Job ID = 11193148 sra ファイルのダウンロード中... Completed: 539568K bytes transferred in 13 seconds (337288K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Read 15093886 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337740/SRR7467863.sra Written 15093886 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337740/SRR7467863.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:07:28 15093886 reads; of these: 15093886 (100.00%) were paired; of these: 12265361 (81.26%) aligned concordantly 0 times 2472680 (16.38%) aligned concordantly exactly 1 time 355845 (2.36%) aligned concordantly >1 times ---- 12265361 pairs aligned concordantly 0 times; of these: 1412463 (11.52%) aligned discordantly 1 time ---- 10852898 pairs aligned 0 times concordantly or discordantly; of these: 21705796 mates make up the pairs; of these: 17407398 (80.20%) aligned 0 times 3634196 (16.74%) aligned exactly 1 time 664202 (3.06%) aligned >1 times 42.34% overall alignment rate Time searching: 00:07:28 Overall time: 00:07:28 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] 1889496 / 3645058 = 0.5184 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 @ Sat, 15 Sep 2018 11:12:48: # Command line: callpeak -t SRX4337740.bam -f BAM -g 12100000 -n SRX4337740.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4337740.10 # format = BAM # ChIP-seq file = ['SRX4337740.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 @ Sat, 15 Sep 2018 11:12:48: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:12:48: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:12:48: # Command line: callpeak -t SRX4337740.bam -f BAM -g 12100000 -n SRX4337740.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4337740.20 # format = BAM # ChIP-seq file = ['SRX4337740.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 @ Sat, 15 Sep 2018 11:12:48: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:12:48: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:12:48: # Command line: callpeak -t SRX4337740.bam -f BAM -g 12100000 -n SRX4337740.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4337740.05 # format = BAM # ChIP-seq file = ['SRX4337740.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 @ Sat, 15 Sep 2018 11:12:48: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:12:48: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:12:55: 1000000 INFO @ Sat, 15 Sep 2018 11:12:55: 1000000 INFO @ Sat, 15 Sep 2018 11:12:55: 1000000 INFO @ Sat, 15 Sep 2018 11:13:01: 2000000 INFO @ Sat, 15 Sep 2018 11:13:01: 2000000 INFO @ Sat, 15 Sep 2018 11:13:01: 2000000 INFO @ Sat, 15 Sep 2018 11:13:07: 3000000 INFO @ Sat, 15 Sep 2018 11:13:08: 3000000 INFO @ Sat, 15 Sep 2018 11:13:08: 3000000 INFO @ Sat, 15 Sep 2018 11:13:13: 4000000 INFO @ Sat, 15 Sep 2018 11:13:14: 4000000 INFO @ Sat, 15 Sep 2018 11:13:15: 4000000 INFO @ Sat, 15 Sep 2018 11:13:19: 5000000 INFO @ Sat, 15 Sep 2018 11:13:21: 5000000 INFO @ Sat, 15 Sep 2018 11:13:21: 5000000 INFO @ Sat, 15 Sep 2018 11:13:26: 6000000 INFO @ Sat, 15 Sep 2018 11:13:28: 6000000 INFO @ Sat, 15 Sep 2018 11:13:28: 6000000 INFO @ Sat, 15 Sep 2018 11:13:32: 7000000 INFO @ Sat, 15 Sep 2018 11:13:34: 7000000 INFO @ Sat, 15 Sep 2018 11:13:35: 7000000 INFO @ Sat, 15 Sep 2018 11:13:38: 8000000 INFO @ Sat, 15 Sep 2018 11:13:41: 8000000 INFO @ Sat, 15 Sep 2018 11:13:41: 8000000 INFO @ Sat, 15 Sep 2018 11:13:44: 9000000 INFO @ Sat, 15 Sep 2018 11:13:44: #1 tag size is determined as 44 bps INFO @ Sat, 15 Sep 2018 11:13:44: #1 tag size = 44 INFO @ Sat, 15 Sep 2018 11:13:44: #1 total tags in treatment: 1355965 INFO @ Sat, 15 Sep 2018 11:13:44: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:13:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:13:44: #1 tags after filtering in treatment: 1218043 INFO @ Sat, 15 Sep 2018 11:13:44: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Sep 2018 11:13:44: #1 finished! INFO @ Sat, 15 Sep 2018 11:13:44: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:13:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:13:44: #2 number of paired peaks: 169 WARNING @ Sat, 15 Sep 2018 11:13:44: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 15 Sep 2018 11:13:44: start model_add_line... INFO @ Sat, 15 Sep 2018 11:13:44: start X-correlation... INFO @ Sat, 15 Sep 2018 11:13:44: end of X-cor INFO @ Sat, 15 Sep 2018 11:13:44: #2 finished! INFO @ Sat, 15 Sep 2018 11:13:44: #2 predicted fragment length is 198 bps INFO @ Sat, 15 Sep 2018 11:13:44: #2 alternative fragment length(s) may be 3,175,198 bps INFO @ Sat, 15 Sep 2018 11:13:44: #2.2 Generate R script for model : SRX4337740.05_model.r INFO @ Sat, 15 Sep 2018 11:13:44: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:13:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:13:47: 9000000 INFO @ Sat, 15 Sep 2018 11:13:47: #1 tag size is determined as 44 bps INFO @ Sat, 15 Sep 2018 11:13:47: #1 tag size = 44 INFO @ Sat, 15 Sep 2018 11:13:47: #1 total tags in treatment: 1355965 INFO @ Sat, 15 Sep 2018 11:13:47: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:13:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:13:47: #1 tags after filtering in treatment: 1218043 INFO @ Sat, 15 Sep 2018 11:13:47: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Sep 2018 11:13:47: #1 finished! INFO @ Sat, 15 Sep 2018 11:13:47: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:13:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:13:47: #2 number of paired peaks: 169 WARNING @ Sat, 15 Sep 2018 11:13:47: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 15 Sep 2018 11:13:47: start model_add_line... INFO @ Sat, 15 Sep 2018 11:13:47: start X-correlation... INFO @ Sat, 15 Sep 2018 11:13:47: end of X-cor INFO @ Sat, 15 Sep 2018 11:13:47: #2 finished! INFO @ Sat, 15 Sep 2018 11:13:47: #2 predicted fragment length is 198 bps INFO @ Sat, 15 Sep 2018 11:13:47: #2 alternative fragment length(s) may be 3,175,198 bps INFO @ Sat, 15 Sep 2018 11:13:47: #2.2 Generate R script for model : SRX4337740.10_model.r INFO @ Sat, 15 Sep 2018 11:13:47: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:13:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:13:48: 9000000 INFO @ Sat, 15 Sep 2018 11:13:48: #1 tag size is determined as 44 bps INFO @ Sat, 15 Sep 2018 11:13:48: #1 tag size = 44 INFO @ Sat, 15 Sep 2018 11:13:48: #1 total tags in treatment: 1355965 INFO @ Sat, 15 Sep 2018 11:13:48: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:13:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:13:48: #1 tags after filtering in treatment: 1218043 INFO @ Sat, 15 Sep 2018 11:13:48: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Sep 2018 11:13:48: #1 finished! INFO @ Sat, 15 Sep 2018 11:13:48: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:13:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:13:48: #2 number of paired peaks: 169 WARNING @ Sat, 15 Sep 2018 11:13:48: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 15 Sep 2018 11:13:48: start model_add_line... INFO @ Sat, 15 Sep 2018 11:13:48: start X-correlation... INFO @ Sat, 15 Sep 2018 11:13:48: end of X-cor INFO @ Sat, 15 Sep 2018 11:13:48: #2 finished! INFO @ Sat, 15 Sep 2018 11:13:48: #2 predicted fragment length is 198 bps INFO @ Sat, 15 Sep 2018 11:13:48: #2 alternative fragment length(s) may be 3,175,198 bps INFO @ Sat, 15 Sep 2018 11:13:48: #2.2 Generate R script for model : SRX4337740.20_model.r INFO @ Sat, 15 Sep 2018 11:13:48: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:13:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:13:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:13:51: #4 Write output xls file... SRX4337740.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:13:51: #4 Write peak in narrowPeak format file... SRX4337740.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:13:51: #4 Write summits bed file... SRX4337740.05_summits.bed INFO @ Sat, 15 Sep 2018 11:13:51: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (527 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:13:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:13:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:13:54: #4 Write output xls file... SRX4337740.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:13:54: #4 Write peak in narrowPeak format file... SRX4337740.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:13:54: #4 Write summits bed file... SRX4337740.10_summits.bed INFO @ Sat, 15 Sep 2018 11:13:54: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (325 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:13:54: #4 Write output xls file... SRX4337740.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:13:54: #4 Write peak in narrowPeak format file... SRX4337740.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:13:54: #4 Write summits bed file... SRX4337740.20_summits.bed INFO @ Sat, 15 Sep 2018 11:13:54: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (172 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。