Job ID = 14521098 SRX = SRX8245358 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9555330 spots for SRR11684569/SRR11684569.sra Written 9555330 spots for SRR11684569/SRR11684569.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: 00:07:36 9555330 reads; of these: 9555330 (100.00%) were paired; of these: 4873835 (51.01%) aligned concordantly 0 times 4164659 (43.58%) aligned concordantly exactly 1 time 516836 (5.41%) aligned concordantly >1 times ---- 4873835 pairs aligned concordantly 0 times; of these: 151597 (3.11%) aligned discordantly 1 time ---- 4722238 pairs aligned 0 times concordantly or discordantly; of these: 9444476 mates make up the pairs; of these: 5573483 (59.01%) aligned 0 times 3337735 (35.34%) aligned exactly 1 time 533258 (5.65%) aligned >1 times 70.84% overall alignment rate Time searching: 00:07:36 Overall time: 00:07:36 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] 266977 / 4832449 = 0.0552 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 20:41:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245358/SRX8245358.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245358/SRX8245358.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245358/SRX8245358.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245358/SRX8245358.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 20:41:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:41:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:41:49: 1000000 INFO @ Sat, 15 Jan 2022 20:42:00: 2000000 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 20:42:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245358/SRX8245358.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245358/SRX8245358.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245358/SRX8245358.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245358/SRX8245358.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 20:42:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:42:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:42:11: 3000000 INFO @ Sat, 15 Jan 2022 20:42:18: 1000000 INFO @ Sat, 15 Jan 2022 20:42:21: 4000000 INFO @ Sat, 15 Jan 2022 20:42:28: 2000000 INFO @ Sat, 15 Jan 2022 20:42:32: 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 20:42:37: 3000000 INFO @ Sat, 15 Jan 2022 20:42:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245358/SRX8245358.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245358/SRX8245358.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245358/SRX8245358.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245358/SRX8245358.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 20:42:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:42:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:42:42: 6000000 INFO @ Sat, 15 Jan 2022 20:42:47: 4000000 INFO @ Sat, 15 Jan 2022 20:42:49: 1000000 INFO @ Sat, 15 Jan 2022 20:42:52: 7000000 INFO @ Sat, 15 Jan 2022 20:42:57: 5000000 INFO @ Sat, 15 Jan 2022 20:42:59: 2000000 INFO @ Sat, 15 Jan 2022 20:43:03: 8000000 INFO @ Sat, 15 Jan 2022 20:43:06: 6000000 INFO @ Sat, 15 Jan 2022 20:43:09: 3000000 INFO @ Sat, 15 Jan 2022 20:43:14: 9000000 INFO @ Sat, 15 Jan 2022 20:43:17: 7000000 INFO @ Sat, 15 Jan 2022 20:43:19: 4000000 INFO @ Sat, 15 Jan 2022 20:43:26: 10000000 INFO @ Sat, 15 Jan 2022 20:43:28: 8000000 INFO @ Sat, 15 Jan 2022 20:43:28: 5000000 INFO @ Sat, 15 Jan 2022 20:43:37: 11000000 INFO @ Sat, 15 Jan 2022 20:43:38: 9000000 INFO @ Sat, 15 Jan 2022 20:43:39: 6000000 INFO @ Sat, 15 Jan 2022 20:43:47: 12000000 INFO @ Sat, 15 Jan 2022 20:43:49: 10000000 INFO @ Sat, 15 Jan 2022 20:43:49: 7000000 INFO @ Sat, 15 Jan 2022 20:43:57: 13000000 INFO @ Sat, 15 Jan 2022 20:43:57: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:43:57: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:43:57: #1 total tags in treatment: 4418437 INFO @ Sat, 15 Jan 2022 20:43:57: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:43:57: #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 20:43:57: #1 tags after filtering in treatment: 2861474 INFO @ Sat, 15 Jan 2022 20:43:57: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 20:43:57: #1 finished! INFO @ Sat, 15 Jan 2022 20:43:57: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:43:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:43:58: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 20:43:58: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 20:43:58: start model_add_line... INFO @ Sat, 15 Jan 2022 20:43:58: start X-correlation... INFO @ Sat, 15 Jan 2022 20:43:58: end of X-cor INFO @ Sat, 15 Jan 2022 20:43:58: #2 finished! INFO @ Sat, 15 Jan 2022 20:43:58: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:43:58: #2 alternative fragment length(s) may be 0,40,78,93,130,153,196,200,239,283,305,307,330,351,402,429,455,480,493,534,564 bps INFO @ Sat, 15 Jan 2022 20:43:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245358/SRX8245358.05_model.r WARNING @ Sat, 15 Jan 2022 20:43:58: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:43:58: #2 You may need to consider one of the other alternative d(s): 0,40,78,93,130,153,196,200,239,283,305,307,330,351,402,429,455,480,493,534,564 WARNING @ Sat, 15 Jan 2022 20:43:58: #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 20:43:58: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:43:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:43:59: 11000000 INFO @ Sat, 15 Jan 2022 20:43:59: 8000000 INFO @ Sat, 15 Jan 2022 20:44:09: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:44:09: 9000000 INFO @ Sat, 15 Jan 2022 20:44:18: 13000000 INFO @ Sat, 15 Jan 2022 20:44:18: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:44:18: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:44:18: #1 total tags in treatment: 4418437 INFO @ Sat, 15 Jan 2022 20:44:18: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:44:18: #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 20:44:18: #1 tags after filtering in treatment: 2861474 INFO @ Sat, 15 Jan 2022 20:44:18: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 20:44:18: #1 finished! INFO @ Sat, 15 Jan 2022 20:44:18: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:44:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:44:18: 10000000 INFO @ Sat, 15 Jan 2022 20:44:18: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 20:44:18: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 20:44:18: start model_add_line... INFO @ Sat, 15 Jan 2022 20:44:18: start X-correlation... INFO @ Sat, 15 Jan 2022 20:44:18: end of X-cor INFO @ Sat, 15 Jan 2022 20:44:18: #2 finished! INFO @ Sat, 15 Jan 2022 20:44:18: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:44:18: #2 alternative fragment length(s) may be 0,40,78,93,130,153,196,200,239,283,305,307,330,351,402,429,455,480,493,534,564 bps INFO @ Sat, 15 Jan 2022 20:44:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245358/SRX8245358.10_model.r WARNING @ Sat, 15 Jan 2022 20:44:18: #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 20:44:18: #2 You may need to consider one of the other alternative d(s): 0,40,78,93,130,153,196,200,239,283,305,307,330,351,402,429,455,480,493,534,564 WARNING @ Sat, 15 Jan 2022 20:44:18: #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 20:44:18: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:44:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at074/job_scripts/14521098: line 297: 54596 Terminated MACS $i /var/spool/uge/at074/job_scripts/14521098: line 297: 55718 Terminated MACS $i /var/spool/uge/at074/job_scripts/14521098: line 297: 55903 Terminated MACS $i ls: cannot access SRX8245358.05.bed: No such file or directory mv: cannot stat ‘SRX8245358.05.bed’: No such file or directory mv: cannot stat ‘SRX8245358.05.bb’: No such file or directory ls: cannot access SRX8245358.10.bed: No such file or directory mv: cannot stat ‘SRX8245358.10.bed’: No such file or directory mv: cannot stat ‘SRX8245358.10.bb’: No such file or directory ls: cannot access SRX8245358.20.bed: No such file or directory mv: cannot stat ‘SRX8245358.20.bed’: No such file or directory mv: cannot stat ‘SRX8245358.20.bb’: No such file or directory