Job ID = 11193146 sra ファイルのダウンロード中... Completed: 270934K bytes transferred in 9 seconds (234537K 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 6716683 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337738/SRR7467865.sra Written 6716683 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337738/SRR7467865.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: 00:04:31 6716683 reads; of these: 6716683 (100.00%) were paired; of these: 6026689 (89.73%) aligned concordantly 0 times 399481 (5.95%) aligned concordantly exactly 1 time 290513 (4.33%) aligned concordantly >1 times ---- 6026689 pairs aligned concordantly 0 times; of these: 133831 (2.22%) aligned discordantly 1 time ---- 5892858 pairs aligned 0 times concordantly or discordantly; of these: 11785716 mates make up the pairs; of these: 9166736 (77.78%) aligned 0 times 1674556 (14.21%) aligned exactly 1 time 944424 (8.01%) aligned >1 times 31.76% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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] 256270 / 755041 = 0.3394 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 11:06:53: # Command line: callpeak -t SRX4337738.bam -f BAM -g 12100000 -n SRX4337738.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4337738.10 # format = BAM # ChIP-seq file = ['SRX4337738.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 11:06:53: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:06:53: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:06:53: # Command line: callpeak -t SRX4337738.bam -f BAM -g 12100000 -n SRX4337738.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4337738.05 # format = BAM # ChIP-seq file = ['SRX4337738.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 11:06:53: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:06:53: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:06:53: # Command line: callpeak -t SRX4337738.bam -f BAM -g 12100000 -n SRX4337738.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4337738.20 # format = BAM # ChIP-seq file = ['SRX4337738.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 11:06:53: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:06:53: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:06:59: 1000000 INFO @ Sat, 15 Sep 2018 11:06:59: 1000000 INFO @ Sat, 15 Sep 2018 11:06:59: 1000000 INFO @ Sat, 15 Sep 2018 11:07:04: 2000000 INFO @ Sat, 15 Sep 2018 11:07:04: 2000000 INFO @ Sat, 15 Sep 2018 11:07:05: 2000000 INFO @ Sat, 15 Sep 2018 11:07:08: 3000000 INFO @ Sat, 15 Sep 2018 11:07:10: 3000000 INFO @ Sat, 15 Sep 2018 11:07:12: #1 tag size is determined as 44 bps INFO @ Sat, 15 Sep 2018 11:07:12: #1 tag size = 44 INFO @ Sat, 15 Sep 2018 11:07:12: #1 total tags in treatment: 460508 INFO @ Sat, 15 Sep 2018 11:07:12: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:07:12: #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 11:07:12: #1 tags after filtering in treatment: 202346 INFO @ Sat, 15 Sep 2018 11:07:12: #1 Redundant rate of treatment: 0.56 INFO @ Sat, 15 Sep 2018 11:07:12: #1 finished! INFO @ Sat, 15 Sep 2018 11:07:12: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:07:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:07:12: 3000000 INFO @ Sat, 15 Sep 2018 11:07:12: #2 number of paired peaks: 409 WARNING @ Sat, 15 Sep 2018 11:07:12: Fewer paired peaks (409) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 409 pairs to build model! INFO @ Sat, 15 Sep 2018 11:07:12: start model_add_line... INFO @ Sat, 15 Sep 2018 11:07:12: start X-correlation... INFO @ Sat, 15 Sep 2018 11:07:12: end of X-cor INFO @ Sat, 15 Sep 2018 11:07:12: #2 finished! INFO @ Sat, 15 Sep 2018 11:07:12: #2 predicted fragment length is 160 bps INFO @ Sat, 15 Sep 2018 11:07:12: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 15 Sep 2018 11:07:12: #2.2 Generate R script for model : SRX4337738.10_model.r INFO @ Sat, 15 Sep 2018 11:07:12: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:07:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:07:13: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:07:13: #4 Write output xls file... SRX4337738.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:07:13: #4 Write peak in narrowPeak format file... SRX4337738.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:07:13: #4 Write summits bed file... SRX4337738.10_summits.bed INFO @ Sat, 15 Sep 2018 11:07:13: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (405 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:07:15: #1 tag size is determined as 44 bps INFO @ Sat, 15 Sep 2018 11:07:15: #1 tag size = 44 INFO @ Sat, 15 Sep 2018 11:07:15: #1 total tags in treatment: 460508 INFO @ Sat, 15 Sep 2018 11:07:15: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:07:15: #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 11:07:15: #1 tags after filtering in treatment: 202346 INFO @ Sat, 15 Sep 2018 11:07:15: #1 Redundant rate of treatment: 0.56 INFO @ Sat, 15 Sep 2018 11:07:15: #1 finished! INFO @ Sat, 15 Sep 2018 11:07:15: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:07:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:07:15: #2 number of paired peaks: 409 WARNING @ Sat, 15 Sep 2018 11:07:15: Fewer paired peaks (409) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 409 pairs to build model! INFO @ Sat, 15 Sep 2018 11:07:15: start model_add_line... INFO @ Sat, 15 Sep 2018 11:07:15: start X-correlation... INFO @ Sat, 15 Sep 2018 11:07:15: end of X-cor INFO @ Sat, 15 Sep 2018 11:07:15: #2 finished! INFO @ Sat, 15 Sep 2018 11:07:15: #2 predicted fragment length is 160 bps INFO @ Sat, 15 Sep 2018 11:07:15: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 15 Sep 2018 11:07:15: #2.2 Generate R script for model : SRX4337738.20_model.r INFO @ Sat, 15 Sep 2018 11:07:15: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:07:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:07:16: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:07:16: #4 Write output xls file... SRX4337738.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:07:16: #4 Write peak in narrowPeak format file... SRX4337738.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:07:16: #4 Write summits bed file... SRX4337738.20_summits.bed INFO @ Sat, 15 Sep 2018 11:07:16: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (341 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:07:17: #1 tag size is determined as 44 bps INFO @ Sat, 15 Sep 2018 11:07:17: #1 tag size = 44 INFO @ Sat, 15 Sep 2018 11:07:17: #1 total tags in treatment: 460508 INFO @ Sat, 15 Sep 2018 11:07:17: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:07:17: #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 11:07:17: #1 tags after filtering in treatment: 202346 INFO @ Sat, 15 Sep 2018 11:07:17: #1 Redundant rate of treatment: 0.56 INFO @ Sat, 15 Sep 2018 11:07:17: #1 finished! INFO @ Sat, 15 Sep 2018 11:07:17: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:07:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:07:17: #2 number of paired peaks: 409 WARNING @ Sat, 15 Sep 2018 11:07:17: Fewer paired peaks (409) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 409 pairs to build model! INFO @ Sat, 15 Sep 2018 11:07:17: start model_add_line... INFO @ Sat, 15 Sep 2018 11:07:17: start X-correlation... INFO @ Sat, 15 Sep 2018 11:07:17: end of X-cor INFO @ Sat, 15 Sep 2018 11:07:17: #2 finished! INFO @ Sat, 15 Sep 2018 11:07:17: #2 predicted fragment length is 160 bps INFO @ Sat, 15 Sep 2018 11:07:17: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 15 Sep 2018 11:07:17: #2.2 Generate R script for model : SRX4337738.05_model.r INFO @ Sat, 15 Sep 2018 11:07:17: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:07:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:07:18: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:07:18: #4 Write output xls file... SRX4337738.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:07:18: #4 Write peak in narrowPeak format file... SRX4337738.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:07:18: #4 Write summits bed file... SRX4337738.05_summits.bed INFO @ Sat, 15 Sep 2018 11:07:18: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (516 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。