Job ID = 2009999 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,409,258 reads read : 10,818,516 reads written : 10,818,516 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5008421.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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:49 5409258 reads; of these: 5409258 (100.00%) were paired; of these: 751857 (13.90%) aligned concordantly 0 times 4057047 (75.00%) aligned concordantly exactly 1 time 600354 (11.10%) aligned concordantly >1 times ---- 751857 pairs aligned concordantly 0 times; of these: 40949 (5.45%) aligned discordantly 1 time ---- 710908 pairs aligned 0 times concordantly or discordantly; of these: 1421816 mates make up the pairs; of these: 1286818 (90.51%) aligned 0 times 90927 (6.40%) aligned exactly 1 time 44071 (3.10%) aligned >1 times 88.11% overall alignment rate Time searching: 00:05:49 Overall time: 00:05:49 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 463429 / 4691021 = 0.0988 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 20:55:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 20:55:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:55:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:55:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 20:55:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:55:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:55:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 20:55:44: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:55:44: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:55:51: 1000000 INFO @ Fri, 05 Jul 2019 20:55:51: 1000000 INFO @ Fri, 05 Jul 2019 20:55:51: 1000000 INFO @ Fri, 05 Jul 2019 20:55:58: 2000000 INFO @ Fri, 05 Jul 2019 20:55:59: 2000000 INFO @ Fri, 05 Jul 2019 20:55:59: 2000000 INFO @ Fri, 05 Jul 2019 20:56:05: 3000000 INFO @ Fri, 05 Jul 2019 20:56:06: 3000000 INFO @ Fri, 05 Jul 2019 20:56:08: 3000000 INFO @ Fri, 05 Jul 2019 20:56:12: 4000000 INFO @ Fri, 05 Jul 2019 20:56:13: 4000000 INFO @ Fri, 05 Jul 2019 20:56:16: 4000000 INFO @ Fri, 05 Jul 2019 20:56:21: 5000000 INFO @ Fri, 05 Jul 2019 20:56:21: 5000000 INFO @ Fri, 05 Jul 2019 20:56:24: 5000000 INFO @ Fri, 05 Jul 2019 20:56:28: 6000000 INFO @ Fri, 05 Jul 2019 20:56:28: 6000000 INFO @ Fri, 05 Jul 2019 20:56:33: 6000000 INFO @ Fri, 05 Jul 2019 20:56:36: 7000000 INFO @ Fri, 05 Jul 2019 20:56:36: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 20:56:41: 7000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 20:56:44: 8000000 INFO @ Fri, 05 Jul 2019 20:56:44: 8000000 INFO @ Fri, 05 Jul 2019 20:56:48: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:56:48: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:56:48: #1 total tags in treatment: 4195285 INFO @ Fri, 05 Jul 2019 20:56:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:56:48: #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 20:56:48: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:56:48: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:56:48: #1 total tags in treatment: 4195285 INFO @ Fri, 05 Jul 2019 20:56:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:56:48: #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 20:56:48: #1 tags after filtering in treatment: 1842555 INFO @ Fri, 05 Jul 2019 20:56:48: #1 Redundant rate of treatment: 0.56 INFO @ Fri, 05 Jul 2019 20:56:48: #1 finished! INFO @ Fri, 05 Jul 2019 20:56:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:56:48: #1 tags after filtering in treatment: 1842555 INFO @ Fri, 05 Jul 2019 20:56:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:56:48: #1 Redundant rate of treatment: 0.56 INFO @ Fri, 05 Jul 2019 20:56:48: #1 finished! INFO @ Fri, 05 Jul 2019 20:56:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:56:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:56:49: #2 number of paired peaks: 1119 INFO @ Fri, 05 Jul 2019 20:56:49: start model_add_line... INFO @ Fri, 05 Jul 2019 20:56:49: #2 number of paired peaks: 1119 INFO @ Fri, 05 Jul 2019 20:56:49: start model_add_line... INFO @ Fri, 05 Jul 2019 20:56:49: start X-correlation... INFO @ Fri, 05 Jul 2019 20:56:49: start X-correlation... INFO @ Fri, 05 Jul 2019 20:56:49: end of X-cor INFO @ Fri, 05 Jul 2019 20:56:49: #2 finished! INFO @ Fri, 05 Jul 2019 20:56:49: #2 predicted fragment length is 237 bps INFO @ Fri, 05 Jul 2019 20:56:49: #2 alternative fragment length(s) may be 1,211,237,260 bps INFO @ Fri, 05 Jul 2019 20:56:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.10_model.r INFO @ Fri, 05 Jul 2019 20:56:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:56:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:56:49: end of X-cor INFO @ Fri, 05 Jul 2019 20:56:49: #2 finished! INFO @ Fri, 05 Jul 2019 20:56:49: #2 predicted fragment length is 237 bps INFO @ Fri, 05 Jul 2019 20:56:49: #2 alternative fragment length(s) may be 1,211,237,260 bps INFO @ Fri, 05 Jul 2019 20:56:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.20_model.r INFO @ Fri, 05 Jul 2019 20:56:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:56:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:56:49: 8000000 INFO @ Fri, 05 Jul 2019 20:56:54: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:56:54: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:56:54: #1 total tags in treatment: 4195285 INFO @ Fri, 05 Jul 2019 20:56:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:56:54: #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 20:56:54: #1 tags after filtering in treatment: 1842555 INFO @ Fri, 05 Jul 2019 20:56:54: #1 Redundant rate of treatment: 0.56 INFO @ Fri, 05 Jul 2019 20:56:54: #1 finished! INFO @ Fri, 05 Jul 2019 20:56:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:56:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:56:55: #2 number of paired peaks: 1119 INFO @ Fri, 05 Jul 2019 20:56:55: start model_add_line... INFO @ Fri, 05 Jul 2019 20:56:55: start X-correlation... INFO @ Fri, 05 Jul 2019 20:56:55: end of X-cor INFO @ Fri, 05 Jul 2019 20:56:55: #2 finished! INFO @ Fri, 05 Jul 2019 20:56:55: #2 predicted fragment length is 237 bps INFO @ Fri, 05 Jul 2019 20:56:55: #2 alternative fragment length(s) may be 1,211,237,260 bps INFO @ Fri, 05 Jul 2019 20:56:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.05_model.r INFO @ Fri, 05 Jul 2019 20:56:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:56:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:57:02: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:57:02: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:57:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.10_peaks.xls INFO @ Fri, 05 Jul 2019 20:57:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:57:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.10_summits.bed INFO @ Fri, 05 Jul 2019 20:57:04: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (443 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 20:57:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.20_peaks.xls INFO @ Fri, 05 Jul 2019 20:57:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:57:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.20_summits.bed INFO @ Fri, 05 Jul 2019 20:57:04: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (319 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:57:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:57:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.05_peaks.xls INFO @ Fri, 05 Jul 2019 20:57:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:57:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339862/SRX2339862.05_summits.bed INFO @ Fri, 05 Jul 2019 20:57:10: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (588 records, 4 fields): 4 millis CompletedMACS2peakCalling