Job ID = 7108234 SRX = SRX7960941 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6453130 spots for SRR11359446/SRR11359446.sra Written 6453130 spots for SRR11359446/SRR11359446.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: 00:02:02 6453130 reads; of these: 6453130 (100.00%) were unpaired; of these: 965115 (14.96%) aligned 0 times 3250889 (50.38%) aligned exactly 1 time 2237126 (34.67%) aligned >1 times 85.04% overall alignment rate Time searching: 00:02:02 Overall time: 00:02:02 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_rmdupse_core] 3142730 / 5488015 = 0.5727 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 13:37:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960941/SRX7960941.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960941/SRX7960941.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960941/SRX7960941.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960941/SRX7960941.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 13:37:33: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:37:33: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:37:44: 1000000 INFO @ Wed, 22 Jul 2020 13:37:54: 2000000 INFO @ Wed, 22 Jul 2020 13:37:58: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:37:58: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:37:58: #1 total tags in treatment: 2345285 INFO @ Wed, 22 Jul 2020 13:37:58: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:37:58: #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 13:37:58: #1 tags after filtering in treatment: 2345285 INFO @ Wed, 22 Jul 2020 13:37:58: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:37:58: #1 finished! INFO @ Wed, 22 Jul 2020 13:37:58: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:37:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:37:58: #2 number of paired peaks: 179 WARNING @ Wed, 22 Jul 2020 13:37:58: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Wed, 22 Jul 2020 13:37:58: start model_add_line... INFO @ Wed, 22 Jul 2020 13:37:58: start X-correlation... INFO @ Wed, 22 Jul 2020 13:37:58: end of X-cor INFO @ Wed, 22 Jul 2020 13:37:58: #2 finished! INFO @ Wed, 22 Jul 2020 13:37:58: #2 predicted fragment length is 0 bps INFO @ Wed, 22 Jul 2020 13:37:58: #2 alternative fragment length(s) may be 0,17,33,74,89,125,167,198,221,251,280,287,309,325,337,390,407,425,467,489,506,528,549,584 bps INFO @ Wed, 22 Jul 2020 13:37:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960941/SRX7960941.05_model.r WARNING @ Wed, 22 Jul 2020 13:37:58: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:37:58: #2 You may need to consider one of the other alternative d(s): 0,17,33,74,89,125,167,198,221,251,280,287,309,325,337,390,407,425,467,489,506,528,549,584 WARNING @ Wed, 22 Jul 2020 13:37:58: #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 13:37:58: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:37:58: #3 Pre-compute pvalue-qvalue table... 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 13:38:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960941/SRX7960941.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960941/SRX7960941.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960941/SRX7960941.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960941/SRX7960941.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 13:38:03: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:38:03: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:38:11: 1000000 INFO @ Wed, 22 Jul 2020 13:38:19: 2000000 INFO @ Wed, 22 Jul 2020 13:38:22: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:38:22: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:38:22: #1 total tags in treatment: 2345285 INFO @ Wed, 22 Jul 2020 13:38:22: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:38:22: #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 13:38:22: #1 tags after filtering in treatment: 2345285 INFO @ Wed, 22 Jul 2020 13:38:22: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:38:22: #1 finished! INFO @ Wed, 22 Jul 2020 13:38:22: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:38:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:38:22: #2 number of paired peaks: 179 WARNING @ Wed, 22 Jul 2020 13:38:22: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Wed, 22 Jul 2020 13:38:22: start model_add_line... INFO @ Wed, 22 Jul 2020 13:38:22: start X-correlation... INFO @ Wed, 22 Jul 2020 13:38:22: end of X-cor INFO @ Wed, 22 Jul 2020 13:38:22: #2 finished! INFO @ Wed, 22 Jul 2020 13:38:22: #2 predicted fragment length is 0 bps INFO @ Wed, 22 Jul 2020 13:38:22: #2 alternative fragment length(s) may be 0,17,33,74,89,125,167,198,221,251,280,287,309,325,337,390,407,425,467,489,506,528,549,584 bps INFO @ Wed, 22 Jul 2020 13:38:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960941/SRX7960941.10_model.r WARNING @ Wed, 22 Jul 2020 13:38:22: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:38:22: #2 You may need to consider one of the other alternative d(s): 0,17,33,74,89,125,167,198,221,251,280,287,309,325,337,390,407,425,467,489,506,528,549,584 WARNING @ Wed, 22 Jul 2020 13:38:22: #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 13:38:22: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:38:22: #3 Pre-compute pvalue-qvalue table... 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 Jul 2020 13:38:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960941/SRX7960941.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960941/SRX7960941.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960941/SRX7960941.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960941/SRX7960941.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 13:38:33: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:38:33: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:38:43: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 /var/spool/uge/at142/job_scripts/7108234: line 297: 112050 Terminated MACS $i /var/spool/uge/at142/job_scripts/7108234: line 297: 112716 Terminated MACS $i /var/spool/uge/at142/job_scripts/7108234: line 297: 112962 Terminated MACS $i ls: cannot access SRX7960941.05.bed: No such file or directory mv: cannot stat ‘SRX7960941.05.bed’: No such file or directory mv: cannot stat ‘SRX7960941.05.bb’: No such file or directory ls: cannot access SRX7960941.10.bed: No such file or directory mv: cannot stat ‘SRX7960941.10.bed’: No such file or directory mv: cannot stat ‘SRX7960941.10.bb’: No such file or directory ls: cannot access SRX7960941.20.bed: No such file or directory mv: cannot stat ‘SRX7960941.20.bed’: No such file or directory mv: cannot stat ‘SRX7960941.20.bb’: No such file or directory