Job ID = 14520794 SRX = SRX8245521 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5601027 spots for SRR11684732/SRR11684732.sra Written 5601027 spots for SRR11684732/SRR11684732.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: 00:03:50 5601027 reads; of these: 5601027 (100.00%) were paired; of these: 3144734 (56.15%) aligned concordantly 0 times 2171933 (38.78%) aligned concordantly exactly 1 time 284360 (5.08%) aligned concordantly >1 times ---- 3144734 pairs aligned concordantly 0 times; of these: 39977 (1.27%) aligned discordantly 1 time ---- 3104757 pairs aligned 0 times concordantly or discordantly; of these: 6209514 mates make up the pairs; of these: 4030914 (64.92%) aligned 0 times 1890815 (30.45%) aligned exactly 1 time 287785 (4.63%) aligned >1 times 64.02% overall alignment rate Time searching: 00:03:50 Overall time: 00:03:50 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] 105796 / 2495879 = 0.0424 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:59:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245521/SRX8245521.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245521/SRX8245521.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245521/SRX8245521.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245521/SRX8245521.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 @ Sat, 15 Jan 2022 19:59:06: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:59:06: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:59:14: 1000000 INFO @ Sat, 15 Jan 2022 19:59:21: 2000000 INFO @ Sat, 15 Jan 2022 19:59:27: 3000000 INFO @ Sat, 15 Jan 2022 19:59:32: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:59:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245521/SRX8245521.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245521/SRX8245521.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245521/SRX8245521.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245521/SRX8245521.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 @ Sat, 15 Jan 2022 19:59:36: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:59:36: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:59:39: 5000000 INFO @ Sat, 15 Jan 2022 19:59:42: 1000000 INFO @ Sat, 15 Jan 2022 19:59:45: 6000000 INFO @ Sat, 15 Jan 2022 19:59:49: 2000000 INFO @ Sat, 15 Jan 2022 19:59:51: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:59:51: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:59:51: #1 total tags in treatment: 2351209 INFO @ Sat, 15 Jan 2022 19:59:51: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:59:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:59:51: #1 tags after filtering in treatment: 1687542 INFO @ Sat, 15 Jan 2022 19:59:51: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 19:59:51: #1 finished! INFO @ Sat, 15 Jan 2022 19:59:51: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:59:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:59:51: #2 number of paired peaks: 175 WARNING @ Sat, 15 Jan 2022 19:59:51: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 15 Jan 2022 19:59:51: start model_add_line... INFO @ Sat, 15 Jan 2022 19:59:51: start X-correlation... INFO @ Sat, 15 Jan 2022 19:59:51: end of X-cor INFO @ Sat, 15 Jan 2022 19:59:51: #2 finished! INFO @ Sat, 15 Jan 2022 19:59:51: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:59:51: #2 alternative fragment length(s) may be 0,62,93,108,113,133,154,175,202,224,243,250,262,277,344,389,498,521,565,588 bps INFO @ Sat, 15 Jan 2022 19:59:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245521/SRX8245521.05_model.r WARNING @ Sat, 15 Jan 2022 19:59:51: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:59:51: #2 You may need to consider one of the other alternative d(s): 0,62,93,108,113,133,154,175,202,224,243,250,262,277,344,389,498,521,565,588 WARNING @ Sat, 15 Jan 2022 19:59:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 19:59:51: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:59:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:59:55: 3000000 INFO @ Sat, 15 Jan 2022 20:00:00: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:00:06: 5000000 INFO @ Sat, 15 Jan 2022 20:00:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245521/SRX8245521.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245521/SRX8245521.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245521/SRX8245521.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245521/SRX8245521.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 @ Sat, 15 Jan 2022 20:00:06: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:00:06: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:00:12: 6000000 INFO @ Sat, 15 Jan 2022 20:00:12: 1000000 INFO @ Sat, 15 Jan 2022 20:00:18: 2000000 INFO @ Sat, 15 Jan 2022 20:00:18: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:00:18: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:00:18: #1 total tags in treatment: 2351209 INFO @ Sat, 15 Jan 2022 20:00:18: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:00:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:00:18: #1 tags after filtering in treatment: 1687542 INFO @ Sat, 15 Jan 2022 20:00:18: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 20:00:18: #1 finished! INFO @ Sat, 15 Jan 2022 20:00:18: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:00:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:00:18: #2 number of paired peaks: 175 WARNING @ Sat, 15 Jan 2022 20:00:18: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 15 Jan 2022 20:00:18: start model_add_line... INFO @ Sat, 15 Jan 2022 20:00:18: start X-correlation... INFO @ Sat, 15 Jan 2022 20:00:18: end of X-cor INFO @ Sat, 15 Jan 2022 20:00:18: #2 finished! INFO @ Sat, 15 Jan 2022 20:00:18: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:00:18: #2 alternative fragment length(s) may be 0,62,93,108,113,133,154,175,202,224,243,250,262,277,344,389,498,521,565,588 bps INFO @ Sat, 15 Jan 2022 20:00:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245521/SRX8245521.10_model.r WARNING @ Sat, 15 Jan 2022 20:00:18: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:00:18: #2 You may need to consider one of the other alternative d(s): 0,62,93,108,113,133,154,175,202,224,243,250,262,277,344,389,498,521,565,588 WARNING @ Sat, 15 Jan 2022 20:00:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 20:00:18: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:00:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:00:23: 3000000 INFO @ Sat, 15 Jan 2022 20:00:28: 4000000 INFO @ Sat, 15 Jan 2022 20:00:34: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:00:39: 6000000 INFO @ Sat, 15 Jan 2022 20:00:44: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:00:44: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:00:44: #1 total tags in treatment: 2351209 INFO @ Sat, 15 Jan 2022 20:00:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:00:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:00:44: #1 tags after filtering in treatment: 1687542 INFO @ Sat, 15 Jan 2022 20:00:44: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 20:00:44: #1 finished! INFO @ Sat, 15 Jan 2022 20:00:44: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:00:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:00:44: #2 number of paired peaks: 175 WARNING @ Sat, 15 Jan 2022 20:00:44: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 15 Jan 2022 20:00:44: start model_add_line... INFO @ Sat, 15 Jan 2022 20:00:44: start X-correlation... INFO @ Sat, 15 Jan 2022 20:00:44: end of X-cor INFO @ Sat, 15 Jan 2022 20:00:44: #2 finished! INFO @ Sat, 15 Jan 2022 20:00:44: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:00:44: #2 alternative fragment length(s) may be 0,62,93,108,113,133,154,175,202,224,243,250,262,277,344,389,498,521,565,588 bps INFO @ Sat, 15 Jan 2022 20:00:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245521/SRX8245521.20_model.r WARNING @ Sat, 15 Jan 2022 20:00:44: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:00:44: #2 You may need to consider one of the other alternative d(s): 0,62,93,108,113,133,154,175,202,224,243,250,262,277,344,389,498,521,565,588 WARNING @ Sat, 15 Jan 2022 20:00:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 20:00:44: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:00:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/it010/job_scripts/14520794: line 297: 942 Terminated MACS $i /var/spool/uge/it010/job_scripts/14520794: line 297: 6936 Terminated MACS $i /var/spool/uge/it010/job_scripts/14520794: line 297: 8088 Terminated MACS $i ls: cannot access SRX8245521.05.bed: No such file or directory mv: cannot stat ‘SRX8245521.05.bed’: No such file or directory mv: cannot stat ‘SRX8245521.05.bb’: No such file or directory ls: cannot access SRX8245521.10.bed: No such file or directory mv: cannot stat ‘SRX8245521.10.bed’: No such file or directory mv: cannot stat ‘SRX8245521.10.bb’: No such file or directory ls: cannot access SRX8245521.20.bed: No such file or directory mv: cannot stat ‘SRX8245521.20.bed’: No such file or directory mv: cannot stat ‘SRX8245521.20.bb’: No such file or directory