Job ID = 14520823 SRX = SRX8245530 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8540093 spots for SRR11684741/SRR11684741.sra Written 8540093 spots for SRR11684741/SRR11684741.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: 00:07:07 8540093 reads; of these: 8540093 (100.00%) were paired; of these: 5123987 (60.00%) aligned concordantly 0 times 3166170 (37.07%) aligned concordantly exactly 1 time 249936 (2.93%) aligned concordantly >1 times ---- 5123987 pairs aligned concordantly 0 times; of these: 105214 (2.05%) aligned discordantly 1 time ---- 5018773 pairs aligned 0 times concordantly or discordantly; of these: 10037546 mates make up the pairs; of these: 6865399 (68.40%) aligned 0 times 2847270 (28.37%) aligned exactly 1 time 324877 (3.24%) aligned >1 times 59.80% overall alignment rate Time searching: 00:07:07 Overall time: 00:07:07 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] 287243 / 3520640 = 0.0816 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 20:07:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245530/SRX8245530.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245530/SRX8245530.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245530/SRX8245530.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245530/SRX8245530.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 20:07:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:07:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:07:47: 1000000 INFO @ Sat, 15 Jan 2022 20:07:52: 2000000 INFO @ Sat, 15 Jan 2022 20:07:57: 3000000 INFO @ Sat, 15 Jan 2022 20:08:02: 4000000 INFO @ Sat, 15 Jan 2022 20:08:07: 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 20:08:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245530/SRX8245530.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245530/SRX8245530.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245530/SRX8245530.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245530/SRX8245530.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 20:08:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:08:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:08:12: 6000000 INFO @ Sat, 15 Jan 2022 20:08:17: 1000000 INFO @ Sat, 15 Jan 2022 20:08:17: 7000000 INFO @ Sat, 15 Jan 2022 20:08:23: 2000000 INFO @ Sat, 15 Jan 2022 20:08:23: 8000000 INFO @ Sat, 15 Jan 2022 20:08:28: 3000000 INFO @ Sat, 15 Jan 2022 20:08:29: 9000000 INFO @ Sat, 15 Jan 2022 20:08:32: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:08:32: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:08:32: #1 total tags in treatment: 3132552 INFO @ Sat, 15 Jan 2022 20:08:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:08:32: #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 20:08:32: #1 tags after filtering in treatment: 2093495 INFO @ Sat, 15 Jan 2022 20:08:32: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 20:08:32: #1 finished! INFO @ Sat, 15 Jan 2022 20:08:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:08:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:08:32: #2 number of paired peaks: 169 WARNING @ Sat, 15 Jan 2022 20:08:32: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 15 Jan 2022 20:08:32: start model_add_line... INFO @ Sat, 15 Jan 2022 20:08:32: start X-correlation... INFO @ Sat, 15 Jan 2022 20:08:32: end of X-cor INFO @ Sat, 15 Jan 2022 20:08:32: #2 finished! INFO @ Sat, 15 Jan 2022 20:08:32: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:08:32: #2 alternative fragment length(s) may be 0,45,79,114,129,173,192,209,225,243,296,320,338,358,386,438,450,477,484,530,543,547,570,583,598 bps INFO @ Sat, 15 Jan 2022 20:08:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245530/SRX8245530.05_model.r WARNING @ Sat, 15 Jan 2022 20:08:32: #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 20:08:32: #2 You may need to consider one of the other alternative d(s): 0,45,79,114,129,173,192,209,225,243,296,320,338,358,386,438,450,477,484,530,543,547,570,583,598 WARNING @ Sat, 15 Jan 2022 20:08:32: #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 20:08:32: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:08:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:08:33: 4000000 INFO @ Sat, 15 Jan 2022 20:08:39: 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 20:08:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245530/SRX8245530.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245530/SRX8245530.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245530/SRX8245530.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245530/SRX8245530.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 20:08:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:08:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:08:45: 6000000 INFO @ Sat, 15 Jan 2022 20:08:47: 1000000 INFO @ Sat, 15 Jan 2022 20:08:50: 7000000 INFO @ Sat, 15 Jan 2022 20:08:52: 2000000 INFO @ Sat, 15 Jan 2022 20:08:56: 8000000 INFO @ Sat, 15 Jan 2022 20:08:56: 3000000 INFO @ Sat, 15 Jan 2022 20:09:01: 4000000 INFO @ Sat, 15 Jan 2022 20:09:02: 9000000 INFO @ Sat, 15 Jan 2022 20:09:06: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:09:06: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:09:06: #1 total tags in treatment: 3132552 INFO @ Sat, 15 Jan 2022 20:09:06: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:09:06: #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 20:09:06: #1 tags after filtering in treatment: 2093495 INFO @ Sat, 15 Jan 2022 20:09:06: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 20:09:06: #1 finished! INFO @ Sat, 15 Jan 2022 20:09:06: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:09:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:09:06: #2 number of paired peaks: 169 WARNING @ Sat, 15 Jan 2022 20:09:06: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 15 Jan 2022 20:09:06: start model_add_line... INFO @ Sat, 15 Jan 2022 20:09:06: start X-correlation... INFO @ Sat, 15 Jan 2022 20:09:06: end of X-cor INFO @ Sat, 15 Jan 2022 20:09:06: #2 finished! INFO @ Sat, 15 Jan 2022 20:09:06: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:09:06: #2 alternative fragment length(s) may be 0,45,79,114,129,173,192,209,225,243,296,320,338,358,386,438,450,477,484,530,543,547,570,583,598 bps INFO @ Sat, 15 Jan 2022 20:09:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245530/SRX8245530.10_model.r WARNING @ Sat, 15 Jan 2022 20:09:06: #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 20:09:06: #2 You may need to consider one of the other alternative d(s): 0,45,79,114,129,173,192,209,225,243,296,320,338,358,386,438,450,477,484,530,543,547,570,583,598 WARNING @ Sat, 15 Jan 2022 20:09:06: #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 20:09:06: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:09:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:09:06: 5000000 INFO @ Sat, 15 Jan 2022 20:09:11: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:09:16: 7000000 INFO @ Sat, 15 Jan 2022 20:09:20: 8000000 BigWig に変換しました。 /var/spool/uge/at155/job_scripts/14520823: line 297: 72621 Terminated MACS $i /var/spool/uge/at155/job_scripts/14520823: line 297: 85400 Terminated MACS $i /var/spool/uge/at155/job_scripts/14520823: line 297: 100278 Terminated MACS $i ls: cannot access SRX8245530.05.bed: No such file or directory mv: cannot stat ‘SRX8245530.05.bed’: No such file or directory mv: cannot stat ‘SRX8245530.05.bb’: No such file or directory ls: cannot access SRX8245530.10.bed: No such file or directory mv: cannot stat ‘SRX8245530.10.bed’: No such file or directory mv: cannot stat ‘SRX8245530.10.bb’: No such file or directory ls: cannot access SRX8245530.20.bed: No such file or directory mv: cannot stat ‘SRX8245530.20.bed’: No such file or directory mv: cannot stat ‘SRX8245530.20.bb’: No such file or directory