Job ID = 5790948 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,917,966 reads read : 5,835,932 reads written : 5,835,932 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: 00:02:21 2917966 reads; of these: 2917966 (100.00%) were paired; of these: 261378 (8.96%) aligned concordantly 0 times 2006196 (68.75%) aligned concordantly exactly 1 time 650392 (22.29%) aligned concordantly >1 times ---- 261378 pairs aligned concordantly 0 times; of these: 9477 (3.63%) aligned discordantly 1 time ---- 251901 pairs aligned 0 times concordantly or discordantly; of these: 503802 mates make up the pairs; of these: 464736 (92.25%) aligned 0 times 21475 (4.26%) aligned exactly 1 time 17591 (3.49%) aligned >1 times 92.04% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 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] 71615 / 2653161 = 0.0270 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 08:12:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.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 08:12:32: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:12:32: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:12:39: 1000000 INFO @ Wed, 22 Apr 2020 08:12:46: 2000000 INFO @ Wed, 22 Apr 2020 08:12:53: 3000000 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 08:13:01: 4000000 INFO @ Wed, 22 Apr 2020 08:13:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.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 08:13:02: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:13:02: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:13:08: 5000000 INFO @ Wed, 22 Apr 2020 08:13:09: 1000000 INFO @ Wed, 22 Apr 2020 08:13:10: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:13:10: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:13:10: #1 total tags in treatment: 2585049 INFO @ Wed, 22 Apr 2020 08:13:10: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:13:10: #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 08:13:10: #1 tags after filtering in treatment: 2131189 INFO @ Wed, 22 Apr 2020 08:13:10: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 22 Apr 2020 08:13:10: #1 finished! INFO @ Wed, 22 Apr 2020 08:13:10: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:13:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:13:10: #2 number of paired peaks: 207 WARNING @ Wed, 22 Apr 2020 08:13:10: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Wed, 22 Apr 2020 08:13:10: start model_add_line... INFO @ Wed, 22 Apr 2020 08:13:10: start X-correlation... INFO @ Wed, 22 Apr 2020 08:13:10: end of X-cor INFO @ Wed, 22 Apr 2020 08:13:10: #2 finished! INFO @ Wed, 22 Apr 2020 08:13:10: #2 predicted fragment length is 147 bps INFO @ Wed, 22 Apr 2020 08:13:10: #2 alternative fragment length(s) may be 2,147,161,181 bps INFO @ Wed, 22 Apr 2020 08:13:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.05_model.r WARNING @ Wed, 22 Apr 2020 08:13:10: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:13:10: #2 You may need to consider one of the other alternative d(s): 2,147,161,181 WARNING @ Wed, 22 Apr 2020 08:13:10: #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 08:13:10: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:13:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:13:15: 2000000 INFO @ Wed, 22 Apr 2020 08:13:16: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:13:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:13:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:13:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.05_summits.bed INFO @ Wed, 22 Apr 2020 08:13:18: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (565 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:13:21: 3000000 INFO @ Wed, 22 Apr 2020 08:13:27: 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 08:13:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.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 08:13:32: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:13:32: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:13:34: 5000000 INFO @ Wed, 22 Apr 2020 08:13:35: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:13:35: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:13:35: #1 total tags in treatment: 2585049 INFO @ Wed, 22 Apr 2020 08:13:35: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:13:35: #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 08:13:35: #1 tags after filtering in treatment: 2131189 INFO @ Wed, 22 Apr 2020 08:13:35: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 22 Apr 2020 08:13:35: #1 finished! INFO @ Wed, 22 Apr 2020 08:13:35: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:13:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:13:35: #2 number of paired peaks: 207 WARNING @ Wed, 22 Apr 2020 08:13:35: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Wed, 22 Apr 2020 08:13:35: start model_add_line... INFO @ Wed, 22 Apr 2020 08:13:35: start X-correlation... INFO @ Wed, 22 Apr 2020 08:13:35: end of X-cor INFO @ Wed, 22 Apr 2020 08:13:36: #2 finished! INFO @ Wed, 22 Apr 2020 08:13:36: #2 predicted fragment length is 147 bps INFO @ Wed, 22 Apr 2020 08:13:36: #2 alternative fragment length(s) may be 2,147,161,181 bps INFO @ Wed, 22 Apr 2020 08:13:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.10_model.r WARNING @ Wed, 22 Apr 2020 08:13:36: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:13:36: #2 You may need to consider one of the other alternative d(s): 2,147,161,181 WARNING @ Wed, 22 Apr 2020 08:13:36: #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 08:13:36: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:13:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:13:39: 1000000 INFO @ Wed, 22 Apr 2020 08:13:41: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:13:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:13:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:13:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.10_summits.bed INFO @ Wed, 22 Apr 2020 08:13:43: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (342 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:13:47: 2000000 INFO @ Wed, 22 Apr 2020 08:13:54: 3000000 INFO @ Wed, 22 Apr 2020 08:14:02: 4000000 INFO @ Wed, 22 Apr 2020 08:14:09: 5000000 INFO @ Wed, 22 Apr 2020 08:14:10: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:14:10: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:14:10: #1 total tags in treatment: 2585049 INFO @ Wed, 22 Apr 2020 08:14:10: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:14:10: #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 08:14:11: #1 tags after filtering in treatment: 2131189 INFO @ Wed, 22 Apr 2020 08:14:11: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 22 Apr 2020 08:14:11: #1 finished! INFO @ Wed, 22 Apr 2020 08:14:11: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:14:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:14:11: #2 number of paired peaks: 207 WARNING @ Wed, 22 Apr 2020 08:14:11: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Wed, 22 Apr 2020 08:14:11: start model_add_line... INFO @ Wed, 22 Apr 2020 08:14:11: start X-correlation... INFO @ Wed, 22 Apr 2020 08:14:11: end of X-cor INFO @ Wed, 22 Apr 2020 08:14:11: #2 finished! INFO @ Wed, 22 Apr 2020 08:14:11: #2 predicted fragment length is 147 bps INFO @ Wed, 22 Apr 2020 08:14:11: #2 alternative fragment length(s) may be 2,147,161,181 bps INFO @ Wed, 22 Apr 2020 08:14:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.20_model.r WARNING @ Wed, 22 Apr 2020 08:14:11: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:14:11: #2 You may need to consider one of the other alternative d(s): 2,147,161,181 WARNING @ Wed, 22 Apr 2020 08:14:11: #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 08:14:11: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:14:11: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 08:14:16: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:14:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.20_peaks.xls BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 08:14:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:14:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874464/SRX5874464.20_summits.bed INFO @ Wed, 22 Apr 2020 08:14:18: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (162 records, 4 fields): 1 millis CompletedMACS2peakCalling