Job ID = 14157994 SRX = SRX7879261 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:05:18 24822282 reads; of these: 24822282 (100.00%) were unpaired; of these: 507701 (2.05%) aligned 0 times 20433768 (82.32%) aligned exactly 1 time 3880813 (15.63%) aligned >1 times 97.95% overall alignment rate Time searching: 00:05:18 Overall time: 00:05:18 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3544882 / 24314581 = 0.1458 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 @ Wed, 08 Dec 2021 13:56:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.bam'] # control file = None # effective genome size = 9.00e+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 @ Wed, 08 Dec 2021 13:56:36: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:56:36: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:56:42: 1000000 INFO @ Wed, 08 Dec 2021 13:56:47: 2000000 INFO @ Wed, 08 Dec 2021 13:56:52: 3000000 INFO @ Wed, 08 Dec 2021 13:56:58: 4000000 INFO @ Wed, 08 Dec 2021 13:57:03: 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 @ Wed, 08 Dec 2021 13:57:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.bam'] # control file = None # effective genome size = 9.00e+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 @ Wed, 08 Dec 2021 13:57:05: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:57:05: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:57:09: 6000000 INFO @ Wed, 08 Dec 2021 13:57:12: 1000000 INFO @ Wed, 08 Dec 2021 13:57:15: 7000000 INFO @ Wed, 08 Dec 2021 13:57:18: 2000000 INFO @ Wed, 08 Dec 2021 13:57:21: 8000000 INFO @ Wed, 08 Dec 2021 13:57:24: 3000000 INFO @ Wed, 08 Dec 2021 13:57:27: 9000000 INFO @ Wed, 08 Dec 2021 13:57:30: 4000000 INFO @ Wed, 08 Dec 2021 13:57:33: 10000000 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 @ Wed, 08 Dec 2021 13:57:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.bam'] # control file = None # effective genome size = 9.00e+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 @ Wed, 08 Dec 2021 13:57:35: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:57:35: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:57:36: 5000000 INFO @ Wed, 08 Dec 2021 13:57:39: 11000000 INFO @ Wed, 08 Dec 2021 13:57:43: 6000000 INFO @ Wed, 08 Dec 2021 13:57:43: 1000000 INFO @ Wed, 08 Dec 2021 13:57:46: 12000000 INFO @ Wed, 08 Dec 2021 13:57:50: 7000000 INFO @ Wed, 08 Dec 2021 13:57:50: 2000000 INFO @ Wed, 08 Dec 2021 13:57:53: 13000000 INFO @ Wed, 08 Dec 2021 13:57:57: 8000000 INFO @ Wed, 08 Dec 2021 13:57:57: 3000000 INFO @ Wed, 08 Dec 2021 13:58:00: 14000000 INFO @ Wed, 08 Dec 2021 13:58:03: 9000000 INFO @ Wed, 08 Dec 2021 13:58:05: 4000000 INFO @ Wed, 08 Dec 2021 13:58:06: 15000000 INFO @ Wed, 08 Dec 2021 13:58:10: 10000000 INFO @ Wed, 08 Dec 2021 13:58:12: 5000000 INFO @ Wed, 08 Dec 2021 13:58:13: 16000000 INFO @ Wed, 08 Dec 2021 13:58:17: 11000000 INFO @ Wed, 08 Dec 2021 13:58:19: 6000000 INFO @ Wed, 08 Dec 2021 13:58:20: 17000000 INFO @ Wed, 08 Dec 2021 13:58:24: 12000000 INFO @ Wed, 08 Dec 2021 13:58:26: 7000000 INFO @ Wed, 08 Dec 2021 13:58:27: 18000000 INFO @ Wed, 08 Dec 2021 13:58:30: 13000000 INFO @ Wed, 08 Dec 2021 13:58:33: 8000000 INFO @ Wed, 08 Dec 2021 13:58:33: 19000000 INFO @ Wed, 08 Dec 2021 13:58:37: 14000000 INFO @ Wed, 08 Dec 2021 13:58:40: 20000000 INFO @ Wed, 08 Dec 2021 13:58:40: 9000000 INFO @ Wed, 08 Dec 2021 13:58:44: 15000000 INFO @ Wed, 08 Dec 2021 13:58:45: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 13:58:45: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 13:58:45: #1 total tags in treatment: 20769699 INFO @ Wed, 08 Dec 2021 13:58:45: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:58:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 13:58:45: #1 tags after filtering in treatment: 20769699 INFO @ Wed, 08 Dec 2021 13:58:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 13:58:45: #1 finished! INFO @ Wed, 08 Dec 2021 13:58:45: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:58:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:58:47: #2 number of paired peaks: 188 WARNING @ Wed, 08 Dec 2021 13:58:47: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Wed, 08 Dec 2021 13:58:47: start model_add_line... INFO @ Wed, 08 Dec 2021 13:58:47: start X-correlation... INFO @ Wed, 08 Dec 2021 13:58:47: end of X-cor INFO @ Wed, 08 Dec 2021 13:58:47: #2 finished! INFO @ Wed, 08 Dec 2021 13:58:47: #2 predicted fragment length is 0 bps INFO @ Wed, 08 Dec 2021 13:58:47: #2 alternative fragment length(s) may be 0,12,45,142,508,532 bps INFO @ Wed, 08 Dec 2021 13:58:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.05_model.r WARNING @ Wed, 08 Dec 2021 13:58:47: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:58:47: #2 You may need to consider one of the other alternative d(s): 0,12,45,142,508,532 WARNING @ Wed, 08 Dec 2021 13:58:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 13:58:47: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:58:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:58:47: 10000000 INFO @ Wed, 08 Dec 2021 13:58:50: 16000000 INFO @ Wed, 08 Dec 2021 13:58:54: 11000000 INFO @ Wed, 08 Dec 2021 13:58:57: 17000000 INFO @ Wed, 08 Dec 2021 13:59:01: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 13:59:03: 18000000 INFO @ Wed, 08 Dec 2021 13:59:08: 13000000 INFO @ Wed, 08 Dec 2021 13:59:10: 19000000 INFO @ Wed, 08 Dec 2021 13:59:15: 14000000 INFO @ Wed, 08 Dec 2021 13:59:16: 20000000 INFO @ Wed, 08 Dec 2021 13:59:21: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 13:59:21: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 13:59:21: #1 total tags in treatment: 20769699 INFO @ Wed, 08 Dec 2021 13:59:21: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:59:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 13:59:21: #1 tags after filtering in treatment: 20769699 INFO @ Wed, 08 Dec 2021 13:59:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 13:59:21: #1 finished! INFO @ Wed, 08 Dec 2021 13:59:21: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:59:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:59:23: 15000000 INFO @ Wed, 08 Dec 2021 13:59:23: #2 number of paired peaks: 188 WARNING @ Wed, 08 Dec 2021 13:59:23: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Wed, 08 Dec 2021 13:59:23: start model_add_line... INFO @ Wed, 08 Dec 2021 13:59:23: start X-correlation... INFO @ Wed, 08 Dec 2021 13:59:23: end of X-cor INFO @ Wed, 08 Dec 2021 13:59:23: #2 finished! INFO @ Wed, 08 Dec 2021 13:59:23: #2 predicted fragment length is 0 bps INFO @ Wed, 08 Dec 2021 13:59:23: #2 alternative fragment length(s) may be 0,12,45,142,508,532 bps INFO @ Wed, 08 Dec 2021 13:59:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.10_model.r WARNING @ Wed, 08 Dec 2021 13:59:23: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:59:23: #2 You may need to consider one of the other alternative d(s): 0,12,45,142,508,532 WARNING @ Wed, 08 Dec 2021 13:59:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 13:59:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:59:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:59:29: 16000000 INFO @ Wed, 08 Dec 2021 13:59:36: 17000000 INFO @ Wed, 08 Dec 2021 13:59:43: 18000000 BigWig に変換しました。 /var/spool/uge/at148/job_scripts/14157994: line 297: 84100 Terminated MACS $i /var/spool/uge/at148/job_scripts/14157994: line 297: 84195 Terminated MACS $i /var/spool/uge/at148/job_scripts/14157994: line 297: 84544 Terminated MACS $i ls: cannot access SRX7879261.05.bed: No such file or directory mv: cannot stat ‘SRX7879261.05.bed’: No such file or directory mv: cannot stat ‘SRX7879261.05.bb’: No such file or directory ls: cannot access SRX7879261.10.bed: No such file or directory mv: cannot stat ‘SRX7879261.10.bed’: No such file or directory mv: cannot stat ‘SRX7879261.10.bb’: No such file or directory ls: cannot access SRX7879261.20.bed: No such file or directory mv: cannot stat ‘SRX7879261.20.bed’: No such file or directory mv: cannot stat ‘SRX7879261.20.bb’: No such file or directory