Job ID = 7108638 SRX = SRX7960947 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 11796609 spots for SRR11359452/SRR11359452.sra Written 11796609 spots for SRR11359452/SRR11359452.sra 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: 00:04:41 11796609 reads; of these: 11796609 (100.00%) were unpaired; of these: 1685855 (14.29%) aligned 0 times 6266495 (53.12%) aligned exactly 1 time 3844259 (32.59%) aligned >1 times 85.71% overall alignment rate Time searching: 00:04:41 Overall time: 00:04:41 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_sort_core] merging from 8 files... [bam_rmdupse_core] 6571671 / 10110754 = 0.6500 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 Jul 2020 13:48:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.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 Jul 2020 13:48:04: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:48:04: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:48:11: 1000000 INFO @ Wed, 22 Jul 2020 13:48:17: 2000000 INFO @ Wed, 22 Jul 2020 13:48:24: 3000000 INFO @ Wed, 22 Jul 2020 13:48:28: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:48:28: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:48:28: #1 total tags in treatment: 3539083 INFO @ Wed, 22 Jul 2020 13:48:28: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:48:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:48:28: #1 tags after filtering in treatment: 3539083 INFO @ Wed, 22 Jul 2020 13:48:28: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:48:28: #1 finished! INFO @ Wed, 22 Jul 2020 13:48:28: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:48:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:48:28: #2 number of paired peaks: 256 WARNING @ Wed, 22 Jul 2020 13:48:28: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Wed, 22 Jul 2020 13:48:28: start model_add_line... INFO @ Wed, 22 Jul 2020 13:48:28: start X-correlation... INFO @ Wed, 22 Jul 2020 13:48:28: end of X-cor INFO @ Wed, 22 Jul 2020 13:48:28: #2 finished! INFO @ Wed, 22 Jul 2020 13:48:28: #2 predicted fragment length is 1 bps INFO @ Wed, 22 Jul 2020 13:48:28: #2 alternative fragment length(s) may be 1,95,109,137,157,177,194,215,231,259,312,330,361,385,388,551,573 bps INFO @ Wed, 22 Jul 2020 13:48:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.05_model.r WARNING @ Wed, 22 Jul 2020 13:48:28: #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 Jul 2020 13:48:28: #2 You may need to consider one of the other alternative d(s): 1,95,109,137,157,177,194,215,231,259,312,330,361,385,388,551,573 WARNING @ Wed, 22 Jul 2020 13:48:28: #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 Jul 2020 13:48:28: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:48:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:48:32: #3 Call peaks for each chromosome... 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 Jul 2020 13:48:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.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 Jul 2020 13:48:34: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:48:34: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:48:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.05_peaks.xls INFO @ Wed, 22 Jul 2020 13:48:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:48:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.05_summits.bed INFO @ Wed, 22 Jul 2020 13:48:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 13:48:41: 1000000 INFO @ Wed, 22 Jul 2020 13:48:47: 2000000 INFO @ Wed, 22 Jul 2020 13:48:54: 3000000 INFO @ Wed, 22 Jul 2020 13:48:58: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:48:58: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:48:58: #1 total tags in treatment: 3539083 INFO @ Wed, 22 Jul 2020 13:48:58: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:48:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:48:58: #1 tags after filtering in treatment: 3539083 INFO @ Wed, 22 Jul 2020 13:48:58: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:48:58: #1 finished! INFO @ Wed, 22 Jul 2020 13:48:58: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:48:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:48:58: #2 number of paired peaks: 256 WARNING @ Wed, 22 Jul 2020 13:48:58: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Wed, 22 Jul 2020 13:48:58: start model_add_line... INFO @ Wed, 22 Jul 2020 13:48:58: start X-correlation... INFO @ Wed, 22 Jul 2020 13:48:58: end of X-cor INFO @ Wed, 22 Jul 2020 13:48:58: #2 finished! INFO @ Wed, 22 Jul 2020 13:48:58: #2 predicted fragment length is 1 bps INFO @ Wed, 22 Jul 2020 13:48:58: #2 alternative fragment length(s) may be 1,95,109,137,157,177,194,215,231,259,312,330,361,385,388,551,573 bps INFO @ Wed, 22 Jul 2020 13:48:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.10_model.r WARNING @ Wed, 22 Jul 2020 13:48:58: #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 Jul 2020 13:48:58: #2 You may need to consider one of the other alternative d(s): 1,95,109,137,157,177,194,215,231,259,312,330,361,385,388,551,573 WARNING @ Wed, 22 Jul 2020 13:48:58: #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 Jul 2020 13:48:58: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:48:58: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... INFO @ Wed, 22 Jul 2020 13:49:02: #3 Call peaks for each chromosome... 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 Jul 2020 13:49:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.10_peaks.xls INFO @ Wed, 22 Jul 2020 13:49:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:49:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.10_summits.bed INFO @ Wed, 22 Jul 2020 13:49:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 13:49:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.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 Jul 2020 13:49:05: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:49:05: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:49:12: 1000000 INFO @ Wed, 22 Jul 2020 13:49:19: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 13:49:25: 3000000 INFO @ Wed, 22 Jul 2020 13:49:29: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:49:29: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:49:29: #1 total tags in treatment: 3539083 INFO @ Wed, 22 Jul 2020 13:49:29: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:49:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:49:29: #1 tags after filtering in treatment: 3539083 INFO @ Wed, 22 Jul 2020 13:49:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:49:29: #1 finished! INFO @ Wed, 22 Jul 2020 13:49:29: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:49:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:49:29: #2 number of paired peaks: 256 WARNING @ Wed, 22 Jul 2020 13:49:29: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Wed, 22 Jul 2020 13:49:29: start model_add_line... INFO @ Wed, 22 Jul 2020 13:49:29: start X-correlation... INFO @ Wed, 22 Jul 2020 13:49:29: end of X-cor INFO @ Wed, 22 Jul 2020 13:49:29: #2 finished! INFO @ Wed, 22 Jul 2020 13:49:29: #2 predicted fragment length is 1 bps INFO @ Wed, 22 Jul 2020 13:49:29: #2 alternative fragment length(s) may be 1,95,109,137,157,177,194,215,231,259,312,330,361,385,388,551,573 bps INFO @ Wed, 22 Jul 2020 13:49:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.20_model.r WARNING @ Wed, 22 Jul 2020 13:49:29: #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 Jul 2020 13:49:29: #2 You may need to consider one of the other alternative d(s): 1,95,109,137,157,177,194,215,231,259,312,330,361,385,388,551,573 WARNING @ Wed, 22 Jul 2020 13:49:29: #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 Jul 2020 13:49:29: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:49:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 13:49:34: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:49:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.20_peaks.xls INFO @ Wed, 22 Jul 2020 13:49:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:49:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960947/SRX7960947.20_summits.bed INFO @ Wed, 22 Jul 2020 13:49:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling