Job ID = 1293128 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,392,638 reads read : 40,785,276 reads written : 20,392,638 reads 0-length : 20,392,638 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:17 20392638 reads; of these: 20392638 (100.00%) were unpaired; of these: 219516 (1.08%) aligned 0 times 15397860 (75.51%) aligned exactly 1 time 4775262 (23.42%) aligned >1 times 98.92% overall alignment rate Time searching: 00:05:18 Overall time: 00:05:18 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_rmdupse_core] 7267712 / 20173122 = 0.3603 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 22:10:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.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 22:10:29: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:10:29: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:10:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.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 22:10:29: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:10:29: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:10:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.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 22:10:29: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:10:29: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:10:37: 1000000 INFO @ Sun, 02 Jun 2019 22:10:39: 1000000 INFO @ Sun, 02 Jun 2019 22:10:39: 1000000 INFO @ Sun, 02 Jun 2019 22:10:44: 2000000 INFO @ Sun, 02 Jun 2019 22:10:48: 2000000 INFO @ Sun, 02 Jun 2019 22:10:49: 2000000 INFO @ Sun, 02 Jun 2019 22:10:51: 3000000 INFO @ Sun, 02 Jun 2019 22:10:58: 3000000 INFO @ Sun, 02 Jun 2019 22:10:58: 4000000 INFO @ Sun, 02 Jun 2019 22:10:59: 3000000 INFO @ Sun, 02 Jun 2019 22:11:05: 5000000 INFO @ Sun, 02 Jun 2019 22:11:07: 4000000 INFO @ Sun, 02 Jun 2019 22:11:10: 4000000 INFO @ Sun, 02 Jun 2019 22:11:13: 6000000 INFO @ Sun, 02 Jun 2019 22:11:17: 5000000 INFO @ Sun, 02 Jun 2019 22:11:20: 7000000 INFO @ Sun, 02 Jun 2019 22:11:20: 5000000 INFO @ Sun, 02 Jun 2019 22:11:27: 6000000 INFO @ Sun, 02 Jun 2019 22:11:27: 8000000 INFO @ Sun, 02 Jun 2019 22:11:30: 6000000 INFO @ Sun, 02 Jun 2019 22:11:35: 9000000 INFO @ Sun, 02 Jun 2019 22:11:36: 7000000 INFO @ Sun, 02 Jun 2019 22:11:41: 7000000 INFO @ Sun, 02 Jun 2019 22:11:42: 10000000 INFO @ Sun, 02 Jun 2019 22:11:47: 8000000 INFO @ Sun, 02 Jun 2019 22:11:49: 11000000 INFO @ Sun, 02 Jun 2019 22:11:51: 8000000 INFO @ Sun, 02 Jun 2019 22:11:57: 9000000 INFO @ Sun, 02 Jun 2019 22:11:57: 12000000 INFO @ Sun, 02 Jun 2019 22:12:01: 9000000 INFO @ Sun, 02 Jun 2019 22:12:03: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:12:03: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:12:03: #1 total tags in treatment: 12905410 INFO @ Sun, 02 Jun 2019 22:12:03: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:12:03: #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 22:12:04: #1 tags after filtering in treatment: 12905410 INFO @ Sun, 02 Jun 2019 22:12:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:12:04: #1 finished! INFO @ Sun, 02 Jun 2019 22:12:04: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:12:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:12:05: #2 number of paired peaks: 608 WARNING @ Sun, 02 Jun 2019 22:12:05: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Sun, 02 Jun 2019 22:12:05: start model_add_line... INFO @ Sun, 02 Jun 2019 22:12:05: start X-correlation... INFO @ Sun, 02 Jun 2019 22:12:05: end of X-cor INFO @ Sun, 02 Jun 2019 22:12:05: #2 finished! INFO @ Sun, 02 Jun 2019 22:12:05: #2 predicted fragment length is 54 bps INFO @ Sun, 02 Jun 2019 22:12:05: #2 alternative fragment length(s) may be 2,54,568 bps INFO @ Sun, 02 Jun 2019 22:12:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.05_model.r WARNING @ Sun, 02 Jun 2019 22:12:05: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:12:05: #2 You may need to consider one of the other alternative d(s): 2,54,568 WARNING @ Sun, 02 Jun 2019 22:12:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:12:05: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:12:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:12:06: 10000000 INFO @ Sun, 02 Jun 2019 22:12:12: 10000000 INFO @ Sun, 02 Jun 2019 22:12:16: 11000000 INFO @ Sun, 02 Jun 2019 22:12:22: 11000000 INFO @ Sun, 02 Jun 2019 22:12:25: 12000000 INFO @ Sun, 02 Jun 2019 22:12:32: 12000000 INFO @ Sun, 02 Jun 2019 22:12:34: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:12:34: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:12:34: #1 total tags in treatment: 12905410 INFO @ Sun, 02 Jun 2019 22:12:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:12:34: #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 22:12:34: #1 tags after filtering in treatment: 12905410 INFO @ Sun, 02 Jun 2019 22:12:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:12:34: #1 finished! INFO @ Sun, 02 Jun 2019 22:12:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:12:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:12:35: #2 number of paired peaks: 608 WARNING @ Sun, 02 Jun 2019 22:12:35: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Sun, 02 Jun 2019 22:12:35: start model_add_line... INFO @ Sun, 02 Jun 2019 22:12:36: start X-correlation... INFO @ Sun, 02 Jun 2019 22:12:36: end of X-cor INFO @ Sun, 02 Jun 2019 22:12:36: #2 finished! INFO @ Sun, 02 Jun 2019 22:12:36: #2 predicted fragment length is 54 bps INFO @ Sun, 02 Jun 2019 22:12:36: #2 alternative fragment length(s) may be 2,54,568 bps INFO @ Sun, 02 Jun 2019 22:12:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.20_model.r WARNING @ Sun, 02 Jun 2019 22:12:36: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:12:36: #2 You may need to consider one of the other alternative d(s): 2,54,568 WARNING @ Sun, 02 Jun 2019 22:12:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:12:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:12:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:12:39: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:12:41: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:12:41: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:12:41: #1 total tags in treatment: 12905410 INFO @ Sun, 02 Jun 2019 22:12:41: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:12:41: #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 22:12:41: #1 tags after filtering in treatment: 12905410 INFO @ Sun, 02 Jun 2019 22:12:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:12:41: #1 finished! INFO @ Sun, 02 Jun 2019 22:12:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:12:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:12:43: #2 number of paired peaks: 608 WARNING @ Sun, 02 Jun 2019 22:12:43: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Sun, 02 Jun 2019 22:12:43: start model_add_line... INFO @ Sun, 02 Jun 2019 22:12:43: start X-correlation... INFO @ Sun, 02 Jun 2019 22:12:43: end of X-cor INFO @ Sun, 02 Jun 2019 22:12:43: #2 finished! INFO @ Sun, 02 Jun 2019 22:12:43: #2 predicted fragment length is 54 bps INFO @ Sun, 02 Jun 2019 22:12:43: #2 alternative fragment length(s) may be 2,54,568 bps INFO @ Sun, 02 Jun 2019 22:12:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.10_model.r WARNING @ Sun, 02 Jun 2019 22:12:43: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:12:43: #2 You may need to consider one of the other alternative d(s): 2,54,568 WARNING @ Sun, 02 Jun 2019 22:12:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:12:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:12:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:12:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:12:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:12:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.05_summits.bed INFO @ Sun, 02 Jun 2019 22:12:56: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2341 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:13:09: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:13:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:13:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:13:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:13:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.20_summits.bed INFO @ Sun, 02 Jun 2019 22:13:26: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (258 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:13:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:13:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:13:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402703/SRX5402703.10_summits.bed INFO @ Sun, 02 Jun 2019 22:13:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (842 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。