Job ID = 5791229 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,327,113 reads read : 2,654,226 reads written : 2,654,226 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: 00:00:17 1327113 reads; of these: 1327113 (100.00%) were paired; of these: 1271389 (95.80%) aligned concordantly 0 times 45544 (3.43%) aligned concordantly exactly 1 time 10180 (0.77%) aligned concordantly >1 times ---- 1271389 pairs aligned concordantly 0 times; of these: 4193 (0.33%) aligned discordantly 1 time ---- 1267196 pairs aligned 0 times concordantly or discordantly; of these: 2534392 mates make up the pairs; of these: 2514204 (99.20%) aligned 0 times 12663 (0.50%) aligned exactly 1 time 7525 (0.30%) aligned >1 times 5.28% overall alignment rate Time searching: 00:00:17 Overall time: 00:00:17 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] 32794 / 59254 = 0.5534 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 09:08:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.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 09:08:53: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:08:53: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:08:53: #1 tag size is determined as 125 bps INFO @ Wed, 22 Apr 2020 09:08:53: #1 tag size = 125 INFO @ Wed, 22 Apr 2020 09:08:53: #1 total tags in treatment: 24780 INFO @ Wed, 22 Apr 2020 09:08:53: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:08:53: #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 09:08:53: #1 tags after filtering in treatment: 20990 INFO @ Wed, 22 Apr 2020 09:08:53: #1 Redundant rate of treatment: 0.15 INFO @ Wed, 22 Apr 2020 09:08:53: #1 finished! INFO @ Wed, 22 Apr 2020 09:08:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:08:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:08:53: #2 number of paired peaks: 206 WARNING @ Wed, 22 Apr 2020 09:08:53: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Wed, 22 Apr 2020 09:08:53: start model_add_line... INFO @ Wed, 22 Apr 2020 09:08:53: start X-correlation... INFO @ Wed, 22 Apr 2020 09:08:53: end of X-cor INFO @ Wed, 22 Apr 2020 09:08:53: #2 finished! INFO @ Wed, 22 Apr 2020 09:08:53: #2 predicted fragment length is 210 bps INFO @ Wed, 22 Apr 2020 09:08:53: #2 alternative fragment length(s) may be 22,156,187,210,259,487,531 bps INFO @ Wed, 22 Apr 2020 09:08:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.05_model.r WARNING @ Wed, 22 Apr 2020 09:08:53: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 09:08:53: #2 You may need to consider one of the other alternative d(s): 22,156,187,210,259,487,531 WARNING @ Wed, 22 Apr 2020 09:08:53: #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 09:08:53: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:08:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:08:53: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:08:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:08:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:08:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.05_summits.bed INFO @ Wed, 22 Apr 2020 09:08:53: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (45 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 09:09:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.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 09:09:23: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:09:23: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:09:23: #1 tag size is determined as 125 bps INFO @ Wed, 22 Apr 2020 09:09:23: #1 tag size = 125 INFO @ Wed, 22 Apr 2020 09:09:23: #1 total tags in treatment: 24780 INFO @ Wed, 22 Apr 2020 09:09:23: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:09:23: #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 09:09:23: #1 tags after filtering in treatment: 20990 INFO @ Wed, 22 Apr 2020 09:09:23: #1 Redundant rate of treatment: 0.15 INFO @ Wed, 22 Apr 2020 09:09:23: #1 finished! INFO @ Wed, 22 Apr 2020 09:09:23: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:09:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:09:23: #2 number of paired peaks: 206 WARNING @ Wed, 22 Apr 2020 09:09:23: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Wed, 22 Apr 2020 09:09:23: start model_add_line... INFO @ Wed, 22 Apr 2020 09:09:23: start X-correlation... INFO @ Wed, 22 Apr 2020 09:09:24: end of X-cor INFO @ Wed, 22 Apr 2020 09:09:24: #2 finished! INFO @ Wed, 22 Apr 2020 09:09:24: #2 predicted fragment length is 210 bps INFO @ Wed, 22 Apr 2020 09:09:24: #2 alternative fragment length(s) may be 22,156,187,210,259,487,531 bps INFO @ Wed, 22 Apr 2020 09:09:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.10_model.r WARNING @ Wed, 22 Apr 2020 09:09:24: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 09:09:24: #2 You may need to consider one of the other alternative d(s): 22,156,187,210,259,487,531 WARNING @ Wed, 22 Apr 2020 09:09:24: #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 09:09:24: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:09:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:09:24: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:09:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:09:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:09:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.10_summits.bed INFO @ Wed, 22 Apr 2020 09:09:24: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (22 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:09:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.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 09:09:53: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:09:53: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:09:53: #1 tag size is determined as 125 bps INFO @ Wed, 22 Apr 2020 09:09:53: #1 tag size = 125 INFO @ Wed, 22 Apr 2020 09:09:53: #1 total tags in treatment: 24780 INFO @ Wed, 22 Apr 2020 09:09:53: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:09:53: #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 09:09:53: #1 tags after filtering in treatment: 20990 INFO @ Wed, 22 Apr 2020 09:09:53: #1 Redundant rate of treatment: 0.15 INFO @ Wed, 22 Apr 2020 09:09:53: #1 finished! INFO @ Wed, 22 Apr 2020 09:09:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:09:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:09:53: #2 number of paired peaks: 206 WARNING @ Wed, 22 Apr 2020 09:09:53: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Wed, 22 Apr 2020 09:09:53: start model_add_line... INFO @ Wed, 22 Apr 2020 09:09:53: start X-correlation... INFO @ Wed, 22 Apr 2020 09:09:53: end of X-cor INFO @ Wed, 22 Apr 2020 09:09:53: #2 finished! INFO @ Wed, 22 Apr 2020 09:09:53: #2 predicted fragment length is 210 bps INFO @ Wed, 22 Apr 2020 09:09:53: #2 alternative fragment length(s) may be 22,156,187,210,259,487,531 bps INFO @ Wed, 22 Apr 2020 09:09:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.20_model.r WARNING @ Wed, 22 Apr 2020 09:09:53: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 09:09:53: #2 You may need to consider one of the other alternative d(s): 22,156,187,210,259,487,531 WARNING @ Wed, 22 Apr 2020 09:09:53: #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 09:09:53: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:09:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:09:53: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:09:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:09:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:09:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7255995/SRX7255995.20_summits.bed INFO @ Wed, 22 Apr 2020 09:09:53: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (15 records, 4 fields): 1 millis CompletedMACS2peakCalling