Job ID = 2590291 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,625,746 reads read : 21,251,492 reads written : 21,251,492 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:04 10625746 reads; of these: 10625746 (100.00%) were paired; of these: 5644802 (53.12%) aligned concordantly 0 times 4592343 (43.22%) aligned concordantly exactly 1 time 388601 (3.66%) aligned concordantly >1 times ---- 5644802 pairs aligned concordantly 0 times; of these: 620796 (11.00%) aligned discordantly 1 time ---- 5024006 pairs aligned 0 times concordantly or discordantly; of these: 10048012 mates make up the pairs; of these: 9723908 (96.77%) aligned 0 times 223742 (2.23%) aligned exactly 1 time 100362 (1.00%) aligned >1 times 54.24% overall alignment rate Time searching: 00:11:04 Overall time: 00:11:04 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 117581 / 5572916 = 0.0211 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 21:02:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.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, 12 Aug 2019 21:02:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:02:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:02:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.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, 12 Aug 2019 21:02:58: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:02:58: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:02:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.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, 12 Aug 2019 21:02:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:02:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:03:07: 1000000 INFO @ Mon, 12 Aug 2019 21:03:08: 1000000 INFO @ Mon, 12 Aug 2019 21:03:09: 1000000 INFO @ Mon, 12 Aug 2019 21:03:17: 2000000 INFO @ Mon, 12 Aug 2019 21:03:19: 2000000 INFO @ Mon, 12 Aug 2019 21:03:20: 2000000 INFO @ Mon, 12 Aug 2019 21:03:27: 3000000 INFO @ Mon, 12 Aug 2019 21:03:30: 3000000 INFO @ Mon, 12 Aug 2019 21:03:31: 3000000 INFO @ Mon, 12 Aug 2019 21:03:38: 4000000 INFO @ Mon, 12 Aug 2019 21:03:41: 4000000 INFO @ Mon, 12 Aug 2019 21:03:41: 4000000 INFO @ Mon, 12 Aug 2019 21:03:48: 5000000 INFO @ Mon, 12 Aug 2019 21:03:51: 5000000 INFO @ Mon, 12 Aug 2019 21:03:52: 5000000 INFO @ Mon, 12 Aug 2019 21:03:59: 6000000 INFO @ Mon, 12 Aug 2019 21:04:01: 6000000 INFO @ Mon, 12 Aug 2019 21:04:03: 6000000 INFO @ Mon, 12 Aug 2019 21:04:09: 7000000 INFO @ Mon, 12 Aug 2019 21:04:12: 7000000 INFO @ Mon, 12 Aug 2019 21:04:13: 7000000 INFO @ Mon, 12 Aug 2019 21:04:19: 8000000 INFO @ Mon, 12 Aug 2019 21:04:22: 8000000 INFO @ Mon, 12 Aug 2019 21:04:24: 8000000 INFO @ Mon, 12 Aug 2019 21:04:29: 9000000 INFO @ Mon, 12 Aug 2019 21:04:32: 9000000 INFO @ Mon, 12 Aug 2019 21:04:35: 9000000 INFO @ Mon, 12 Aug 2019 21:04:40: 10000000 INFO @ Mon, 12 Aug 2019 21:04:42: 10000000 INFO @ Mon, 12 Aug 2019 21:04:45: 10000000 INFO @ Mon, 12 Aug 2019 21:04:50: 11000000 INFO @ Mon, 12 Aug 2019 21:04:53: 11000000 INFO @ Mon, 12 Aug 2019 21:04:53: #1 tag size is determined as 101 bps INFO @ Mon, 12 Aug 2019 21:04:53: #1 tag size = 101 INFO @ Mon, 12 Aug 2019 21:04:53: #1 total tags in treatment: 4873669 INFO @ Mon, 12 Aug 2019 21:04:53: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:04:53: #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 21:04:53: #1 tags after filtering in treatment: 4774282 INFO @ Mon, 12 Aug 2019 21:04:53: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 12 Aug 2019 21:04:53: #1 finished! INFO @ Mon, 12 Aug 2019 21:04:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:04:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:04:54: #2 number of paired peaks: 468 WARNING @ Mon, 12 Aug 2019 21:04:54: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Mon, 12 Aug 2019 21:04:54: start model_add_line... INFO @ Mon, 12 Aug 2019 21:04:54: start X-correlation... INFO @ Mon, 12 Aug 2019 21:04:54: end of X-cor INFO @ Mon, 12 Aug 2019 21:04:54: #2 finished! INFO @ Mon, 12 Aug 2019 21:04:54: #2 predicted fragment length is 230 bps INFO @ Mon, 12 Aug 2019 21:04:54: #2 alternative fragment length(s) may be 230 bps INFO @ Mon, 12 Aug 2019 21:04:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.05_model.r INFO @ Mon, 12 Aug 2019 21:04:54: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:04:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:04:55: #1 tag size is determined as 101 bps INFO @ Mon, 12 Aug 2019 21:04:55: #1 tag size = 101 INFO @ Mon, 12 Aug 2019 21:04:55: #1 total tags in treatment: 4873669 INFO @ Mon, 12 Aug 2019 21:04:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:04:55: #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 21:04:56: #1 tags after filtering in treatment: 4774282 INFO @ Mon, 12 Aug 2019 21:04:56: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 12 Aug 2019 21:04:56: #1 finished! INFO @ Mon, 12 Aug 2019 21:04:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:04:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:04:56: 11000000 INFO @ Mon, 12 Aug 2019 21:04:56: #2 number of paired peaks: 468 WARNING @ Mon, 12 Aug 2019 21:04:56: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Mon, 12 Aug 2019 21:04:56: start model_add_line... INFO @ Mon, 12 Aug 2019 21:04:56: start X-correlation... INFO @ Mon, 12 Aug 2019 21:04:56: end of X-cor INFO @ Mon, 12 Aug 2019 21:04:56: #2 finished! INFO @ Mon, 12 Aug 2019 21:04:56: #2 predicted fragment length is 230 bps INFO @ Mon, 12 Aug 2019 21:04:56: #2 alternative fragment length(s) may be 230 bps INFO @ Mon, 12 Aug 2019 21:04:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.20_model.r INFO @ Mon, 12 Aug 2019 21:04:56: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:04:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:04:59: #1 tag size is determined as 101 bps INFO @ Mon, 12 Aug 2019 21:04:59: #1 tag size = 101 INFO @ Mon, 12 Aug 2019 21:04:59: #1 total tags in treatment: 4873669 INFO @ Mon, 12 Aug 2019 21:04:59: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:04:59: #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 21:04:59: #1 tags after filtering in treatment: 4774282 INFO @ Mon, 12 Aug 2019 21:04:59: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 12 Aug 2019 21:04:59: #1 finished! INFO @ Mon, 12 Aug 2019 21:04:59: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:04:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:04:59: #2 number of paired peaks: 468 WARNING @ Mon, 12 Aug 2019 21:04:59: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Mon, 12 Aug 2019 21:04:59: start model_add_line... INFO @ Mon, 12 Aug 2019 21:04:59: start X-correlation... INFO @ Mon, 12 Aug 2019 21:05:00: end of X-cor INFO @ Mon, 12 Aug 2019 21:05:00: #2 finished! INFO @ Mon, 12 Aug 2019 21:05:00: #2 predicted fragment length is 230 bps INFO @ Mon, 12 Aug 2019 21:05:00: #2 alternative fragment length(s) may be 230 bps INFO @ Mon, 12 Aug 2019 21:05:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.10_model.r INFO @ Mon, 12 Aug 2019 21:05:00: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:05:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:05:08: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:05:11: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:05:14: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:05:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:05:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:05:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.05_summits.bed INFO @ Mon, 12 Aug 2019 21:05:16: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (1933 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:05:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:05:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:05:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.20_summits.bed INFO @ Mon, 12 Aug 2019 21:05:18: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (111 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:05:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:05:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:05:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2950505/SRX2950505.10_summits.bed INFO @ Mon, 12 Aug 2019 21:05:21: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (532 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。