Job ID = 14159228 SRX = SRX9120619 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 25413202 spots for SRR12638562/SRR12638562.sra Written 25413202 spots for SRR12638562/SRR12638562.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159437 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:57 25413202 reads; of these: 25413202 (100.00%) were unpaired; of these: 1413575 (5.56%) aligned 0 times 20008967 (78.73%) aligned exactly 1 time 3990660 (15.70%) aligned >1 times 94.44% overall alignment rate Time searching: 00:04:57 Overall time: 00:04:57 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] 3479652 / 23999627 = 0.1450 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 20:27:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.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 20:27:45: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:27:45: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:27:50: 1000000 INFO @ Wed, 08 Dec 2021 20:27:56: 2000000 INFO @ Wed, 08 Dec 2021 20:28:01: 3000000 INFO @ Wed, 08 Dec 2021 20:28:06: 4000000 INFO @ Wed, 08 Dec 2021 20:28:11: 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 20:28:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.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 20:28:15: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:28:15: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:28:17: 6000000 INFO @ Wed, 08 Dec 2021 20:28:21: 1000000 INFO @ Wed, 08 Dec 2021 20:28:23: 7000000 INFO @ Wed, 08 Dec 2021 20:28:27: 2000000 INFO @ Wed, 08 Dec 2021 20:28:29: 8000000 INFO @ Wed, 08 Dec 2021 20:28:33: 3000000 INFO @ Wed, 08 Dec 2021 20:28:35: 9000000 INFO @ Wed, 08 Dec 2021 20:28:39: 4000000 INFO @ Wed, 08 Dec 2021 20:28:41: 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 20:28:45: 5000000 INFO @ Wed, 08 Dec 2021 20:28:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.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 20:28:45: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:28:45: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:28:47: 11000000 INFO @ Wed, 08 Dec 2021 20:28:51: 6000000 INFO @ Wed, 08 Dec 2021 20:28:51: 1000000 INFO @ Wed, 08 Dec 2021 20:28:53: 12000000 INFO @ Wed, 08 Dec 2021 20:28:57: 7000000 INFO @ Wed, 08 Dec 2021 20:28:57: 2000000 INFO @ Wed, 08 Dec 2021 20:28:59: 13000000 INFO @ Wed, 08 Dec 2021 20:29:03: 8000000 INFO @ Wed, 08 Dec 2021 20:29:03: 3000000 INFO @ Wed, 08 Dec 2021 20:29:05: 14000000 INFO @ Wed, 08 Dec 2021 20:29:09: 9000000 INFO @ Wed, 08 Dec 2021 20:29:09: 4000000 INFO @ Wed, 08 Dec 2021 20:29:11: 15000000 INFO @ Wed, 08 Dec 2021 20:29:15: 10000000 INFO @ Wed, 08 Dec 2021 20:29:15: 5000000 INFO @ Wed, 08 Dec 2021 20:29:16: 16000000 INFO @ Wed, 08 Dec 2021 20:29:21: 11000000 INFO @ Wed, 08 Dec 2021 20:29:21: 6000000 INFO @ Wed, 08 Dec 2021 20:29:22: 17000000 INFO @ Wed, 08 Dec 2021 20:29:27: 12000000 INFO @ Wed, 08 Dec 2021 20:29:27: 7000000 INFO @ Wed, 08 Dec 2021 20:29:28: 18000000 INFO @ Wed, 08 Dec 2021 20:29:33: 13000000 INFO @ Wed, 08 Dec 2021 20:29:33: 8000000 INFO @ Wed, 08 Dec 2021 20:29:34: 19000000 INFO @ Wed, 08 Dec 2021 20:29:39: 14000000 INFO @ Wed, 08 Dec 2021 20:29:39: 9000000 INFO @ Wed, 08 Dec 2021 20:29:40: 20000000 INFO @ Wed, 08 Dec 2021 20:29:43: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 20:29:43: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 20:29:43: #1 total tags in treatment: 20519975 INFO @ Wed, 08 Dec 2021 20:29:43: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:29:43: #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 20:29:44: #1 tags after filtering in treatment: 20519975 INFO @ Wed, 08 Dec 2021 20:29:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:29:44: #1 finished! INFO @ Wed, 08 Dec 2021 20:29:44: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:29:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:29:45: #2 number of paired peaks: 176 WARNING @ Wed, 08 Dec 2021 20:29:45: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Wed, 08 Dec 2021 20:29:45: start model_add_line... INFO @ Wed, 08 Dec 2021 20:29:45: start X-correlation... INFO @ Wed, 08 Dec 2021 20:29:45: end of X-cor INFO @ Wed, 08 Dec 2021 20:29:45: #2 finished! INFO @ Wed, 08 Dec 2021 20:29:45: #2 predicted fragment length is 0 bps INFO @ Wed, 08 Dec 2021 20:29:45: #2 alternative fragment length(s) may be 0,14,46,586 bps INFO @ Wed, 08 Dec 2021 20:29:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.05_model.r WARNING @ Wed, 08 Dec 2021 20:29:45: #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 20:29:45: #2 You may need to consider one of the other alternative d(s): 0,14,46,586 WARNING @ Wed, 08 Dec 2021 20:29:45: #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 20:29:45: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:29:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:29:45: 15000000 INFO @ Wed, 08 Dec 2021 20:29:45: 10000000 INFO @ Wed, 08 Dec 2021 20:29:50: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:29:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:29:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:29:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.05_summits.bed INFO @ Wed, 08 Dec 2021 20:29:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:29:51: 16000000 INFO @ Wed, 08 Dec 2021 20:29:51: 11000000 INFO @ Wed, 08 Dec 2021 20:29:57: 17000000 INFO @ Wed, 08 Dec 2021 20:29:57: 12000000 INFO @ Wed, 08 Dec 2021 20:30:03: 18000000 INFO @ Wed, 08 Dec 2021 20:30:03: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:30:09: 19000000 INFO @ Wed, 08 Dec 2021 20:30:09: 14000000 INFO @ Wed, 08 Dec 2021 20:30:15: 20000000 INFO @ Wed, 08 Dec 2021 20:30:16: 15000000 INFO @ Wed, 08 Dec 2021 20:30:19: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 20:30:19: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 20:30:19: #1 total tags in treatment: 20519975 INFO @ Wed, 08 Dec 2021 20:30:19: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:30:19: #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 20:30:19: #1 tags after filtering in treatment: 20519975 INFO @ Wed, 08 Dec 2021 20:30:19: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:30:19: #1 finished! INFO @ Wed, 08 Dec 2021 20:30:19: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:30:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:30:20: #2 number of paired peaks: 176 WARNING @ Wed, 08 Dec 2021 20:30:20: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Wed, 08 Dec 2021 20:30:20: start model_add_line... INFO @ Wed, 08 Dec 2021 20:30:20: start X-correlation... INFO @ Wed, 08 Dec 2021 20:30:20: end of X-cor INFO @ Wed, 08 Dec 2021 20:30:20: #2 finished! INFO @ Wed, 08 Dec 2021 20:30:20: #2 predicted fragment length is 0 bps INFO @ Wed, 08 Dec 2021 20:30:20: #2 alternative fragment length(s) may be 0,14,46,586 bps INFO @ Wed, 08 Dec 2021 20:30:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.10_model.r WARNING @ Wed, 08 Dec 2021 20:30:20: #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 20:30:20: #2 You may need to consider one of the other alternative d(s): 0,14,46,586 WARNING @ Wed, 08 Dec 2021 20:30:20: #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 20:30:20: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:30:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:30:22: 16000000 INFO @ Wed, 08 Dec 2021 20:30:25: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:30:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:30:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:30:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.10_summits.bed INFO @ Wed, 08 Dec 2021 20:30:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:30:28: 17000000 INFO @ Wed, 08 Dec 2021 20:30:33: 18000000 INFO @ Wed, 08 Dec 2021 20:30:39: 19000000 INFO @ Wed, 08 Dec 2021 20:30:45: 20000000 INFO @ Wed, 08 Dec 2021 20:30:48: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 20:30:48: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 20:30:48: #1 total tags in treatment: 20519975 INFO @ Wed, 08 Dec 2021 20:30:48: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:30:48: #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 20:30:48: #1 tags after filtering in treatment: 20519975 INFO @ Wed, 08 Dec 2021 20:30:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:30:48: #1 finished! INFO @ Wed, 08 Dec 2021 20:30:48: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:30:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:30:50: #2 number of paired peaks: 176 WARNING @ Wed, 08 Dec 2021 20:30:50: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Wed, 08 Dec 2021 20:30:50: start model_add_line... INFO @ Wed, 08 Dec 2021 20:30:50: start X-correlation... INFO @ Wed, 08 Dec 2021 20:30:50: end of X-cor INFO @ Wed, 08 Dec 2021 20:30:50: #2 finished! INFO @ Wed, 08 Dec 2021 20:30:50: #2 predicted fragment length is 0 bps INFO @ Wed, 08 Dec 2021 20:30:50: #2 alternative fragment length(s) may be 0,14,46,586 bps INFO @ Wed, 08 Dec 2021 20:30:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.20_model.r WARNING @ Wed, 08 Dec 2021 20:30:50: #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 20:30:50: #2 You may need to consider one of the other alternative d(s): 0,14,46,586 WARNING @ Wed, 08 Dec 2021 20:30:50: #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 20:30:50: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:30:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:30:55: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:30:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:30:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:30:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.20_summits.bed INFO @ Wed, 08 Dec 2021 20:30:55: Done! BigWig に変換しました。 /var/spool/uge/at152/job_scripts/14159228: line 284: kill: (2531) - No such process /var/spool/uge/at152/job_scripts/14159228: line 284: kill: (3641) - No such process /var/spool/uge/at152/job_scripts/14159228: line 297: 3768 Terminated MACS $i ls: cannot access SRX9120619.20.bed: No such file or directory mv: cannot stat ‘SRX9120619.20.bed’: No such file or directory mv: cannot stat ‘SRX9120619.20.bb’: No such file or directory