Job ID = 2009742 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,213,812 reads read : 24,427,624 reads written : 24,427,624 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: 00:10:33 12213812 reads; of these: 12213812 (100.00%) were paired; of these: 3984146 (32.62%) aligned concordantly 0 times 7167036 (58.68%) aligned concordantly exactly 1 time 1062630 (8.70%) aligned concordantly >1 times ---- 3984146 pairs aligned concordantly 0 times; of these: 533937 (13.40%) aligned discordantly 1 time ---- 3450209 pairs aligned 0 times concordantly or discordantly; of these: 6900418 mates make up the pairs; of these: 6483718 (93.96%) aligned 0 times 199394 (2.89%) aligned exactly 1 time 217306 (3.15%) aligned >1 times 73.46% overall alignment rate Time searching: 00:10:33 Overall time: 00:10:33 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_sort_core] merging from 8 files... [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] 4989031 / 8735889 = 0.5711 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 05 Jul 2019 20:01:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.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 20:01:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:01:30: #1 read treatment tags... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 20:01:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.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 20:01:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:01:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:01:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.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 20:01:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:01:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:01:35: 1000000 INFO @ Fri, 05 Jul 2019 20:01:36: 1000000 INFO @ Fri, 05 Jul 2019 20:01:37: 1000000 INFO @ Fri, 05 Jul 2019 20:01:39: 2000000 INFO @ Fri, 05 Jul 2019 20:01:41: 2000000 INFO @ Fri, 05 Jul 2019 20:01:41: 2000000 INFO @ Fri, 05 Jul 2019 20:01:44: 3000000 INFO @ Fri, 05 Jul 2019 20:01:46: 3000000 INFO @ Fri, 05 Jul 2019 20:01:46: 3000000 INFO @ Fri, 05 Jul 2019 20:01:48: 4000000 INFO @ Fri, 05 Jul 2019 20:01:51: 4000000 INFO @ Fri, 05 Jul 2019 20:01:51: 4000000 INFO @ Fri, 05 Jul 2019 20:01:53: 5000000 INFO @ Fri, 05 Jul 2019 20:01:56: 5000000 INFO @ Fri, 05 Jul 2019 20:01:57: 5000000 INFO @ Fri, 05 Jul 2019 20:01:58: 6000000 INFO @ Fri, 05 Jul 2019 20:02:00: 6000000 INFO @ Fri, 05 Jul 2019 20:02:01: 6000000 INFO @ Fri, 05 Jul 2019 20:02:02: 7000000 INFO @ Fri, 05 Jul 2019 20:02:05: 7000000 INFO @ Fri, 05 Jul 2019 20:02:06: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 20:02:06: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 20:02:06: #1 total tags in treatment: 3484510 INFO @ Fri, 05 Jul 2019 20:02:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:02:06: #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 20:02:06: #1 tags after filtering in treatment: 2823188 INFO @ Fri, 05 Jul 2019 20:02:06: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 05 Jul 2019 20:02:06: #1 finished! INFO @ Fri, 05 Jul 2019 20:02:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:02:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:02:07: 7000000 INFO @ Fri, 05 Jul 2019 20:02:07: #2 number of paired peaks: 158 WARNING @ Fri, 05 Jul 2019 20:02:07: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Fri, 05 Jul 2019 20:02:07: start model_add_line... INFO @ Fri, 05 Jul 2019 20:02:07: start X-correlation... INFO @ Fri, 05 Jul 2019 20:02:07: end of X-cor INFO @ Fri, 05 Jul 2019 20:02:07: #2 finished! INFO @ Fri, 05 Jul 2019 20:02:07: #2 predicted fragment length is 154 bps INFO @ Fri, 05 Jul 2019 20:02:07: #2 alternative fragment length(s) may be 2,85,87,106,154,180,221,236 bps INFO @ Fri, 05 Jul 2019 20:02:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.05_model.r INFO @ Fri, 05 Jul 2019 20:02:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:02:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:02:08: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 20:02:08: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 20:02:08: #1 total tags in treatment: 3484510 INFO @ Fri, 05 Jul 2019 20:02:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:02:08: #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 20:02:09: #1 tags after filtering in treatment: 2823188 INFO @ Fri, 05 Jul 2019 20:02:09: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 05 Jul 2019 20:02:09: #1 finished! INFO @ Fri, 05 Jul 2019 20:02:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:02:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:02:09: #2 number of paired peaks: 158 WARNING @ Fri, 05 Jul 2019 20:02:09: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Fri, 05 Jul 2019 20:02:09: start model_add_line... INFO @ Fri, 05 Jul 2019 20:02:09: start X-correlation... INFO @ Fri, 05 Jul 2019 20:02:09: end of X-cor INFO @ Fri, 05 Jul 2019 20:02:09: #2 finished! INFO @ Fri, 05 Jul 2019 20:02:09: #2 predicted fragment length is 154 bps INFO @ Fri, 05 Jul 2019 20:02:09: #2 alternative fragment length(s) may be 2,85,87,106,154,180,221,236 bps INFO @ Fri, 05 Jul 2019 20:02:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.20_model.r INFO @ Fri, 05 Jul 2019 20:02:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:02:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:02:11: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 20:02:11: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 20:02:11: #1 total tags in treatment: 3484510 INFO @ Fri, 05 Jul 2019 20:02:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:02:11: #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 20:02:11: #1 tags after filtering in treatment: 2823188 INFO @ Fri, 05 Jul 2019 20:02:11: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 05 Jul 2019 20:02:11: #1 finished! INFO @ Fri, 05 Jul 2019 20:02:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:02:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:02:11: #2 number of paired peaks: 158 WARNING @ Fri, 05 Jul 2019 20:02:11: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Fri, 05 Jul 2019 20:02:11: start model_add_line... INFO @ Fri, 05 Jul 2019 20:02:11: start X-correlation... INFO @ Fri, 05 Jul 2019 20:02:11: end of X-cor INFO @ Fri, 05 Jul 2019 20:02:11: #2 finished! INFO @ Fri, 05 Jul 2019 20:02:11: #2 predicted fragment length is 154 bps INFO @ Fri, 05 Jul 2019 20:02:11: #2 alternative fragment length(s) may be 2,85,87,106,154,180,221,236 bps INFO @ Fri, 05 Jul 2019 20:02:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.10_model.r INFO @ Fri, 05 Jul 2019 20:02:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:02:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:02:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:02:16: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:02:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.05_peaks.xls INFO @ Fri, 05 Jul 2019 20:02:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:02:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.05_summits.bed INFO @ Fri, 05 Jul 2019 20:02:16: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1125 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 20:02:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.20_peaks.xls INFO @ Fri, 05 Jul 2019 20:02:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:02:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.20_summits.bed INFO @ Fri, 05 Jul 2019 20:02:18: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (265 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:02:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:02:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.10_peaks.xls INFO @ Fri, 05 Jul 2019 20:02:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:02:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX1462591/SRX1462591.10_summits.bed INFO @ Fri, 05 Jul 2019 20:02:20: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (578 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。