Job ID = 4288824 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,601,242 reads read : 61,202,484 reads written : 30,601,242 reads 0-length : 30,601,242 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:36 30601242 reads; of these: 30601242 (100.00%) were unpaired; of these: 20287917 (66.30%) aligned 0 times 7309761 (23.89%) aligned exactly 1 time 3003564 (9.82%) aligned >1 times 33.70% overall alignment rate Time searching: 00:13:37 Overall time: 00:13:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2210003 / 10313325 = 0.2143 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 12:34:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Tue, 10 Dec 2019 12:34:04: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:34:04: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:34:16: 1000000 INFO @ Tue, 10 Dec 2019 12:34:28: 2000000 INFO @ Tue, 10 Dec 2019 12:34:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Tue, 10 Dec 2019 12:34:34: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:34:34: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:34:40: 3000000 INFO @ Tue, 10 Dec 2019 12:34:46: 1000000 INFO @ Tue, 10 Dec 2019 12:34:51: 4000000 INFO @ Tue, 10 Dec 2019 12:34:58: 2000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 12:35:03: 5000000 INFO @ Tue, 10 Dec 2019 12:35:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Tue, 10 Dec 2019 12:35:04: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:35:04: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:35:10: 3000000 INFO @ Tue, 10 Dec 2019 12:35:15: 6000000 INFO @ Tue, 10 Dec 2019 12:35:18: 1000000 INFO @ Tue, 10 Dec 2019 12:35:24: 4000000 INFO @ Tue, 10 Dec 2019 12:35:26: 7000000 INFO @ Tue, 10 Dec 2019 12:35:32: 2000000 INFO @ Tue, 10 Dec 2019 12:35:37: 5000000 INFO @ Tue, 10 Dec 2019 12:35:39: 8000000 INFO @ Tue, 10 Dec 2019 12:35:40: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:35:40: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:35:40: #1 total tags in treatment: 8103322 INFO @ Tue, 10 Dec 2019 12:35:40: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:35:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 12:35:40: #1 tags after filtering in treatment: 8103103 INFO @ Tue, 10 Dec 2019 12:35:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:35:40: #1 finished! INFO @ Tue, 10 Dec 2019 12:35:40: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:35:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:35:42: #2 number of paired peaks: 40214 INFO @ Tue, 10 Dec 2019 12:35:42: start model_add_line... INFO @ Tue, 10 Dec 2019 12:35:42: start X-correlation... INFO @ Tue, 10 Dec 2019 12:35:42: end of X-cor INFO @ Tue, 10 Dec 2019 12:35:42: #2 finished! INFO @ Tue, 10 Dec 2019 12:35:42: #2 predicted fragment length is 52 bps INFO @ Tue, 10 Dec 2019 12:35:42: #2 alternative fragment length(s) may be 52 bps INFO @ Tue, 10 Dec 2019 12:35:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.05_model.r WARNING @ Tue, 10 Dec 2019 12:35:42: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:35:42: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Tue, 10 Dec 2019 12:35:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 12:35:42: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:35:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:35:45: 3000000 INFO @ Tue, 10 Dec 2019 12:35:51: 6000000 INFO @ Tue, 10 Dec 2019 12:35:58: 4000000 INFO @ Tue, 10 Dec 2019 12:36:04: 7000000 INFO @ Tue, 10 Dec 2019 12:36:08: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:36:12: 5000000 INFO @ Tue, 10 Dec 2019 12:36:18: 8000000 INFO @ Tue, 10 Dec 2019 12:36:19: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:36:19: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:36:19: #1 total tags in treatment: 8103322 INFO @ Tue, 10 Dec 2019 12:36:19: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:36:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 12:36:19: #1 tags after filtering in treatment: 8103103 INFO @ Tue, 10 Dec 2019 12:36:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:36:19: #1 finished! INFO @ Tue, 10 Dec 2019 12:36:19: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:36:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:36:21: #2 number of paired peaks: 40214 INFO @ Tue, 10 Dec 2019 12:36:21: start model_add_line... INFO @ Tue, 10 Dec 2019 12:36:22: start X-correlation... INFO @ Tue, 10 Dec 2019 12:36:22: end of X-cor INFO @ Tue, 10 Dec 2019 12:36:22: #2 finished! INFO @ Tue, 10 Dec 2019 12:36:22: #2 predicted fragment length is 52 bps INFO @ Tue, 10 Dec 2019 12:36:22: #2 alternative fragment length(s) may be 52 bps INFO @ Tue, 10 Dec 2019 12:36:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.10_model.r WARNING @ Tue, 10 Dec 2019 12:36:22: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:36:22: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Tue, 10 Dec 2019 12:36:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 12:36:22: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:36:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:36:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.05_peaks.xls INFO @ Tue, 10 Dec 2019 12:36:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:36:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.05_summits.bed INFO @ Tue, 10 Dec 2019 12:36:23: Done! pass1 - making usageList (132 chroms): 11 millis pass2 - checking and writing primary data (32737 records, 4 fields): 45 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:36:24: 6000000 INFO @ Tue, 10 Dec 2019 12:36:35: 7000000 INFO @ Tue, 10 Dec 2019 12:36:46: 8000000 INFO @ Tue, 10 Dec 2019 12:36:47: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:36:47: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:36:47: #1 total tags in treatment: 8103322 INFO @ Tue, 10 Dec 2019 12:36:47: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:36:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 12:36:48: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:36:48: #1 tags after filtering in treatment: 8103103 INFO @ Tue, 10 Dec 2019 12:36:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:36:48: #1 finished! INFO @ Tue, 10 Dec 2019 12:36:48: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:36:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:36:50: #2 number of paired peaks: 40214 INFO @ Tue, 10 Dec 2019 12:36:50: start model_add_line... INFO @ Tue, 10 Dec 2019 12:36:50: start X-correlation... INFO @ Tue, 10 Dec 2019 12:36:50: end of X-cor INFO @ Tue, 10 Dec 2019 12:36:50: #2 finished! INFO @ Tue, 10 Dec 2019 12:36:50: #2 predicted fragment length is 52 bps INFO @ Tue, 10 Dec 2019 12:36:50: #2 alternative fragment length(s) may be 52 bps INFO @ Tue, 10 Dec 2019 12:36:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.20_model.r WARNING @ Tue, 10 Dec 2019 12:36:50: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:36:50: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Tue, 10 Dec 2019 12:36:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 12:36:50: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:36:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:37:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.10_peaks.xls INFO @ Tue, 10 Dec 2019 12:37:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:37:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.10_summits.bed INFO @ Tue, 10 Dec 2019 12:37:01: Done! pass1 - making usageList (93 chroms): 8 millis pass2 - checking and writing primary data (14526 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:37:16: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 12:37:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.20_peaks.xls INFO @ Tue, 10 Dec 2019 12:37:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:37:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654071/SRX4654071.20_summits.bed INFO @ Tue, 10 Dec 2019 12:37:29: Done! pass1 - making usageList (47 chroms): 2 millis pass2 - checking and writing primary data (4386 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。