Job ID = 5790997 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,035,284 reads read : 10,070,568 reads written : 10,070,568 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: 00:02:29 5035284 reads; of these: 5035284 (100.00%) were paired; of these: 364199 (7.23%) aligned concordantly 0 times 3590625 (71.31%) aligned concordantly exactly 1 time 1080460 (21.46%) aligned concordantly >1 times ---- 364199 pairs aligned concordantly 0 times; of these: 2409 (0.66%) aligned discordantly 1 time ---- 361790 pairs aligned 0 times concordantly or discordantly; of these: 723580 mates make up the pairs; of these: 685393 (94.72%) aligned 0 times 23502 (3.25%) aligned exactly 1 time 14685 (2.03%) aligned >1 times 93.19% overall alignment rate Time searching: 00:02:29 Overall time: 00:02:29 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] 479249 / 4672482 = 0.1026 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 08:15:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.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 08:15:12: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:15:12: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:15:17: 1000000 INFO @ Wed, 22 Apr 2020 08:15:22: 2000000 INFO @ Wed, 22 Apr 2020 08:15:26: 3000000 INFO @ Wed, 22 Apr 2020 08:15:31: 4000000 INFO @ Wed, 22 Apr 2020 08:15:36: 5000000 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 08:15:41: 6000000 INFO @ Wed, 22 Apr 2020 08:15:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.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 08:15:42: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:15:42: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:15:46: 7000000 INFO @ Wed, 22 Apr 2020 08:15:48: 1000000 INFO @ Wed, 22 Apr 2020 08:15:51: 8000000 INFO @ Wed, 22 Apr 2020 08:15:53: #1 tag size is determined as 42 bps INFO @ Wed, 22 Apr 2020 08:15:53: #1 tag size = 42 INFO @ Wed, 22 Apr 2020 08:15:53: #1 total tags in treatment: 4191952 INFO @ Wed, 22 Apr 2020 08:15:53: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:15:53: #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 08:15:53: #1 tags after filtering in treatment: 3314471 INFO @ Wed, 22 Apr 2020 08:15:53: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 08:15:53: #1 finished! INFO @ Wed, 22 Apr 2020 08:15:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:15:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:15:53: #2 number of paired peaks: 144 WARNING @ Wed, 22 Apr 2020 08:15:53: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Wed, 22 Apr 2020 08:15:53: start model_add_line... INFO @ Wed, 22 Apr 2020 08:15:53: start X-correlation... INFO @ Wed, 22 Apr 2020 08:15:53: end of X-cor INFO @ Wed, 22 Apr 2020 08:15:53: #2 finished! INFO @ Wed, 22 Apr 2020 08:15:53: #2 predicted fragment length is 1 bps INFO @ Wed, 22 Apr 2020 08:15:53: #2 alternative fragment length(s) may be 1,60,104,133,155,162,206 bps INFO @ Wed, 22 Apr 2020 08:15:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.05_model.r WARNING @ Wed, 22 Apr 2020 08:15:53: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:15:53: #2 You may need to consider one of the other alternative d(s): 1,60,104,133,155,162,206 WARNING @ Wed, 22 Apr 2020 08:15:53: #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 08:15:53: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:15:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:15:54: 2000000 INFO @ Wed, 22 Apr 2020 08:15:58: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:15:59: 3000000 INFO @ Wed, 22 Apr 2020 08:16:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:16:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:16:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.05_summits.bed INFO @ Wed, 22 Apr 2020 08:16:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:16:05: 4000000 INFO @ Wed, 22 Apr 2020 08:16:10: 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 08:16:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.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 08:16:12: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:16:12: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:16:16: 6000000 INFO @ Wed, 22 Apr 2020 08:16:19: 1000000 INFO @ Wed, 22 Apr 2020 08:16:22: 7000000 INFO @ Wed, 22 Apr 2020 08:16:24: 2000000 INFO @ Wed, 22 Apr 2020 08:16:27: 8000000 INFO @ Wed, 22 Apr 2020 08:16:29: #1 tag size is determined as 42 bps INFO @ Wed, 22 Apr 2020 08:16:29: #1 tag size = 42 INFO @ Wed, 22 Apr 2020 08:16:29: #1 total tags in treatment: 4191952 INFO @ Wed, 22 Apr 2020 08:16:29: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:16:29: #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 08:16:30: #1 tags after filtering in treatment: 3314471 INFO @ Wed, 22 Apr 2020 08:16:30: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 08:16:30: #1 finished! INFO @ Wed, 22 Apr 2020 08:16:30: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:16:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:16:30: #2 number of paired peaks: 144 WARNING @ Wed, 22 Apr 2020 08:16:30: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Wed, 22 Apr 2020 08:16:30: start model_add_line... INFO @ Wed, 22 Apr 2020 08:16:30: start X-correlation... INFO @ Wed, 22 Apr 2020 08:16:30: end of X-cor INFO @ Wed, 22 Apr 2020 08:16:30: #2 finished! INFO @ Wed, 22 Apr 2020 08:16:30: #2 predicted fragment length is 1 bps INFO @ Wed, 22 Apr 2020 08:16:30: #2 alternative fragment length(s) may be 1,60,104,133,155,162,206 bps INFO @ Wed, 22 Apr 2020 08:16:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.10_model.r WARNING @ Wed, 22 Apr 2020 08:16:30: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:16:30: #2 You may need to consider one of the other alternative d(s): 1,60,104,133,155,162,206 WARNING @ Wed, 22 Apr 2020 08:16:30: #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 08:16:30: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:16:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:16:30: 3000000 INFO @ Wed, 22 Apr 2020 08:16:34: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:16:36: 4000000 INFO @ Wed, 22 Apr 2020 08:16:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:16:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:16:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.10_summits.bed INFO @ Wed, 22 Apr 2020 08:16:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:16:41: 5000000 INFO @ Wed, 22 Apr 2020 08:16:47: 6000000 INFO @ Wed, 22 Apr 2020 08:16:52: 7000000 INFO @ Wed, 22 Apr 2020 08:16:58: 8000000 INFO @ Wed, 22 Apr 2020 08:17:00: #1 tag size is determined as 42 bps INFO @ Wed, 22 Apr 2020 08:17:00: #1 tag size = 42 INFO @ Wed, 22 Apr 2020 08:17:00: #1 total tags in treatment: 4191952 INFO @ Wed, 22 Apr 2020 08:17:00: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:17:00: #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 08:17:00: #1 tags after filtering in treatment: 3314471 INFO @ Wed, 22 Apr 2020 08:17:00: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 08:17:00: #1 finished! INFO @ Wed, 22 Apr 2020 08:17:00: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:17:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:17:00: #2 number of paired peaks: 144 WARNING @ Wed, 22 Apr 2020 08:17:00: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Wed, 22 Apr 2020 08:17:00: start model_add_line... INFO @ Wed, 22 Apr 2020 08:17:00: start X-correlation... INFO @ Wed, 22 Apr 2020 08:17:00: end of X-cor INFO @ Wed, 22 Apr 2020 08:17:00: #2 finished! INFO @ Wed, 22 Apr 2020 08:17:00: #2 predicted fragment length is 1 bps INFO @ Wed, 22 Apr 2020 08:17:00: #2 alternative fragment length(s) may be 1,60,104,133,155,162,206 bps INFO @ Wed, 22 Apr 2020 08:17:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.20_model.r WARNING @ Wed, 22 Apr 2020 08:17:00: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:17:00: #2 You may need to consider one of the other alternative d(s): 1,60,104,133,155,162,206 WARNING @ Wed, 22 Apr 2020 08:17:00: #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 08:17:00: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:17:00: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 08:17:05: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:17:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:17:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:17:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874496/SRX5874496.20_summits.bed INFO @ Wed, 22 Apr 2020 08:17:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。