Job ID = 14520433 SRX = SRX11781028 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8805101 spots for SRR15480971/SRR15480971.sra Written 8805101 spots for SRR15480971/SRR15480971.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: 00:06:37 8805101 reads; of these: 8805101 (100.00%) were paired; of these: 1851747 (21.03%) aligned concordantly 0 times 6311953 (71.69%) aligned concordantly exactly 1 time 641401 (7.28%) aligned concordantly >1 times ---- 1851747 pairs aligned concordantly 0 times; of these: 135008 (7.29%) aligned discordantly 1 time ---- 1716739 pairs aligned 0 times concordantly or discordantly; of these: 3433478 mates make up the pairs; of these: 2736293 (79.69%) aligned 0 times 654678 (19.07%) aligned exactly 1 time 42507 (1.24%) aligned >1 times 84.46% overall alignment rate Time searching: 00:06:37 Overall time: 00:06:37 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_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] 2383600 / 7070999 = 0.3371 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 19:16:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781028/SRX11781028.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781028/SRX11781028.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781028/SRX11781028.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781028/SRX11781028.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 19:16:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:16:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:16:54: 1000000 INFO @ Sat, 15 Jan 2022 19:16:59: 2000000 INFO @ Sat, 15 Jan 2022 19:17:04: 3000000 INFO @ Sat, 15 Jan 2022 19:17:09: 4000000 INFO @ Sat, 15 Jan 2022 19:17:13: 5000000 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 19:17:18: 6000000 INFO @ Sat, 15 Jan 2022 19:17:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781028/SRX11781028.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781028/SRX11781028.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781028/SRX11781028.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781028/SRX11781028.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 19:17:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:17:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:17:23: 7000000 INFO @ Sat, 15 Jan 2022 19:17:25: 1000000 INFO @ Sat, 15 Jan 2022 19:17:28: 8000000 INFO @ Sat, 15 Jan 2022 19:17:30: 2000000 INFO @ Sat, 15 Jan 2022 19:17:34: 9000000 INFO @ Sat, 15 Jan 2022 19:17:35: 3000000 INFO @ Sat, 15 Jan 2022 19:17:39: 10000000 INFO @ Sat, 15 Jan 2022 19:17:40: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:17:40: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:17:40: #1 total tags in treatment: 4614505 INFO @ Sat, 15 Jan 2022 19:17:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:17:40: #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 19:17:40: #1 tags after filtering in treatment: 2465574 INFO @ Sat, 15 Jan 2022 19:17:40: #1 Redundant rate of treatment: 0.47 INFO @ Sat, 15 Jan 2022 19:17:40: #1 finished! INFO @ Sat, 15 Jan 2022 19:17:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:17:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:17:40: #2 number of paired peaks: 177 WARNING @ Sat, 15 Jan 2022 19:17:40: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sat, 15 Jan 2022 19:17:40: start model_add_line... INFO @ Sat, 15 Jan 2022 19:17:40: start X-correlation... INFO @ Sat, 15 Jan 2022 19:17:40: end of X-cor INFO @ Sat, 15 Jan 2022 19:17:40: #2 finished! INFO @ Sat, 15 Jan 2022 19:17:40: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:17:40: #2 alternative fragment length(s) may be 0,21,67,82,85,129,145,225,239,299,379,401,459,480,504,545,588 bps INFO @ Sat, 15 Jan 2022 19:17:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781028/SRX11781028.05_model.r WARNING @ Sat, 15 Jan 2022 19:17:40: #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 19:17:40: #2 You may need to consider one of the other alternative d(s): 0,21,67,82,85,129,145,225,239,299,379,401,459,480,504,545,588 WARNING @ Sat, 15 Jan 2022 19:17:40: #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 19:17:40: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:17:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:17:40: 4000000 INFO @ Sat, 15 Jan 2022 19:17:45: 5000000 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 19:17:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781028/SRX11781028.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781028/SRX11781028.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781028/SRX11781028.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781028/SRX11781028.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 19:17:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:17:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:17:50: 6000000 INFO @ Sat, 15 Jan 2022 19:17:55: 1000000 INFO @ Sat, 15 Jan 2022 19:17:55: 7000000 INFO @ Sat, 15 Jan 2022 19:18:00: 2000000 INFO @ Sat, 15 Jan 2022 19:18:00: 8000000 INFO @ Sat, 15 Jan 2022 19:18:05: 3000000 INFO @ Sat, 15 Jan 2022 19:18:05: 9000000 INFO @ Sat, 15 Jan 2022 19:18:10: 4000000 INFO @ Sat, 15 Jan 2022 19:18:10: 10000000 INFO @ Sat, 15 Jan 2022 19:18:11: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:18:11: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:18:11: #1 total tags in treatment: 4614505 INFO @ Sat, 15 Jan 2022 19:18:11: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:18:11: #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 19:18:11: #1 tags after filtering in treatment: 2465574 INFO @ Sat, 15 Jan 2022 19:18:11: #1 Redundant rate of treatment: 0.47 INFO @ Sat, 15 Jan 2022 19:18:11: #1 finished! INFO @ Sat, 15 Jan 2022 19:18:11: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:18:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:18:11: #2 number of paired peaks: 177 WARNING @ Sat, 15 Jan 2022 19:18:11: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sat, 15 Jan 2022 19:18:11: start model_add_line... INFO @ Sat, 15 Jan 2022 19:18:11: start X-correlation... INFO @ Sat, 15 Jan 2022 19:18:11: end of X-cor INFO @ Sat, 15 Jan 2022 19:18:11: #2 finished! INFO @ Sat, 15 Jan 2022 19:18:11: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:18:11: #2 alternative fragment length(s) may be 0,21,67,82,85,129,145,225,239,299,379,401,459,480,504,545,588 bps INFO @ Sat, 15 Jan 2022 19:18:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781028/SRX11781028.10_model.r WARNING @ Sat, 15 Jan 2022 19:18:11: #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 19:18:11: #2 You may need to consider one of the other alternative d(s): 0,21,67,82,85,129,145,225,239,299,379,401,459,480,504,545,588 WARNING @ Sat, 15 Jan 2022 19:18:11: #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 19:18:11: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:18:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:18:15: 5000000 INFO @ Sat, 15 Jan 2022 19:18:19: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:18:24: 7000000 INFO @ Sat, 15 Jan 2022 19:18:29: 8000000 BigWig に変換しました。 /var/spool/uge/at157/job_scripts/14520433: line 297: 100245 Terminated MACS $i /var/spool/uge/at157/job_scripts/14520433: line 297: 100381 Terminated MACS $i /var/spool/uge/at157/job_scripts/14520433: line 297: 100539 Terminated MACS $i ls: cannot access SRX11781028.05.bed: No such file or directory mv: cannot stat ‘SRX11781028.05.bed’: No such file or directory mv: cannot stat ‘SRX11781028.05.bb’: No such file or directory ls: cannot access SRX11781028.10.bed: No such file or directory mv: cannot stat ‘SRX11781028.10.bed’: No such file or directory mv: cannot stat ‘SRX11781028.10.bb’: No such file or directory ls: cannot access SRX11781028.20.bed: No such file or directory mv: cannot stat ‘SRX11781028.20.bed’: No such file or directory mv: cannot stat ‘SRX11781028.20.bb’: No such file or directory