INFO @ Mon, 12 Aug 2019 19:17:05: 17000000 INFO @ Mon, 12 Aug 2019 19:17:06: 17000000 INFO @ Mon, 12 Aug 2019 19:17:06: 17000000 INFO @ Mon, 12 Aug 2019 19:17:13: 18000000 INFO @ Mon, 12 Aug 2019 19:17:14: 18000000 INFO @ Mon, 12 Aug 2019 19:17:14: 18000000 INFO @ Mon, 12 Aug 2019 19:17:21: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:17:21: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:17:21: #1 total tags in treatment: 18937490 INFO @ Mon, 12 Aug 2019 19:17:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:17:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:17:21: #1 tags after filtering in treatment: 18937490 INFO @ Mon, 12 Aug 2019 19:17:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:17:21: #1 finished! INFO @ Mon, 12 Aug 2019 19:17:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:17:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:17:21: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:17:21: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:17:21: #1 total tags in treatment: 18937490 INFO @ Mon, 12 Aug 2019 19:17:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:17:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:17:22: #1 tags after filtering in treatment: 18937490 INFO @ Mon, 12 Aug 2019 19:17:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:17:22: #1 finished! INFO @ Mon, 12 Aug 2019 19:17:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:17:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:17:22: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:17:22: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:17:22: #1 total tags in treatment: 18937490 INFO @ Mon, 12 Aug 2019 19:17:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:17:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:17:22: #1 tags after filtering in treatment: 18937490 INFO @ Mon, 12 Aug 2019 19:17:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:17:22: #1 finished! INFO @ Mon, 12 Aug 2019 19:17:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:17:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:17:23: #2 number of paired peaks: 1486 INFO @ Mon, 12 Aug 2019 19:17:23: start model_add_line... INFO @ Mon, 12 Aug 2019 19:17:23: start X-correlation... INFO @ Mon, 12 Aug 2019 19:17:23: end of X-cor INFO @ Mon, 12 Aug 2019 19:17:23: #2 finished! INFO @ Mon, 12 Aug 2019 19:17:23: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 19:17:23: #2 alternative fragment length(s) may be 2,50 bps INFO @ Mon, 12 Aug 2019 19:17:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.05_model.r WARNING @ Mon, 12 Aug 2019 19:17:23: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:17:23: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Mon, 12 Aug 2019 19:17:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:17:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:17:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:17:23: #2 number of paired peaks: 1486 INFO @ Mon, 12 Aug 2019 19:17:23: start model_add_line... INFO @ Mon, 12 Aug 2019 19:17:24: start X-correlation... INFO @ Mon, 12 Aug 2019 19:17:24: end of X-cor INFO @ Mon, 12 Aug 2019 19:17:24: #2 finished! INFO @ Mon, 12 Aug 2019 19:17:24: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 19:17:24: #2 alternative fragment length(s) may be 2,50 bps INFO @ Mon, 12 Aug 2019 19:17:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.10_model.r WARNING @ Mon, 12 Aug 2019 19:17:24: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:17:24: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Mon, 12 Aug 2019 19:17:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:17:24: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:17:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:17:24: #2 number of paired peaks: 1486 INFO @ Mon, 12 Aug 2019 19:17:24: start model_add_line... INFO @ Mon, 12 Aug 2019 19:17:24: start X-correlation... INFO @ Mon, 12 Aug 2019 19:17:24: end of X-cor INFO @ Mon, 12 Aug 2019 19:17:24: #2 finished! INFO @ Mon, 12 Aug 2019 19:17:24: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 19:17:24: #2 alternative fragment length(s) may be 2,50 bps INFO @ Mon, 12 Aug 2019 19:17:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.20_model.r WARNING @ Mon, 12 Aug 2019 19:17:24: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:17:24: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Mon, 12 Aug 2019 19:17:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:17:24: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:17:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:18:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:18:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:18:10: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:18:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:18:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:18:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.05_summits.bed INFO @ Mon, 12 Aug 2019 19:18:30: Done! INFO @ Mon, 12 Aug 2019 19:18:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:18:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:18:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.10_summits.bed INFO @ Mon, 12 Aug 2019 19:18:30: Done! pass1 - making usageList (6 chroms): 4 millis pass2 - checking and writing primary data (5834 records, 4 fields): 11 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2447 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:18:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:18:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:18:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466498/SRX466498.20_summits.bed INFO @ Mon, 12 Aug 2019 19:18:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (676 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。