Job ID = 16434795 SRX = SRX11633402 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 22364902 spots for SRR15329111/SRR15329111.sra Written 22364902 spots for SRR15329111/SRR15329111.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434873 ("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: 00:07:10 22364902 reads; of these: 22364902 (100.00%) were unpaired; of these: 2278649 (10.19%) aligned 0 times 17160195 (76.73%) aligned exactly 1 time 2926058 (13.08%) aligned >1 times 89.81% overall alignment rate Time searching: 00:07:10 Overall time: 00:07:10 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] 2832217 / 20086253 = 0.1410 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:12:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.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 @ Tue, 02 Aug 2022 10:12:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:12:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:12:34: 1000000 INFO @ Tue, 02 Aug 2022 10:12:41: 2000000 INFO @ Tue, 02 Aug 2022 10:12:48: 3000000 INFO @ Tue, 02 Aug 2022 10:12:55: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:12:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.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 @ Tue, 02 Aug 2022 10:12:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:12:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:13:02: 5000000 INFO @ Tue, 02 Aug 2022 10:13:05: 1000000 INFO @ Tue, 02 Aug 2022 10:13:10: 6000000 INFO @ Tue, 02 Aug 2022 10:13:13: 2000000 INFO @ Tue, 02 Aug 2022 10:13:18: 7000000 INFO @ Tue, 02 Aug 2022 10:13:21: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:13:25: 8000000 INFO @ Tue, 02 Aug 2022 10:13:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.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 @ Tue, 02 Aug 2022 10:13:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:13:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:13:29: 4000000 INFO @ Tue, 02 Aug 2022 10:13:33: 9000000 INFO @ Tue, 02 Aug 2022 10:13:35: 1000000 INFO @ Tue, 02 Aug 2022 10:13:37: 5000000 INFO @ Tue, 02 Aug 2022 10:13:41: 10000000 INFO @ Tue, 02 Aug 2022 10:13:43: 2000000 INFO @ Tue, 02 Aug 2022 10:13:45: 6000000 INFO @ Tue, 02 Aug 2022 10:13:48: 11000000 INFO @ Tue, 02 Aug 2022 10:13:51: 3000000 INFO @ Tue, 02 Aug 2022 10:13:53: 7000000 INFO @ Tue, 02 Aug 2022 10:13:56: 12000000 INFO @ Tue, 02 Aug 2022 10:14:00: 4000000 INFO @ Tue, 02 Aug 2022 10:14:01: 8000000 INFO @ Tue, 02 Aug 2022 10:14:04: 13000000 INFO @ Tue, 02 Aug 2022 10:14:08: 5000000 INFO @ Tue, 02 Aug 2022 10:14:09: 9000000 INFO @ Tue, 02 Aug 2022 10:14:11: 14000000 INFO @ Tue, 02 Aug 2022 10:14:16: 6000000 INFO @ Tue, 02 Aug 2022 10:14:16: 10000000 INFO @ Tue, 02 Aug 2022 10:14:19: 15000000 INFO @ Tue, 02 Aug 2022 10:14:24: 7000000 INFO @ Tue, 02 Aug 2022 10:14:24: 11000000 INFO @ Tue, 02 Aug 2022 10:14:27: 16000000 INFO @ Tue, 02 Aug 2022 10:14:31: 8000000 INFO @ Tue, 02 Aug 2022 10:14:32: 12000000 INFO @ Tue, 02 Aug 2022 10:14:35: 17000000 INFO @ Tue, 02 Aug 2022 10:14:37: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:14:37: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:14:37: #1 total tags in treatment: 17254036 INFO @ Tue, 02 Aug 2022 10:14:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:14:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:14:37: #1 tags after filtering in treatment: 17254036 INFO @ Tue, 02 Aug 2022 10:14:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:14:37: #1 finished! INFO @ Tue, 02 Aug 2022 10:14:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:14:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:14:38: #2 number of paired peaks: 182 WARNING @ Tue, 02 Aug 2022 10:14:38: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Tue, 02 Aug 2022 10:14:38: start model_add_line... INFO @ Tue, 02 Aug 2022 10:14:38: start X-correlation... INFO @ Tue, 02 Aug 2022 10:14:38: end of X-cor INFO @ Tue, 02 Aug 2022 10:14:38: #2 finished! INFO @ Tue, 02 Aug 2022 10:14:38: #2 predicted fragment length is 2 bps INFO @ Tue, 02 Aug 2022 10:14:38: #2 alternative fragment length(s) may be 2,35,40,536 bps INFO @ Tue, 02 Aug 2022 10:14:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.05_model.r WARNING @ Tue, 02 Aug 2022 10:14:38: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:14:38: #2 You may need to consider one of the other alternative d(s): 2,35,40,536 WARNING @ Tue, 02 Aug 2022 10:14:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:14:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:14:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:14:39: 9000000 INFO @ Tue, 02 Aug 2022 10:14:39: 13000000 INFO @ Tue, 02 Aug 2022 10:14:47: 10000000 INFO @ Tue, 02 Aug 2022 10:14:47: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:14:54: 11000000 INFO @ Tue, 02 Aug 2022 10:14:54: 15000000 INFO @ Tue, 02 Aug 2022 10:15:02: 12000000 INFO @ Tue, 02 Aug 2022 10:15:02: 16000000 INFO @ Tue, 02 Aug 2022 10:15:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:15:09: 13000000 INFO @ Tue, 02 Aug 2022 10:15:09: 17000000 INFO @ Tue, 02 Aug 2022 10:15:11: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:15:11: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:15:11: #1 total tags in treatment: 17254036 INFO @ Tue, 02 Aug 2022 10:15:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:15:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:15:12: #1 tags after filtering in treatment: 17254036 INFO @ Tue, 02 Aug 2022 10:15:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:15:12: #1 finished! INFO @ Tue, 02 Aug 2022 10:15:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:15:13: #2 number of paired peaks: 182 WARNING @ Tue, 02 Aug 2022 10:15:13: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Tue, 02 Aug 2022 10:15:13: start model_add_line... INFO @ Tue, 02 Aug 2022 10:15:13: start X-correlation... INFO @ Tue, 02 Aug 2022 10:15:13: end of X-cor INFO @ Tue, 02 Aug 2022 10:15:13: #2 finished! INFO @ Tue, 02 Aug 2022 10:15:13: #2 predicted fragment length is 2 bps INFO @ Tue, 02 Aug 2022 10:15:13: #2 alternative fragment length(s) may be 2,35,40,536 bps INFO @ Tue, 02 Aug 2022 10:15:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.10_model.r WARNING @ Tue, 02 Aug 2022 10:15:13: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:15:13: #2 You may need to consider one of the other alternative d(s): 2,35,40,536 WARNING @ Tue, 02 Aug 2022 10:15:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:15:13: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:15:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:15:16: 14000000 INFO @ Tue, 02 Aug 2022 10:15:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:15:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:15:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.05_summits.bed INFO @ Tue, 02 Aug 2022 10:15:21: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:15:23: 15000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:15:30: 16000000 INFO @ Tue, 02 Aug 2022 10:15:37: 17000000 INFO @ Tue, 02 Aug 2022 10:15:39: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:15:39: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:15:39: #1 total tags in treatment: 17254036 INFO @ Tue, 02 Aug 2022 10:15:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:15:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:15:39: #1 tags after filtering in treatment: 17254036 INFO @ Tue, 02 Aug 2022 10:15:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:15:39: #1 finished! INFO @ Tue, 02 Aug 2022 10:15:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:15:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:15:40: #2 number of paired peaks: 182 WARNING @ Tue, 02 Aug 2022 10:15:40: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Tue, 02 Aug 2022 10:15:40: start model_add_line... INFO @ Tue, 02 Aug 2022 10:15:40: start X-correlation... INFO @ Tue, 02 Aug 2022 10:15:40: end of X-cor INFO @ Tue, 02 Aug 2022 10:15:40: #2 finished! INFO @ Tue, 02 Aug 2022 10:15:40: #2 predicted fragment length is 2 bps INFO @ Tue, 02 Aug 2022 10:15:40: #2 alternative fragment length(s) may be 2,35,40,536 bps INFO @ Tue, 02 Aug 2022 10:15:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.20_model.r WARNING @ Tue, 02 Aug 2022 10:15:40: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:15:40: #2 You may need to consider one of the other alternative d(s): 2,35,40,536 WARNING @ Tue, 02 Aug 2022 10:15:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:15:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:15:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:15:41: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:15:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:15:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:15:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.10_summits.bed INFO @ Tue, 02 Aug 2022 10:15:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:16:08: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:16:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:16:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:16:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633402/SRX11633402.20_summits.bed INFO @ Tue, 02 Aug 2022 10:16:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling