Job ID = 5790854 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,901,689 reads read : 7,803,378 reads written : 7,803,378 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: 00:01:48 3901689 reads; of these: 3901689 (100.00%) were paired; of these: 186843 (4.79%) aligned concordantly 0 times 3175490 (81.39%) aligned concordantly exactly 1 time 539356 (13.82%) aligned concordantly >1 times ---- 186843 pairs aligned concordantly 0 times; of these: 4706 (2.52%) aligned discordantly 1 time ---- 182137 pairs aligned 0 times concordantly or discordantly; of these: 364274 mates make up the pairs; of these: 329970 (90.58%) aligned 0 times 29929 (8.22%) aligned exactly 1 time 4375 (1.20%) aligned >1 times 95.77% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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] 76664 / 3716476 = 0.0206 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 07:59:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.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 07:59:22: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:59:22: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:59:26: 1000000 INFO @ Wed, 22 Apr 2020 07:59:31: 2000000 INFO @ Wed, 22 Apr 2020 07:59:35: 3000000 INFO @ Wed, 22 Apr 2020 07:59:40: 4000000 INFO @ Wed, 22 Apr 2020 07:59:44: 5000000 INFO @ Wed, 22 Apr 2020 07:59:48: 6000000 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 07:59:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.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 07:59:52: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:59:52: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:59:53: 7000000 INFO @ Wed, 22 Apr 2020 07:59:55: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 07:59:55: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 07:59:55: #1 total tags in treatment: 3638542 INFO @ Wed, 22 Apr 2020 07:59:55: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:59:55: #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 07:59:55: #1 tags after filtering in treatment: 2884797 INFO @ Wed, 22 Apr 2020 07:59:55: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 07:59:55: #1 finished! INFO @ Wed, 22 Apr 2020 07:59:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:59:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:59:55: #2 number of paired peaks: 160 WARNING @ Wed, 22 Apr 2020 07:59:55: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Wed, 22 Apr 2020 07:59:55: start model_add_line... INFO @ Wed, 22 Apr 2020 07:59:55: start X-correlation... INFO @ Wed, 22 Apr 2020 07:59:55: end of X-cor INFO @ Wed, 22 Apr 2020 07:59:55: #2 finished! INFO @ Wed, 22 Apr 2020 07:59:55: #2 predicted fragment length is 2 bps INFO @ Wed, 22 Apr 2020 07:59:55: #2 alternative fragment length(s) may be 2 bps INFO @ Wed, 22 Apr 2020 07:59:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.05_model.r WARNING @ Wed, 22 Apr 2020 07:59:55: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:59:55: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Wed, 22 Apr 2020 07:59:55: #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 07:59:55: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:59:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:59:57: 1000000 INFO @ Wed, 22 Apr 2020 07:59:59: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:00:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:00:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:00:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.05_summits.bed INFO @ Wed, 22 Apr 2020 08:00:01: Done! pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:00:02: 2000000 INFO @ Wed, 22 Apr 2020 08:00:07: 3000000 INFO @ Wed, 22 Apr 2020 08:00:12: 4000000 INFO @ Wed, 22 Apr 2020 08:00:16: 5000000 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 08:00:21: 6000000 INFO @ Wed, 22 Apr 2020 08:00:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.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 08:00:22: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:00:22: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:00:26: 7000000 INFO @ Wed, 22 Apr 2020 08:00:27: 1000000 INFO @ Wed, 22 Apr 2020 08:00:28: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 08:00:28: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 08:00:28: #1 total tags in treatment: 3638542 INFO @ Wed, 22 Apr 2020 08:00:28: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:00:28: #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 08:00:28: #1 tags after filtering in treatment: 2884797 INFO @ Wed, 22 Apr 2020 08:00:28: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 08:00:28: #1 finished! INFO @ Wed, 22 Apr 2020 08:00:28: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:00:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:00:28: #2 number of paired peaks: 160 WARNING @ Wed, 22 Apr 2020 08:00:28: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Wed, 22 Apr 2020 08:00:28: start model_add_line... INFO @ Wed, 22 Apr 2020 08:00:28: start X-correlation... INFO @ Wed, 22 Apr 2020 08:00:28: end of X-cor INFO @ Wed, 22 Apr 2020 08:00:28: #2 finished! INFO @ Wed, 22 Apr 2020 08:00:28: #2 predicted fragment length is 2 bps INFO @ Wed, 22 Apr 2020 08:00:28: #2 alternative fragment length(s) may be 2 bps INFO @ Wed, 22 Apr 2020 08:00:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.10_model.r WARNING @ Wed, 22 Apr 2020 08:00:28: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:00:28: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Wed, 22 Apr 2020 08:00:28: #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 08:00:28: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:00:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:00:32: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:00:32: 2000000 INFO @ Wed, 22 Apr 2020 08:00:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:00:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:00:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.10_summits.bed INFO @ Wed, 22 Apr 2020 08:00:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:00:37: 3000000 INFO @ Wed, 22 Apr 2020 08:00:42: 4000000 INFO @ Wed, 22 Apr 2020 08:00:47: 5000000 INFO @ Wed, 22 Apr 2020 08:00:52: 6000000 INFO @ Wed, 22 Apr 2020 08:00:56: 7000000 INFO @ Wed, 22 Apr 2020 08:00:58: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 08:00:58: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 08:00:58: #1 total tags in treatment: 3638542 INFO @ Wed, 22 Apr 2020 08:00:58: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:00:58: #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 08:00:58: #1 tags after filtering in treatment: 2884797 INFO @ Wed, 22 Apr 2020 08:00:58: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 08:00:58: #1 finished! INFO @ Wed, 22 Apr 2020 08:00:58: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:00:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:00:58: #2 number of paired peaks: 160 WARNING @ Wed, 22 Apr 2020 08:00:58: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Wed, 22 Apr 2020 08:00:58: start model_add_line... INFO @ Wed, 22 Apr 2020 08:00:58: start X-correlation... INFO @ Wed, 22 Apr 2020 08:00:58: end of X-cor INFO @ Wed, 22 Apr 2020 08:00:58: #2 finished! INFO @ Wed, 22 Apr 2020 08:00:58: #2 predicted fragment length is 2 bps INFO @ Wed, 22 Apr 2020 08:00:58: #2 alternative fragment length(s) may be 2 bps INFO @ Wed, 22 Apr 2020 08:00:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.20_model.r WARNING @ Wed, 22 Apr 2020 08:00:58: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:00:58: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Wed, 22 Apr 2020 08:00:58: #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 08:00:58: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:00:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:01:02: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:01:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:01:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:01:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521502/SRX5521502.20_summits.bed INFO @ Wed, 22 Apr 2020 08:01:04: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。