Job ID = 2003691 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,594,541 reads read : 27,594,541 reads written : 27,594,541 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1103817.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: 00:00:05 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:23:49 27594541 reads; of these: 27594541 (100.00%) were unpaired; of these: 1703491 (6.17%) aligned 0 times 17973455 (65.13%) aligned exactly 1 time 7917595 (28.69%) aligned >1 times 93.83% overall alignment rate Time searching: 00:23:56 Overall time: 00:23:56 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 12 files... [bam_rmdupse_core] 1085506 / 25891050 = 0.0419 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 @ Fri, 05 Jul 2019 13:55:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.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 @ Fri, 05 Jul 2019 13:55:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:55:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:55:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.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 @ Fri, 05 Jul 2019 13:55:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:55:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:55:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.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 @ Fri, 05 Jul 2019 13:55:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:55:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:55:38: 1000000 INFO @ Fri, 05 Jul 2019 13:55:39: 1000000 INFO @ Fri, 05 Jul 2019 13:55:41: 1000000 INFO @ Fri, 05 Jul 2019 13:55:46: 2000000 INFO @ Fri, 05 Jul 2019 13:55:47: 2000000 INFO @ Fri, 05 Jul 2019 13:55:50: 2000000 INFO @ Fri, 05 Jul 2019 13:55:53: 3000000 INFO @ Fri, 05 Jul 2019 13:55:54: 3000000 INFO @ Fri, 05 Jul 2019 13:55:58: 3000000 INFO @ Fri, 05 Jul 2019 13:56:00: 4000000 INFO @ Fri, 05 Jul 2019 13:56:02: 4000000 INFO @ Fri, 05 Jul 2019 13:56:07: 5000000 INFO @ Fri, 05 Jul 2019 13:56:07: 4000000 INFO @ Fri, 05 Jul 2019 13:56:10: 5000000 INFO @ Fri, 05 Jul 2019 13:56:14: 6000000 INFO @ Fri, 05 Jul 2019 13:56:16: 5000000 INFO @ Fri, 05 Jul 2019 13:56:17: 6000000 INFO @ Fri, 05 Jul 2019 13:56:21: 7000000 INFO @ Fri, 05 Jul 2019 13:56:24: 6000000 INFO @ Fri, 05 Jul 2019 13:56:25: 7000000 INFO @ Fri, 05 Jul 2019 13:56:28: 8000000 INFO @ Fri, 05 Jul 2019 13:56:33: 8000000 INFO @ Fri, 05 Jul 2019 13:56:33: 7000000 INFO @ Fri, 05 Jul 2019 13:56:35: 9000000 INFO @ Fri, 05 Jul 2019 13:56:40: 9000000 INFO @ Fri, 05 Jul 2019 13:56:41: 8000000 INFO @ Fri, 05 Jul 2019 13:56:42: 10000000 INFO @ Fri, 05 Jul 2019 13:56:48: 10000000 INFO @ Fri, 05 Jul 2019 13:56:49: 11000000 INFO @ Fri, 05 Jul 2019 13:56:50: 9000000 INFO @ Fri, 05 Jul 2019 13:56:55: 11000000 INFO @ Fri, 05 Jul 2019 13:56:56: 12000000 INFO @ Fri, 05 Jul 2019 13:56:58: 10000000 INFO @ Fri, 05 Jul 2019 13:57:03: 12000000 INFO @ Fri, 05 Jul 2019 13:57:03: 13000000 INFO @ Fri, 05 Jul 2019 13:57:07: 11000000 INFO @ Fri, 05 Jul 2019 13:57:11: 14000000 INFO @ Fri, 05 Jul 2019 13:57:11: 13000000 INFO @ Fri, 05 Jul 2019 13:57:16: 12000000 INFO @ Fri, 05 Jul 2019 13:57:18: 15000000 INFO @ Fri, 05 Jul 2019 13:57:18: 14000000 INFO @ Fri, 05 Jul 2019 13:57:24: 13000000 INFO @ Fri, 05 Jul 2019 13:57:25: 16000000 INFO @ Fri, 05 Jul 2019 13:57:26: 15000000 INFO @ Fri, 05 Jul 2019 13:57:32: 17000000 INFO @ Fri, 05 Jul 2019 13:57:33: 14000000 INFO @ Fri, 05 Jul 2019 13:57:34: 16000000 INFO @ Fri, 05 Jul 2019 13:57:39: 18000000 INFO @ Fri, 05 Jul 2019 13:57:41: 17000000 INFO @ Fri, 05 Jul 2019 13:57:42: 15000000 INFO @ Fri, 05 Jul 2019 13:57:46: 19000000 INFO @ Fri, 05 Jul 2019 13:57:49: 18000000 INFO @ Fri, 05 Jul 2019 13:57:52: 16000000 INFO @ Fri, 05 Jul 2019 13:57:53: 20000000 INFO @ Fri, 05 Jul 2019 13:57:58: 19000000 INFO @ Fri, 05 Jul 2019 13:58:00: 21000000 INFO @ Fri, 05 Jul 2019 13:58:01: 17000000 INFO @ Fri, 05 Jul 2019 13:58:07: 22000000 INFO @ Fri, 05 Jul 2019 13:58:09: 20000000 INFO @ Fri, 05 Jul 2019 13:58:11: 18000000 INFO @ Fri, 05 Jul 2019 13:58:14: 23000000 INFO @ Fri, 05 Jul 2019 13:58:20: 21000000 INFO @ Fri, 05 Jul 2019 13:58:21: 19000000 INFO @ Fri, 05 Jul 2019 13:58:21: 24000000 INFO @ Fri, 05 Jul 2019 13:58:27: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:58:27: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:58:27: #1 total tags in treatment: 24805544 INFO @ Fri, 05 Jul 2019 13:58:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:58:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 13:58:28: #1 tags after filtering in treatment: 24805436 INFO @ Fri, 05 Jul 2019 13:58:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:58:28: #1 finished! INFO @ Fri, 05 Jul 2019 13:58:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:58:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:58:30: 22000000 INFO @ Fri, 05 Jul 2019 13:58:31: 20000000 INFO @ Fri, 05 Jul 2019 13:58:31: #2 number of paired peaks: 6260 INFO @ Fri, 05 Jul 2019 13:58:31: start model_add_line... INFO @ Fri, 05 Jul 2019 13:58:31: start X-correlation... INFO @ Fri, 05 Jul 2019 13:58:31: end of X-cor INFO @ Fri, 05 Jul 2019 13:58:31: #2 finished! INFO @ Fri, 05 Jul 2019 13:58:31: #2 predicted fragment length is 97 bps INFO @ Fri, 05 Jul 2019 13:58:31: #2 alternative fragment length(s) may be 97 bps INFO @ Fri, 05 Jul 2019 13:58:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.05_model.r WARNING @ Fri, 05 Jul 2019 13:58:31: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 13:58:31: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Fri, 05 Jul 2019 13:58:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 13:58:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:58:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:58:40: 21000000 INFO @ Fri, 05 Jul 2019 13:58:41: 23000000 INFO @ Fri, 05 Jul 2019 13:58:50: 22000000 INFO @ Fri, 05 Jul 2019 13:58:52: 24000000 INFO @ Fri, 05 Jul 2019 13:59:00: 23000000 INFO @ Fri, 05 Jul 2019 13:59:00: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:59:00: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:59:00: #1 total tags in treatment: 24805544 INFO @ Fri, 05 Jul 2019 13:59:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:59:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 13:59:01: #1 tags after filtering in treatment: 24805436 INFO @ Fri, 05 Jul 2019 13:59:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:59:01: #1 finished! INFO @ Fri, 05 Jul 2019 13:59:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:59:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:59:04: #2 number of paired peaks: 6260 INFO @ Fri, 05 Jul 2019 13:59:04: start model_add_line... INFO @ Fri, 05 Jul 2019 13:59:04: start X-correlation... INFO @ Fri, 05 Jul 2019 13:59:04: end of X-cor INFO @ Fri, 05 Jul 2019 13:59:04: #2 finished! INFO @ Fri, 05 Jul 2019 13:59:04: #2 predicted fragment length is 97 bps INFO @ Fri, 05 Jul 2019 13:59:04: #2 alternative fragment length(s) may be 97 bps INFO @ Fri, 05 Jul 2019 13:59:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.10_model.r WARNING @ Fri, 05 Jul 2019 13:59:04: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 13:59:04: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Fri, 05 Jul 2019 13:59:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 13:59:04: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:59:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:59:08: 24000000 INFO @ Fri, 05 Jul 2019 13:59:15: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:59:15: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:59:15: #1 total tags in treatment: 24805544 INFO @ Fri, 05 Jul 2019 13:59:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:59:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 13:59:16: #1 tags after filtering in treatment: 24805436 INFO @ Fri, 05 Jul 2019 13:59:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:59:16: #1 finished! INFO @ Fri, 05 Jul 2019 13:59:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:59:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:59:19: #2 number of paired peaks: 6260 INFO @ Fri, 05 Jul 2019 13:59:19: start model_add_line... INFO @ Fri, 05 Jul 2019 13:59:19: start X-correlation... INFO @ Fri, 05 Jul 2019 13:59:19: end of X-cor INFO @ Fri, 05 Jul 2019 13:59:19: #2 finished! INFO @ Fri, 05 Jul 2019 13:59:19: #2 predicted fragment length is 97 bps INFO @ Fri, 05 Jul 2019 13:59:19: #2 alternative fragment length(s) may be 97 bps INFO @ Fri, 05 Jul 2019 13:59:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.20_model.r WARNING @ Fri, 05 Jul 2019 13:59:19: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 13:59:19: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Fri, 05 Jul 2019 13:59:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 13:59:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:59:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:59:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:00:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:00:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.05_peaks.xls INFO @ Fri, 05 Jul 2019 14:00:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:00:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.05_summits.bed INFO @ Fri, 05 Jul 2019 14:00:27: Done! pass1 - making usageList (47 chroms): 3 millis pass2 - checking and writing primary data (1869 records, 4 fields): 70 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 14:00:37: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:01:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.10_peaks.xls INFO @ Fri, 05 Jul 2019 14:01:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:01:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.10_summits.bed INFO @ Fri, 05 Jul 2019 14:01:01: Done! pass1 - making usageList (40 chroms): 2 millis pass2 - checking and writing primary data (928 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 14:01:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.20_peaks.xls INFO @ Fri, 05 Jul 2019 14:01:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:01:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX423108/SRX423108.20_summits.bed INFO @ Fri, 05 Jul 2019 14:01:15: Done! pass1 - making usageList (30 chroms): 2 millis pass2 - checking and writing primary data (318 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。