Job ID = 11633576 sra ファイルのダウンロード中... Completed: 169864K bytes transferred in 4 seconds (287112K 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 3142396 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1303538/ERR1231599.sra Written 3142396 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1303538/ERR1231599.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: 00:03:13 3142396 reads; of these: 3142396 (100.00%) were paired; of these: 2026311 (64.48%) aligned concordantly 0 times 754580 (24.01%) aligned concordantly exactly 1 time 361505 (11.50%) aligned concordantly >1 times ---- 2026311 pairs aligned concordantly 0 times; of these: 864141 (42.65%) aligned discordantly 1 time ---- 1162170 pairs aligned 0 times concordantly or discordantly; of these: 2324340 mates make up the pairs; of these: 1313175 (56.50%) aligned 0 times 593753 (25.55%) aligned exactly 1 time 417412 (17.96%) aligned >1 times 79.11% overall alignment rate Time searching: 00:03:13 Overall time: 00:03:13 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] 217141 / 1293329 = 0.1679 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, 15 Feb 2019 09:09:45: # Command line: callpeak -t ERX1303538.bam -f BAM -g 12100000 -n ERX1303538.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1303538.10 # format = BAM # ChIP-seq file = ['ERX1303538.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, 15 Feb 2019 09:09:45: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:09:45: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:09:45: # Command line: callpeak -t ERX1303538.bam -f BAM -g 12100000 -n ERX1303538.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1303538.05 # format = BAM # ChIP-seq file = ['ERX1303538.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, 15 Feb 2019 09:09:45: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:09:45: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:09:45: # Command line: callpeak -t ERX1303538.bam -f BAM -g 12100000 -n ERX1303538.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1303538.20 # format = BAM # ChIP-seq file = ['ERX1303538.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, 15 Feb 2019 09:09:45: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:09:45: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:09:51: 1000000 INFO @ Fri, 15 Feb 2019 09:09:51: 1000000 INFO @ Fri, 15 Feb 2019 09:09:51: 1000000 INFO @ Fri, 15 Feb 2019 09:09:57: 2000000 INFO @ Fri, 15 Feb 2019 09:09:58: 2000000 INFO @ Fri, 15 Feb 2019 09:09:58: 2000000 INFO @ Fri, 15 Feb 2019 09:10:03: 3000000 INFO @ Fri, 15 Feb 2019 09:10:04: 3000000 INFO @ Fri, 15 Feb 2019 09:10:04: 3000000 INFO @ Fri, 15 Feb 2019 09:10:08: 4000000 INFO @ Fri, 15 Feb 2019 09:10:10: 4000000 INFO @ Fri, 15 Feb 2019 09:10:10: 4000000 INFO @ Fri, 15 Feb 2019 09:10:11: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:10:11: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:10:11: #1 total tags in treatment: 927881 INFO @ Fri, 15 Feb 2019 09:10:11: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:10:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 09:10:11: #1 tags after filtering in treatment: 713128 INFO @ Fri, 15 Feb 2019 09:10:11: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 15 Feb 2019 09:10:11: #1 finished! INFO @ Fri, 15 Feb 2019 09:10:11: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:10:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:10:12: #2 number of paired peaks: 177 WARNING @ Fri, 15 Feb 2019 09:10:12: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Fri, 15 Feb 2019 09:10:12: start model_add_line... INFO @ Fri, 15 Feb 2019 09:10:12: start X-correlation... INFO @ Fri, 15 Feb 2019 09:10:12: end of X-cor INFO @ Fri, 15 Feb 2019 09:10:12: #2 finished! INFO @ Fri, 15 Feb 2019 09:10:12: #2 predicted fragment length is 324 bps INFO @ Fri, 15 Feb 2019 09:10:12: #2 alternative fragment length(s) may be 4,324 bps INFO @ Fri, 15 Feb 2019 09:10:12: #2.2 Generate R script for model : ERX1303538.20_model.r INFO @ Fri, 15 Feb 2019 09:10:12: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:10:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:10:13: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:10:13: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:10:13: #1 total tags in treatment: 927881 INFO @ Fri, 15 Feb 2019 09:10:13: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:10:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 09:10:13: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:10:13: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:10:13: #1 total tags in treatment: 927881 INFO @ Fri, 15 Feb 2019 09:10:13: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:10:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 09:10:13: #1 tags after filtering in treatment: 713128 INFO @ Fri, 15 Feb 2019 09:10:13: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 15 Feb 2019 09:10:13: #1 finished! INFO @ Fri, 15 Feb 2019 09:10:13: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:10:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:10:13: #1 tags after filtering in treatment: 713128 INFO @ Fri, 15 Feb 2019 09:10:13: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 15 Feb 2019 09:10:13: #1 finished! INFO @ Fri, 15 Feb 2019 09:10:13: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:10:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:10:13: #2 number of paired peaks: 177 WARNING @ Fri, 15 Feb 2019 09:10:13: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Fri, 15 Feb 2019 09:10:13: start model_add_line... INFO @ Fri, 15 Feb 2019 09:10:13: start X-correlation... INFO @ Fri, 15 Feb 2019 09:10:13: end of X-cor INFO @ Fri, 15 Feb 2019 09:10:13: #2 finished! INFO @ Fri, 15 Feb 2019 09:10:13: #2 predicted fragment length is 324 bps INFO @ Fri, 15 Feb 2019 09:10:13: #2 alternative fragment length(s) may be 4,324 bps INFO @ Fri, 15 Feb 2019 09:10:13: #2.2 Generate R script for model : ERX1303538.10_model.r INFO @ Fri, 15 Feb 2019 09:10:13: #2 number of paired peaks: 177 WARNING @ Fri, 15 Feb 2019 09:10:13: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Fri, 15 Feb 2019 09:10:13: start model_add_line... INFO @ Fri, 15 Feb 2019 09:10:13: start X-correlation... INFO @ Fri, 15 Feb 2019 09:10:13: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:10:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:10:13: end of X-cor INFO @ Fri, 15 Feb 2019 09:10:13: #2 finished! INFO @ Fri, 15 Feb 2019 09:10:13: #2 predicted fragment length is 324 bps INFO @ Fri, 15 Feb 2019 09:10:13: #2 alternative fragment length(s) may be 4,324 bps INFO @ Fri, 15 Feb 2019 09:10:13: #2.2 Generate R script for model : ERX1303538.05_model.r INFO @ Fri, 15 Feb 2019 09:10:13: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:10:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:10:14: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:10:15: #4 Write output xls file... ERX1303538.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:10:15: #4 Write peak in narrowPeak format file... ERX1303538.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:10:15: #4 Write summits bed file... ERX1303538.20_summits.bed INFO @ Fri, 15 Feb 2019 09:10:15: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (76 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:10:16: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:10:16: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:10:17: #4 Write output xls file... ERX1303538.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:10:17: #4 Write peak in narrowPeak format file... ERX1303538.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:10:17: #4 Write summits bed file... ERX1303538.10_summits.bed INFO @ Fri, 15 Feb 2019 09:10:17: Done! INFO @ Fri, 15 Feb 2019 09:10:17: #4 Write output xls file... ERX1303538.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:10:17: #4 Write peak in narrowPeak format file... ERX1303538.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:10:17: #4 Write summits bed file... ERX1303538.05_summits.bed INFO @ Fri, 15 Feb 2019 09:10:17: Done! pass1 - making usageList (16 chroms): 4 millis pass2 - checking and writing primary data (152 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (240 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。