Job ID = 6368733 SRX = SRX5402757 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:35:49 prefetch.2.10.7: 1) Downloading 'SRR8602991'... 2020-06-16T00:35:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:39:21 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:39:21 prefetch.2.10.7: 1) 'SRR8602991' was downloaded successfully Read 26961904 spots for SRR8602991/SRR8602991.sra Written 26961904 spots for SRR8602991/SRR8602991.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: 00:05:56 26961904 reads; of these: 26961904 (100.00%) were unpaired; of these: 2907433 (10.78%) aligned 0 times 19228715 (71.32%) aligned exactly 1 time 4825756 (17.90%) aligned >1 times 89.22% overall alignment rate Time searching: 00:05:56 Overall time: 00:05:56 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] 4679743 / 24054471 = 0.1945 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:52:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.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, 16 Jun 2020 09:52:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:16: 1000000 INFO @ Tue, 16 Jun 2020 09:52:21: 2000000 INFO @ Tue, 16 Jun 2020 09:52:26: 3000000 INFO @ Tue, 16 Jun 2020 09:52:31: 4000000 INFO @ Tue, 16 Jun 2020 09:52:36: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:52:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.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, 16 Jun 2020 09:52:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:42: 6000000 INFO @ Tue, 16 Jun 2020 09:52:47: 1000000 INFO @ Tue, 16 Jun 2020 09:52:47: 7000000 INFO @ Tue, 16 Jun 2020 09:52:53: 8000000 INFO @ Tue, 16 Jun 2020 09:52:53: 2000000 INFO @ Tue, 16 Jun 2020 09:52:59: 9000000 INFO @ Tue, 16 Jun 2020 09:52:59: 3000000 INFO @ Tue, 16 Jun 2020 09:53:04: 10000000 INFO @ Tue, 16 Jun 2020 09:53:05: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:53:10: 11000000 INFO @ Tue, 16 Jun 2020 09:53:10: 5000000 INFO @ Tue, 16 Jun 2020 09:53:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.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, 16 Jun 2020 09:53:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:16: 12000000 INFO @ Tue, 16 Jun 2020 09:53:16: 6000000 INFO @ Tue, 16 Jun 2020 09:53:17: 1000000 INFO @ Tue, 16 Jun 2020 09:53:22: 13000000 INFO @ Tue, 16 Jun 2020 09:53:22: 7000000 INFO @ Tue, 16 Jun 2020 09:53:23: 2000000 INFO @ Tue, 16 Jun 2020 09:53:28: 14000000 INFO @ Tue, 16 Jun 2020 09:53:28: 8000000 INFO @ Tue, 16 Jun 2020 09:53:30: 3000000 INFO @ Tue, 16 Jun 2020 09:53:34: 15000000 INFO @ Tue, 16 Jun 2020 09:53:34: 9000000 INFO @ Tue, 16 Jun 2020 09:53:36: 4000000 INFO @ Tue, 16 Jun 2020 09:53:40: 16000000 INFO @ Tue, 16 Jun 2020 09:53:40: 10000000 INFO @ Tue, 16 Jun 2020 09:53:42: 5000000 INFO @ Tue, 16 Jun 2020 09:53:46: 17000000 INFO @ Tue, 16 Jun 2020 09:53:46: 11000000 INFO @ Tue, 16 Jun 2020 09:53:49: 6000000 INFO @ Tue, 16 Jun 2020 09:53:51: 18000000 INFO @ Tue, 16 Jun 2020 09:53:52: 12000000 INFO @ Tue, 16 Jun 2020 09:53:55: 7000000 INFO @ Tue, 16 Jun 2020 09:53:57: 19000000 INFO @ Tue, 16 Jun 2020 09:53:58: 13000000 INFO @ Tue, 16 Jun 2020 09:54:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:54:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:54:00: #1 total tags in treatment: 19374728 INFO @ Tue, 16 Jun 2020 09:54:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:54:00: #1 tags after filtering in treatment: 19374728 INFO @ Tue, 16 Jun 2020 09:54:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:01: #2 number of paired peaks: 191 WARNING @ Tue, 16 Jun 2020 09:54:01: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Tue, 16 Jun 2020 09:54:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:01: 8000000 INFO @ Tue, 16 Jun 2020 09:54:01: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:01: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:01: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:01: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:54:01: #2 alternative fragment length(s) may be 1,40,512,514,566 bps INFO @ Tue, 16 Jun 2020 09:54:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.05_model.r WARNING @ Tue, 16 Jun 2020 09:54:01: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:54:01: #2 You may need to consider one of the other alternative d(s): 1,40,512,514,566 WARNING @ Tue, 16 Jun 2020 09:54:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:54:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:04: 14000000 INFO @ Tue, 16 Jun 2020 09:54:08: 9000000 INFO @ Tue, 16 Jun 2020 09:54:10: 15000000 INFO @ Tue, 16 Jun 2020 09:54:14: 10000000 INFO @ Tue, 16 Jun 2020 09:54:16: 16000000 INFO @ Tue, 16 Jun 2020 09:54:20: 11000000 INFO @ Tue, 16 Jun 2020 09:54:22: 17000000 INFO @ Tue, 16 Jun 2020 09:54:27: 12000000 INFO @ Tue, 16 Jun 2020 09:54:28: 18000000 INFO @ Tue, 16 Jun 2020 09:54:33: 13000000 INFO @ Tue, 16 Jun 2020 09:54:34: 19000000 INFO @ Tue, 16 Jun 2020 09:54:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:54:37: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:54:37: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:54:37: #1 total tags in treatment: 19374728 INFO @ Tue, 16 Jun 2020 09:54:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:54:37: #1 tags after filtering in treatment: 19374728 INFO @ Tue, 16 Jun 2020 09:54:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:38: #2 number of paired peaks: 191 WARNING @ Tue, 16 Jun 2020 09:54:38: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Tue, 16 Jun 2020 09:54:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:39: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:39: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:39: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:54:39: #2 alternative fragment length(s) may be 1,40,512,514,566 bps INFO @ Tue, 16 Jun 2020 09:54:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.10_model.r WARNING @ Tue, 16 Jun 2020 09:54:39: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:54:39: #2 You may need to consider one of the other alternative d(s): 1,40,512,514,566 WARNING @ Tue, 16 Jun 2020 09:54:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:54:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:39: 14000000 INFO @ Tue, 16 Jun 2020 09:54:45: 15000000 INFO @ Tue, 16 Jun 2020 09:54:50: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:54:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.05_summits.bed INFO @ Tue, 16 Jun 2020 09:54:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:54:56: 17000000 INFO @ Tue, 16 Jun 2020 09:55:01: 18000000 INFO @ Tue, 16 Jun 2020 09:55:07: 19000000 INFO @ Tue, 16 Jun 2020 09:55:09: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:55:09: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:55:09: #1 total tags in treatment: 19374728 INFO @ Tue, 16 Jun 2020 09:55:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:55:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:55:09: #1 tags after filtering in treatment: 19374728 INFO @ Tue, 16 Jun 2020 09:55:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:55:09: #1 finished! INFO @ Tue, 16 Jun 2020 09:55:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:55:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:55:11: #2 number of paired peaks: 191 WARNING @ Tue, 16 Jun 2020 09:55:11: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Tue, 16 Jun 2020 09:55:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:55:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:55:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:55:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:55:11: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:55:11: #2 alternative fragment length(s) may be 1,40,512,514,566 bps INFO @ Tue, 16 Jun 2020 09:55:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.20_model.r WARNING @ Tue, 16 Jun 2020 09:55:11: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:55:11: #2 You may need to consider one of the other alternative d(s): 1,40,512,514,566 WARNING @ Tue, 16 Jun 2020 09:55:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:55:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:55:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:55:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:55:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:55:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:55:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.10_summits.bed INFO @ Tue, 16 Jun 2020 09:55:28: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:55:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:56:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:56:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:56:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402757/SRX5402757.20_summits.bed INFO @ Tue, 16 Jun 2020 09:56:00: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling