Job ID = 6368731 SRX = SRX5402755 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:23:36 prefetch.2.10.7: 1) Downloading 'SRR8602989'... 2020-06-16T00:23:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:26:04 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:26:04 prefetch.2.10.7: 1) 'SRR8602989' was downloaded successfully Read 29239844 spots for SRR8602989/SRR8602989.sra Written 29239844 spots for SRR8602989/SRR8602989.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: 00:06:01 29239844 reads; of these: 29239844 (100.00%) were unpaired; of these: 2502314 (8.56%) aligned 0 times 21333743 (72.96%) aligned exactly 1 time 5403787 (18.48%) aligned >1 times 91.44% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 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] 3581217 / 26737530 = 0.1339 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 09:39:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.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 09:39:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:20: 1000000 INFO @ Tue, 16 Jun 2020 09:39:25: 2000000 INFO @ Tue, 16 Jun 2020 09:39:30: 3000000 INFO @ Tue, 16 Jun 2020 09:39:35: 4000000 INFO @ Tue, 16 Jun 2020 09:39:41: 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 09:39:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.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 09:39:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:46: 6000000 INFO @ Tue, 16 Jun 2020 09:39:52: 1000000 INFO @ Tue, 16 Jun 2020 09:39:52: 7000000 INFO @ Tue, 16 Jun 2020 09:39:59: 2000000 INFO @ Tue, 16 Jun 2020 09:39:59: 8000000 INFO @ Tue, 16 Jun 2020 09:40:05: 9000000 INFO @ Tue, 16 Jun 2020 09:40:06: 3000000 INFO @ Tue, 16 Jun 2020 09:40:11: 10000000 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 09:40:12: 4000000 INFO @ Tue, 16 Jun 2020 09:40:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.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 09:40:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:18: 11000000 INFO @ Tue, 16 Jun 2020 09:40:20: 5000000 INFO @ Tue, 16 Jun 2020 09:40:22: 1000000 INFO @ Tue, 16 Jun 2020 09:40:24: 12000000 INFO @ Tue, 16 Jun 2020 09:40:27: 6000000 INFO @ Tue, 16 Jun 2020 09:40:29: 2000000 INFO @ Tue, 16 Jun 2020 09:40:30: 13000000 INFO @ Tue, 16 Jun 2020 09:40:34: 7000000 INFO @ Tue, 16 Jun 2020 09:40:36: 3000000 INFO @ Tue, 16 Jun 2020 09:40:37: 14000000 INFO @ Tue, 16 Jun 2020 09:40:41: 8000000 INFO @ Tue, 16 Jun 2020 09:40:43: 4000000 INFO @ Tue, 16 Jun 2020 09:40:43: 15000000 INFO @ Tue, 16 Jun 2020 09:40:48: 9000000 INFO @ Tue, 16 Jun 2020 09:40:49: 16000000 INFO @ Tue, 16 Jun 2020 09:40:50: 5000000 INFO @ Tue, 16 Jun 2020 09:40:54: 10000000 INFO @ Tue, 16 Jun 2020 09:40:56: 17000000 INFO @ Tue, 16 Jun 2020 09:40:57: 6000000 INFO @ Tue, 16 Jun 2020 09:41:01: 11000000 INFO @ Tue, 16 Jun 2020 09:41:02: 18000000 INFO @ Tue, 16 Jun 2020 09:41:04: 7000000 INFO @ Tue, 16 Jun 2020 09:41:08: 12000000 INFO @ Tue, 16 Jun 2020 09:41:09: 19000000 INFO @ Tue, 16 Jun 2020 09:41:11: 8000000 INFO @ Tue, 16 Jun 2020 09:41:15: 20000000 INFO @ Tue, 16 Jun 2020 09:41:15: 13000000 INFO @ Tue, 16 Jun 2020 09:41:17: 9000000 INFO @ Tue, 16 Jun 2020 09:41:21: 21000000 INFO @ Tue, 16 Jun 2020 09:41:22: 14000000 INFO @ Tue, 16 Jun 2020 09:41:24: 10000000 INFO @ Tue, 16 Jun 2020 09:41:28: 22000000 INFO @ Tue, 16 Jun 2020 09:41:29: 15000000 INFO @ Tue, 16 Jun 2020 09:41:31: 11000000 INFO @ Tue, 16 Jun 2020 09:41:34: 23000000 INFO @ Tue, 16 Jun 2020 09:41:35: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:41:35: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:41:35: #1 total tags in treatment: 23156313 INFO @ Tue, 16 Jun 2020 09:41:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:35: #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 09:41:35: 16000000 INFO @ Tue, 16 Jun 2020 09:41:36: #1 tags after filtering in treatment: 23156313 INFO @ Tue, 16 Jun 2020 09:41:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:36: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:37: #2 number of paired peaks: 176 WARNING @ Tue, 16 Jun 2020 09:41:37: 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 @ Tue, 16 Jun 2020 09:41:37: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:37: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:37: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:37: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:37: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:41:37: #2 alternative fragment length(s) may be 1,35,533,550,572,597 bps INFO @ Tue, 16 Jun 2020 09:41:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.05_model.r WARNING @ Tue, 16 Jun 2020 09:41:37: #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 09:41:37: #2 You may need to consider one of the other alternative d(s): 1,35,533,550,572,597 WARNING @ Tue, 16 Jun 2020 09:41:37: #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 09:41:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:38: 12000000 INFO @ Tue, 16 Jun 2020 09:41:42: 17000000 INFO @ Tue, 16 Jun 2020 09:41:45: 13000000 INFO @ Tue, 16 Jun 2020 09:41:49: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:41:52: 14000000 INFO @ Tue, 16 Jun 2020 09:41:56: 19000000 INFO @ Tue, 16 Jun 2020 09:41:59: 15000000 INFO @ Tue, 16 Jun 2020 09:42:03: 20000000 INFO @ Tue, 16 Jun 2020 09:42:06: 16000000 INFO @ Tue, 16 Jun 2020 09:42:10: 21000000 INFO @ Tue, 16 Jun 2020 09:42:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:13: 17000000 INFO @ Tue, 16 Jun 2020 09:42:16: 22000000 INFO @ Tue, 16 Jun 2020 09:42:20: 18000000 INFO @ Tue, 16 Jun 2020 09:42:23: 23000000 INFO @ Tue, 16 Jun 2020 09:42:24: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:42:24: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:42:24: #1 total tags in treatment: 23156313 INFO @ Tue, 16 Jun 2020 09:42:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:24: #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 09:42:24: #1 tags after filtering in treatment: 23156313 INFO @ Tue, 16 Jun 2020 09:42:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:26: #2 number of paired peaks: 176 WARNING @ Tue, 16 Jun 2020 09:42:26: 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 @ Tue, 16 Jun 2020 09:42:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:26: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:42:26: #2 alternative fragment length(s) may be 1,35,533,550,572,597 bps INFO @ Tue, 16 Jun 2020 09:42:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.10_model.r WARNING @ Tue, 16 Jun 2020 09:42:26: #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 09:42:26: #2 You may need to consider one of the other alternative d(s): 1,35,533,550,572,597 WARNING @ Tue, 16 Jun 2020 09:42:26: #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 09:42:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:26: 19000000 INFO @ Tue, 16 Jun 2020 09:42:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.05_summits.bed INFO @ Tue, 16 Jun 2020 09:42:27: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:42:33: 20000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:42:39: 21000000 INFO @ Tue, 16 Jun 2020 09:42:45: 22000000 INFO @ Tue, 16 Jun 2020 09:42:51: 23000000 INFO @ Tue, 16 Jun 2020 09:42:52: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:42:52: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:42:52: #1 total tags in treatment: 23156313 INFO @ Tue, 16 Jun 2020 09:42:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:52: #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 09:42:53: #1 tags after filtering in treatment: 23156313 INFO @ Tue, 16 Jun 2020 09:42:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:53: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:54: #2 number of paired peaks: 176 WARNING @ Tue, 16 Jun 2020 09:42:54: 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 @ Tue, 16 Jun 2020 09:42:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:54: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:42:54: #2 alternative fragment length(s) may be 1,35,533,550,572,597 bps INFO @ Tue, 16 Jun 2020 09:42:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.20_model.r WARNING @ Tue, 16 Jun 2020 09:42:54: #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 09:42:54: #2 You may need to consider one of the other alternative d(s): 1,35,533,550,572,597 WARNING @ Tue, 16 Jun 2020 09:42:54: #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 09:42:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.10_summits.bed INFO @ Tue, 16 Jun 2020 09:43:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:43:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402755/SRX5402755.20_summits.bed INFO @ Tue, 16 Jun 2020 09:43:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling