Job ID = 5791032 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,591,747 reads read : 5,183,494 reads written : 5,183,494 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: 00:02:07 2591747 reads; of these: 2591747 (100.00%) were paired; of these: 122918 (4.74%) aligned concordantly 0 times 1696835 (65.47%) aligned concordantly exactly 1 time 771994 (29.79%) aligned concordantly >1 times ---- 122918 pairs aligned concordantly 0 times; of these: 1867 (1.52%) aligned discordantly 1 time ---- 121051 pairs aligned 0 times concordantly or discordantly; of these: 242102 mates make up the pairs; of these: 217967 (90.03%) aligned 0 times 13158 (5.43%) aligned exactly 1 time 10977 (4.53%) aligned >1 times 95.79% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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] 72133 / 2457974 = 0.0293 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 08:24:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.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 @ Wed, 22 Apr 2020 08:24:52: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:24:52: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:24:58: 1000000 INFO @ Wed, 22 Apr 2020 08:25:03: 2000000 INFO @ Wed, 22 Apr 2020 08:25:08: 3000000 INFO @ Wed, 22 Apr 2020 08:25:13: 4000000 INFO @ Wed, 22 Apr 2020 08:25:18: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:25:18: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:25:18: #1 total tags in treatment: 2396697 INFO @ Wed, 22 Apr 2020 08:25:18: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:25:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:25:18: #1 tags after filtering in treatment: 1834848 INFO @ Wed, 22 Apr 2020 08:25:18: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 22 Apr 2020 08:25:18: #1 finished! INFO @ Wed, 22 Apr 2020 08:25:18: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:25:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:25:18: #2 number of paired peaks: 169 WARNING @ Wed, 22 Apr 2020 08:25:18: 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 @ Wed, 22 Apr 2020 08:25:18: start model_add_line... INFO @ Wed, 22 Apr 2020 08:25:18: start X-correlation... INFO @ Wed, 22 Apr 2020 08:25:18: end of X-cor INFO @ Wed, 22 Apr 2020 08:25:18: #2 finished! INFO @ Wed, 22 Apr 2020 08:25:18: #2 predicted fragment length is 122 bps INFO @ Wed, 22 Apr 2020 08:25:18: #2 alternative fragment length(s) may be 2,117,120,122 bps INFO @ Wed, 22 Apr 2020 08:25:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.05_model.r WARNING @ Wed, 22 Apr 2020 08:25:18: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:25:18: #2 You may need to consider one of the other alternative d(s): 2,117,120,122 WARNING @ Wed, 22 Apr 2020 08:25:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:25:18: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:25:18: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 08:25:22: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:25:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.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 @ Wed, 22 Apr 2020 08:25:22: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:25:22: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:25:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:25:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:25:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.05_summits.bed INFO @ Wed, 22 Apr 2020 08:25:24: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (522 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:25:29: 1000000 INFO @ Wed, 22 Apr 2020 08:25:35: 2000000 INFO @ Wed, 22 Apr 2020 08:25:41: 3000000 INFO @ Wed, 22 Apr 2020 08:25:47: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 08:25:52: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:25:52: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:25:52: #1 total tags in treatment: 2396697 INFO @ Wed, 22 Apr 2020 08:25:52: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:25:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:25:52: #1 tags after filtering in treatment: 1834848 INFO @ Wed, 22 Apr 2020 08:25:52: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 22 Apr 2020 08:25:52: #1 finished! INFO @ Wed, 22 Apr 2020 08:25:52: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:25:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:25:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.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 @ Wed, 22 Apr 2020 08:25:52: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:25:52: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:25:53: #2 number of paired peaks: 169 WARNING @ Wed, 22 Apr 2020 08:25:53: 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 @ Wed, 22 Apr 2020 08:25:53: start model_add_line... INFO @ Wed, 22 Apr 2020 08:25:53: start X-correlation... INFO @ Wed, 22 Apr 2020 08:25:53: end of X-cor INFO @ Wed, 22 Apr 2020 08:25:53: #2 finished! INFO @ Wed, 22 Apr 2020 08:25:53: #2 predicted fragment length is 122 bps INFO @ Wed, 22 Apr 2020 08:25:53: #2 alternative fragment length(s) may be 2,117,120,122 bps INFO @ Wed, 22 Apr 2020 08:25:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.10_model.r WARNING @ Wed, 22 Apr 2020 08:25:53: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:25:53: #2 You may need to consider one of the other alternative d(s): 2,117,120,122 WARNING @ Wed, 22 Apr 2020 08:25:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:25:53: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:25:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:25:57: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:25:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:25:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:25:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.10_summits.bed INFO @ Wed, 22 Apr 2020 08:25:58: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (262 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:25:59: 1000000 INFO @ Wed, 22 Apr 2020 08:26:05: 2000000 INFO @ Wed, 22 Apr 2020 08:26:11: 3000000 INFO @ Wed, 22 Apr 2020 08:26:17: 4000000 INFO @ Wed, 22 Apr 2020 08:26:22: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:26:22: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:26:22: #1 total tags in treatment: 2396697 INFO @ Wed, 22 Apr 2020 08:26:22: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:26:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:26:22: #1 tags after filtering in treatment: 1834848 INFO @ Wed, 22 Apr 2020 08:26:22: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 22 Apr 2020 08:26:22: #1 finished! INFO @ Wed, 22 Apr 2020 08:26:22: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:26:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:26:22: #2 number of paired peaks: 169 WARNING @ Wed, 22 Apr 2020 08:26:22: 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 @ Wed, 22 Apr 2020 08:26:22: start model_add_line... INFO @ Wed, 22 Apr 2020 08:26:22: start X-correlation... INFO @ Wed, 22 Apr 2020 08:26:22: end of X-cor INFO @ Wed, 22 Apr 2020 08:26:22: #2 finished! INFO @ Wed, 22 Apr 2020 08:26:22: #2 predicted fragment length is 122 bps INFO @ Wed, 22 Apr 2020 08:26:22: #2 alternative fragment length(s) may be 2,117,120,122 bps INFO @ Wed, 22 Apr 2020 08:26:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.20_model.r WARNING @ Wed, 22 Apr 2020 08:26:22: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:26:22: #2 You may need to consider one of the other alternative d(s): 2,117,120,122 WARNING @ Wed, 22 Apr 2020 08:26:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:26:22: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:26:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:26:26: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 08:26:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:26:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:26:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874528/SRX5874528.20_summits.bed INFO @ Wed, 22 Apr 2020 08:26:28: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (124 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。