Job ID = 6366964 SRX = SRX2576663 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:09:01 prefetch.2.10.7: 1) Downloading 'SRR5272620'... 2020-06-15T23:09:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:11:57 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:11:57 prefetch.2.10.7: 1) 'SRR5272620' was downloaded successfully Read 23882510 spots for SRR5272620/SRR5272620.sra Written 23882510 spots for SRR5272620/SRR5272620.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: 00:05:28 23882510 reads; of these: 23882510 (100.00%) were unpaired; of these: 342758 (1.44%) aligned 0 times 19591525 (82.03%) aligned exactly 1 time 3948227 (16.53%) aligned >1 times 98.56% overall alignment rate Time searching: 00:05:28 Overall time: 00:05:28 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] 3278485 / 23539752 = 0.1393 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 08:24:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.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 08:24:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:36: 1000000 INFO @ Tue, 16 Jun 2020 08:24:41: 2000000 INFO @ Tue, 16 Jun 2020 08:24:46: 3000000 INFO @ Tue, 16 Jun 2020 08:24:51: 4000000 INFO @ Tue, 16 Jun 2020 08:24:56: 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 08:25:01: 6000000 INFO @ Tue, 16 Jun 2020 08:25:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.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 08:25:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:06: 7000000 INFO @ Tue, 16 Jun 2020 08:25:07: 1000000 INFO @ Tue, 16 Jun 2020 08:25:11: 8000000 INFO @ Tue, 16 Jun 2020 08:25:12: 2000000 INFO @ Tue, 16 Jun 2020 08:25:16: 9000000 INFO @ Tue, 16 Jun 2020 08:25:17: 3000000 INFO @ Tue, 16 Jun 2020 08:25:21: 10000000 INFO @ Tue, 16 Jun 2020 08:25:22: 4000000 INFO @ Tue, 16 Jun 2020 08:25:26: 11000000 INFO @ Tue, 16 Jun 2020 08:25:27: 5000000 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 08:25:31: 12000000 INFO @ Tue, 16 Jun 2020 08:25:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.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 08:25:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:32: 6000000 INFO @ Tue, 16 Jun 2020 08:25:36: 13000000 INFO @ Tue, 16 Jun 2020 08:25:37: 1000000 INFO @ Tue, 16 Jun 2020 08:25:38: 7000000 INFO @ Tue, 16 Jun 2020 08:25:42: 14000000 INFO @ Tue, 16 Jun 2020 08:25:42: 2000000 INFO @ Tue, 16 Jun 2020 08:25:43: 8000000 INFO @ Tue, 16 Jun 2020 08:25:47: 15000000 INFO @ Tue, 16 Jun 2020 08:25:47: 3000000 INFO @ Tue, 16 Jun 2020 08:25:48: 9000000 INFO @ Tue, 16 Jun 2020 08:25:52: 16000000 INFO @ Tue, 16 Jun 2020 08:25:53: 4000000 INFO @ Tue, 16 Jun 2020 08:25:53: 10000000 INFO @ Tue, 16 Jun 2020 08:25:58: 17000000 INFO @ Tue, 16 Jun 2020 08:25:58: 5000000 INFO @ Tue, 16 Jun 2020 08:25:59: 11000000 INFO @ Tue, 16 Jun 2020 08:26:03: 18000000 INFO @ Tue, 16 Jun 2020 08:26:03: 6000000 INFO @ Tue, 16 Jun 2020 08:26:04: 12000000 INFO @ Tue, 16 Jun 2020 08:26:08: 19000000 INFO @ Tue, 16 Jun 2020 08:26:09: 7000000 INFO @ Tue, 16 Jun 2020 08:26:09: 13000000 INFO @ Tue, 16 Jun 2020 08:26:13: 20000000 INFO @ Tue, 16 Jun 2020 08:26:14: 8000000 INFO @ Tue, 16 Jun 2020 08:26:14: 14000000 INFO @ Tue, 16 Jun 2020 08:26:15: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:26:15: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:26:15: #1 total tags in treatment: 20261267 INFO @ Tue, 16 Jun 2020 08:26:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:15: #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 08:26:15: #1 tags after filtering in treatment: 20261267 INFO @ Tue, 16 Jun 2020 08:26:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:17: #2 number of paired peaks: 190 WARNING @ Tue, 16 Jun 2020 08:26:17: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:17: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:26:17: #2 alternative fragment length(s) may be 1,49,577 bps INFO @ Tue, 16 Jun 2020 08:26:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.05_model.r WARNING @ Tue, 16 Jun 2020 08:26:17: #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 08:26:17: #2 You may need to consider one of the other alternative d(s): 1,49,577 WARNING @ Tue, 16 Jun 2020 08:26:17: #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 08:26:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:19: 9000000 INFO @ Tue, 16 Jun 2020 08:26:20: 15000000 INFO @ Tue, 16 Jun 2020 08:26:24: 10000000 INFO @ Tue, 16 Jun 2020 08:26:25: 16000000 INFO @ Tue, 16 Jun 2020 08:26:30: 11000000 INFO @ Tue, 16 Jun 2020 08:26:30: 17000000 INFO @ Tue, 16 Jun 2020 08:26:35: 12000000 INFO @ Tue, 16 Jun 2020 08:26:35: 18000000 INFO @ Tue, 16 Jun 2020 08:26:40: 13000000 INFO @ Tue, 16 Jun 2020 08:26:41: 19000000 INFO @ Tue, 16 Jun 2020 08:26:46: 14000000 INFO @ Tue, 16 Jun 2020 08:26:46: 20000000 INFO @ Tue, 16 Jun 2020 08:26:48: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:26:48: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:26:48: #1 total tags in treatment: 20261267 INFO @ Tue, 16 Jun 2020 08:26:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:48: #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 08:26:48: #1 tags after filtering in treatment: 20261267 INFO @ Tue, 16 Jun 2020 08:26:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:49: #2 number of paired peaks: 190 WARNING @ Tue, 16 Jun 2020 08:26:49: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:49: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:26:49: #2 alternative fragment length(s) may be 1,49,577 bps INFO @ Tue, 16 Jun 2020 08:26:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.10_model.r WARNING @ Tue, 16 Jun 2020 08:26:49: #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 08:26:49: #2 You may need to consider one of the other alternative d(s): 1,49,577 WARNING @ Tue, 16 Jun 2020 08:26:49: #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 08:26:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:51: 15000000 INFO @ Tue, 16 Jun 2020 08:26:56: 16000000 INFO @ Tue, 16 Jun 2020 08:27:01: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:27:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.05_summits.bed INFO @ Tue, 16 Jun 2020 08:27:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:27:06: 18000000 INFO @ Tue, 16 Jun 2020 08:27:11: 19000000 INFO @ Tue, 16 Jun 2020 08:27:17: 20000000 INFO @ Tue, 16 Jun 2020 08:27:18: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:27:18: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:27:18: #1 total tags in treatment: 20261267 INFO @ Tue, 16 Jun 2020 08:27:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:18: #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 08:27:18: #1 tags after filtering in treatment: 20261267 INFO @ Tue, 16 Jun 2020 08:27:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:20: #2 number of paired peaks: 190 WARNING @ Tue, 16 Jun 2020 08:27:20: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:20: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:27:20: #2 alternative fragment length(s) may be 1,49,577 bps INFO @ Tue, 16 Jun 2020 08:27:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.20_model.r WARNING @ Tue, 16 Jun 2020 08:27:20: #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 08:27:20: #2 You may need to consider one of the other alternative d(s): 1,49,577 WARNING @ Tue, 16 Jun 2020 08:27:20: #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 08:27:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.10_summits.bed INFO @ Tue, 16 Jun 2020 08:27:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:27:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:28:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576663/SRX2576663.20_summits.bed INFO @ Tue, 16 Jun 2020 08:28:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling