Job ID = 14521146 SRX = SRX8245368 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12653289 spots for SRR11684579/SRR11684579.sra Written 12653289 spots for SRR11684579/SRR11684579.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: 00:06:54 12653289 reads; of these: 12653289 (100.00%) were paired; of these: 7658349 (60.52%) aligned concordantly 0 times 4388327 (34.68%) aligned concordantly exactly 1 time 606613 (4.79%) aligned concordantly >1 times ---- 7658349 pairs aligned concordantly 0 times; of these: 110349 (1.44%) aligned discordantly 1 time ---- 7548000 pairs aligned 0 times concordantly or discordantly; of these: 15096000 mates make up the pairs; of these: 8803460 (58.32%) aligned 0 times 5408055 (35.82%) aligned exactly 1 time 884485 (5.86%) aligned >1 times 65.21% overall alignment rate Time searching: 00:06:54 Overall time: 00:06:54 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] 379024 / 5104582 = 0.0743 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 20:44:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245368/SRX8245368.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245368/SRX8245368.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245368/SRX8245368.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245368/SRX8245368.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 20:44:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:44:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:44:41: 1000000 INFO @ Sat, 15 Jan 2022 20:44:47: 2000000 INFO @ Sat, 15 Jan 2022 20:44:52: 3000000 INFO @ Sat, 15 Jan 2022 20:44:58: 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 20:45:03: 5000000 INFO @ Sat, 15 Jan 2022 20:45:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245368/SRX8245368.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245368/SRX8245368.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245368/SRX8245368.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245368/SRX8245368.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 20:45:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:45:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:45:09: 6000000 INFO @ Sat, 15 Jan 2022 20:45:10: 1000000 INFO @ Sat, 15 Jan 2022 20:45:15: 7000000 INFO @ Sat, 15 Jan 2022 20:45:16: 2000000 INFO @ Sat, 15 Jan 2022 20:45:21: 3000000 INFO @ Sat, 15 Jan 2022 20:45:21: 8000000 INFO @ Sat, 15 Jan 2022 20:45:26: 4000000 INFO @ Sat, 15 Jan 2022 20:45:28: 9000000 INFO @ Sat, 15 Jan 2022 20:45:31: 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 20:45:34: 10000000 INFO @ Sat, 15 Jan 2022 20:45:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245368/SRX8245368.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245368/SRX8245368.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245368/SRX8245368.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245368/SRX8245368.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 20:45:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:45:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:45:37: 6000000 INFO @ Sat, 15 Jan 2022 20:45:40: 1000000 INFO @ Sat, 15 Jan 2022 20:45:41: 11000000 INFO @ Sat, 15 Jan 2022 20:45:42: 7000000 INFO @ Sat, 15 Jan 2022 20:45:46: 2000000 INFO @ Sat, 15 Jan 2022 20:45:47: 8000000 INFO @ Sat, 15 Jan 2022 20:45:47: 12000000 INFO @ Sat, 15 Jan 2022 20:45:51: 3000000 INFO @ Sat, 15 Jan 2022 20:45:52: 9000000 INFO @ Sat, 15 Jan 2022 20:45:53: 13000000 INFO @ Sat, 15 Jan 2022 20:45:56: 4000000 INFO @ Sat, 15 Jan 2022 20:45:58: 10000000 INFO @ Sat, 15 Jan 2022 20:46:00: 14000000 INFO @ Sat, 15 Jan 2022 20:46:02: 5000000 INFO @ Sat, 15 Jan 2022 20:46:03: 11000000 INFO @ Sat, 15 Jan 2022 20:46:06: 15000000 INFO @ Sat, 15 Jan 2022 20:46:07: 6000000 INFO @ Sat, 15 Jan 2022 20:46:08: 12000000 INFO @ Sat, 15 Jan 2022 20:46:11: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:46:11: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:46:11: #1 total tags in treatment: 4619392 INFO @ Sat, 15 Jan 2022 20:46:11: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:46:11: #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 20:46:11: #1 tags after filtering in treatment: 2895014 INFO @ Sat, 15 Jan 2022 20:46:11: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 15 Jan 2022 20:46:11: #1 finished! INFO @ Sat, 15 Jan 2022 20:46:11: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:46:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:46:11: #2 number of paired peaks: 175 WARNING @ Sat, 15 Jan 2022 20:46:11: 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 20:46:11: start model_add_line... INFO @ Sat, 15 Jan 2022 20:46:11: start X-correlation... INFO @ Sat, 15 Jan 2022 20:46:11: end of X-cor INFO @ Sat, 15 Jan 2022 20:46:11: #2 finished! INFO @ Sat, 15 Jan 2022 20:46:11: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:46:11: #2 alternative fragment length(s) may be 0,32,58,85,99,101,108,111,117,138,169,193,203,225,257,298,331,362,379,423,476,489,527,548,570,585 bps INFO @ Sat, 15 Jan 2022 20:46:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245368/SRX8245368.05_model.r WARNING @ Sat, 15 Jan 2022 20:46:11: #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 20:46:11: #2 You may need to consider one of the other alternative d(s): 0,32,58,85,99,101,108,111,117,138,169,193,203,225,257,298,331,362,379,423,476,489,527,548,570,585 WARNING @ Sat, 15 Jan 2022 20:46:11: #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 20:46:11: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:46:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:46:12: 7000000 INFO @ Sat, 15 Jan 2022 20:46:14: 13000000 INFO @ Sat, 15 Jan 2022 20:46:17: 8000000 INFO @ Sat, 15 Jan 2022 20:46:19: 14000000 INFO @ Sat, 15 Jan 2022 20:46:22: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:46:24: 15000000 INFO @ Sat, 15 Jan 2022 20:46:28: 10000000 INFO @ Sat, 15 Jan 2022 20:46:28: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:46:28: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:46:28: #1 total tags in treatment: 4619392 INFO @ Sat, 15 Jan 2022 20:46:28: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:46:28: #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 20:46:28: #1 tags after filtering in treatment: 2895014 INFO @ Sat, 15 Jan 2022 20:46:28: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 15 Jan 2022 20:46:28: #1 finished! INFO @ Sat, 15 Jan 2022 20:46:28: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:46:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:46:28: #2 number of paired peaks: 175 WARNING @ Sat, 15 Jan 2022 20:46:28: 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 20:46:28: start model_add_line... INFO @ Sat, 15 Jan 2022 20:46:28: start X-correlation... INFO @ Sat, 15 Jan 2022 20:46:28: end of X-cor INFO @ Sat, 15 Jan 2022 20:46:28: #2 finished! INFO @ Sat, 15 Jan 2022 20:46:28: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:46:28: #2 alternative fragment length(s) may be 0,32,58,85,99,101,108,111,117,138,169,193,203,225,257,298,331,362,379,423,476,489,527,548,570,585 bps INFO @ Sat, 15 Jan 2022 20:46:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245368/SRX8245368.10_model.r WARNING @ Sat, 15 Jan 2022 20:46:28: #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 20:46:28: #2 You may need to consider one of the other alternative d(s): 0,32,58,85,99,101,108,111,117,138,169,193,203,225,257,298,331,362,379,423,476,489,527,548,570,585 WARNING @ Sat, 15 Jan 2022 20:46:28: #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 20:46:28: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:46:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:46:33: 11000000 BigWig に変換しました。 /var/spool/uge/at155/job_scripts/14521146: line 297: 33677 Terminated MACS $i /var/spool/uge/at155/job_scripts/14521146: line 297: 42111 Terminated MACS $i /var/spool/uge/at155/job_scripts/14521146: line 297: 50595 Terminated MACS $i ls: cannot access SRX8245368.05.bed: No such file or directory mv: cannot stat ‘SRX8245368.05.bed’: No such file or directory mv: cannot stat ‘SRX8245368.05.bb’: No such file or directory ls: cannot access SRX8245368.10.bed: No such file or directory mv: cannot stat ‘SRX8245368.10.bed’: No such file or directory mv: cannot stat ‘SRX8245368.10.bb’: No such file or directory ls: cannot access SRX8245368.20.bed: No such file or directory mv: cannot stat ‘SRX8245368.20.bed’: No such file or directory mv: cannot stat ‘SRX8245368.20.bb’: No such file or directory