Job ID = 1293864 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,057,618 reads read : 14,057,618 reads written : 14,057,618 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: 00:04:37 14057618 reads; of these: 14057618 (100.00%) were unpaired; of these: 601730 (4.28%) aligned 0 times 11258948 (80.09%) aligned exactly 1 time 2196940 (15.63%) aligned >1 times 95.72% overall alignment rate Time searching: 00:04:37 Overall time: 00:04:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1820271 / 13455888 = 0.1353 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, 03 Jun 2019 02:59:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 02:59:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:59:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 02:59:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:59:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:59:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:59:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 02:59:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:59:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:59:59: 1000000 INFO @ Mon, 03 Jun 2019 03:00:00: 1000000 INFO @ Mon, 03 Jun 2019 03:00:01: 1000000 INFO @ Mon, 03 Jun 2019 03:00:06: 2000000 INFO @ Mon, 03 Jun 2019 03:00:08: 2000000 INFO @ Mon, 03 Jun 2019 03:00:10: 2000000 INFO @ Mon, 03 Jun 2019 03:00:13: 3000000 INFO @ Mon, 03 Jun 2019 03:00:15: 3000000 INFO @ Mon, 03 Jun 2019 03:00:19: 3000000 INFO @ Mon, 03 Jun 2019 03:00:20: 4000000 INFO @ Mon, 03 Jun 2019 03:00:23: 4000000 INFO @ Mon, 03 Jun 2019 03:00:27: 5000000 INFO @ Mon, 03 Jun 2019 03:00:27: 4000000 INFO @ Mon, 03 Jun 2019 03:00:31: 5000000 INFO @ Mon, 03 Jun 2019 03:00:34: 6000000 INFO @ Mon, 03 Jun 2019 03:00:36: 5000000 INFO @ Mon, 03 Jun 2019 03:00:39: 6000000 INFO @ Mon, 03 Jun 2019 03:00:41: 7000000 INFO @ Mon, 03 Jun 2019 03:00:45: 6000000 INFO @ Mon, 03 Jun 2019 03:00:46: 7000000 INFO @ Mon, 03 Jun 2019 03:00:48: 8000000 INFO @ Mon, 03 Jun 2019 03:00:54: 7000000 INFO @ Mon, 03 Jun 2019 03:00:54: 8000000 INFO @ Mon, 03 Jun 2019 03:00:55: 9000000 INFO @ Mon, 03 Jun 2019 03:01:02: 10000000 INFO @ Mon, 03 Jun 2019 03:01:02: 9000000 INFO @ Mon, 03 Jun 2019 03:01:02: 8000000 INFO @ Mon, 03 Jun 2019 03:01:09: 11000000 INFO @ Mon, 03 Jun 2019 03:01:10: 10000000 INFO @ Mon, 03 Jun 2019 03:01:11: 9000000 INFO @ Mon, 03 Jun 2019 03:01:13: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 03:01:13: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 03:01:13: #1 total tags in treatment: 11635617 INFO @ Mon, 03 Jun 2019 03:01:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:01:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 03:01:14: #1 tags after filtering in treatment: 11635617 INFO @ Mon, 03 Jun 2019 03:01:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:01:14: #1 finished! INFO @ Mon, 03 Jun 2019 03:01:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:01:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:01:15: #2 number of paired peaks: 316 WARNING @ Mon, 03 Jun 2019 03:01:15: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Mon, 03 Jun 2019 03:01:15: start model_add_line... INFO @ Mon, 03 Jun 2019 03:01:15: start X-correlation... INFO @ Mon, 03 Jun 2019 03:01:15: end of X-cor INFO @ Mon, 03 Jun 2019 03:01:15: #2 finished! INFO @ Mon, 03 Jun 2019 03:01:15: #2 predicted fragment length is 121 bps INFO @ Mon, 03 Jun 2019 03:01:15: #2 alternative fragment length(s) may be 121 bps INFO @ Mon, 03 Jun 2019 03:01:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.05_model.r INFO @ Mon, 03 Jun 2019 03:01:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:01:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:01:18: 11000000 INFO @ Mon, 03 Jun 2019 03:01:20: 10000000 INFO @ Mon, 03 Jun 2019 03:01:23: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 03:01:23: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 03:01:23: #1 total tags in treatment: 11635617 INFO @ Mon, 03 Jun 2019 03:01:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:01:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 03:01:24: #1 tags after filtering in treatment: 11635617 INFO @ Mon, 03 Jun 2019 03:01:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:01:24: #1 finished! INFO @ Mon, 03 Jun 2019 03:01:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:01:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:01:25: #2 number of paired peaks: 316 WARNING @ Mon, 03 Jun 2019 03:01:25: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Mon, 03 Jun 2019 03:01:25: start model_add_line... INFO @ Mon, 03 Jun 2019 03:01:25: start X-correlation... INFO @ Mon, 03 Jun 2019 03:01:25: end of X-cor INFO @ Mon, 03 Jun 2019 03:01:25: #2 finished! INFO @ Mon, 03 Jun 2019 03:01:25: #2 predicted fragment length is 121 bps INFO @ Mon, 03 Jun 2019 03:01:25: #2 alternative fragment length(s) may be 121 bps INFO @ Mon, 03 Jun 2019 03:01:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.10_model.r INFO @ Mon, 03 Jun 2019 03:01:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:01:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:01:29: 11000000 INFO @ Mon, 03 Jun 2019 03:01:34: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 03:01:34: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 03:01:34: #1 total tags in treatment: 11635617 INFO @ Mon, 03 Jun 2019 03:01:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:01:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 03:01:34: #1 tags after filtering in treatment: 11635617 INFO @ Mon, 03 Jun 2019 03:01:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:01:34: #1 finished! INFO @ Mon, 03 Jun 2019 03:01:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:01:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:01:35: #2 number of paired peaks: 316 WARNING @ Mon, 03 Jun 2019 03:01:35: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Mon, 03 Jun 2019 03:01:35: start model_add_line... INFO @ Mon, 03 Jun 2019 03:01:35: start X-correlation... INFO @ Mon, 03 Jun 2019 03:01:35: end of X-cor INFO @ Mon, 03 Jun 2019 03:01:35: #2 finished! INFO @ Mon, 03 Jun 2019 03:01:35: #2 predicted fragment length is 121 bps INFO @ Mon, 03 Jun 2019 03:01:35: #2 alternative fragment length(s) may be 121 bps INFO @ Mon, 03 Jun 2019 03:01:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.20_model.r INFO @ Mon, 03 Jun 2019 03:01:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:01:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:01:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:01:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:02:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:02:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:02:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.05_summits.bed INFO @ Mon, 03 Jun 2019 03:02:03: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3241 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:02:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:02:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:02:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:02:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.10_summits.bed INFO @ Mon, 03 Jun 2019 03:02:15: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1143 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:02:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:02:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:02:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299942/SRX1299942.20_summits.bed INFO @ Mon, 03 Jun 2019 03:02:24: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (400 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。