Job ID = 6368653 SRX = SRX529213 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:27:31 prefetch.2.10.7: 1) Downloading 'SRR1265817'... 2020-06-16T00:27:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:29:07 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:29:08 prefetch.2.10.7: 'SRR1265817' is valid 2020-06-16T00:29:08 prefetch.2.10.7: 1) 'SRR1265817' was downloaded successfully Read 19253374 spots for SRR1265817/SRR1265817.sra Written 19253374 spots for SRR1265817/SRR1265817.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: 00:03:15 19253374 reads; of these: 19253374 (100.00%) were unpaired; of these: 167031 (0.87%) aligned 0 times 16239996 (84.35%) aligned exactly 1 time 2846347 (14.78%) aligned >1 times 99.13% overall alignment rate Time searching: 00:03:15 Overall time: 00:03:15 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 8 files... [bam_rmdupse_core] 1844761 / 19086343 = 0.0967 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 09:37:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.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 09:37:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:35: 1000000 INFO @ Tue, 16 Jun 2020 09:37:40: 2000000 INFO @ Tue, 16 Jun 2020 09:37:46: 3000000 INFO @ Tue, 16 Jun 2020 09:37:51: 4000000 INFO @ Tue, 16 Jun 2020 09:37:56: 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 09:38:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.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 09:38:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:02: 6000000 INFO @ Tue, 16 Jun 2020 09:38:06: 1000000 INFO @ Tue, 16 Jun 2020 09:38:08: 7000000 INFO @ Tue, 16 Jun 2020 09:38:12: 2000000 INFO @ Tue, 16 Jun 2020 09:38:14: 8000000 INFO @ Tue, 16 Jun 2020 09:38:18: 3000000 INFO @ Tue, 16 Jun 2020 09:38:20: 9000000 INFO @ Tue, 16 Jun 2020 09:38:24: 4000000 INFO @ Tue, 16 Jun 2020 09:38:26: 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 09:38:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.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 09:38:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:30: 5000000 INFO @ Tue, 16 Jun 2020 09:38:32: 11000000 INFO @ Tue, 16 Jun 2020 09:38:36: 6000000 INFO @ Tue, 16 Jun 2020 09:38:37: 1000000 INFO @ Tue, 16 Jun 2020 09:38:39: 12000000 INFO @ Tue, 16 Jun 2020 09:38:43: 7000000 INFO @ Tue, 16 Jun 2020 09:38:44: 2000000 INFO @ Tue, 16 Jun 2020 09:38:46: 13000000 INFO @ Tue, 16 Jun 2020 09:38:50: 8000000 INFO @ Tue, 16 Jun 2020 09:38:51: 3000000 INFO @ Tue, 16 Jun 2020 09:38:52: 14000000 INFO @ Tue, 16 Jun 2020 09:38:56: 9000000 INFO @ Tue, 16 Jun 2020 09:38:58: 4000000 INFO @ Tue, 16 Jun 2020 09:38:59: 15000000 INFO @ Tue, 16 Jun 2020 09:39:03: 10000000 INFO @ Tue, 16 Jun 2020 09:39:05: 5000000 INFO @ Tue, 16 Jun 2020 09:39:06: 16000000 INFO @ Tue, 16 Jun 2020 09:39:10: 11000000 INFO @ Tue, 16 Jun 2020 09:39:12: 6000000 INFO @ Tue, 16 Jun 2020 09:39:13: 17000000 INFO @ Tue, 16 Jun 2020 09:39:14: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:39:14: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:39:14: #1 total tags in treatment: 17241582 INFO @ Tue, 16 Jun 2020 09:39:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:14: #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 09:39:15: #1 tags after filtering in treatment: 17241582 INFO @ Tue, 16 Jun 2020 09:39:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:16: #2 number of paired peaks: 202 WARNING @ Tue, 16 Jun 2020 09:39:16: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:16: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:16: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:39:16: #2 alternative fragment length(s) may be 1,32 bps INFO @ Tue, 16 Jun 2020 09:39:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.05_model.r WARNING @ Tue, 16 Jun 2020 09:39:16: #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 09:39:16: #2 You may need to consider one of the other alternative d(s): 1,32 WARNING @ Tue, 16 Jun 2020 09:39:16: #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 09:39:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:39:17: 12000000 INFO @ Tue, 16 Jun 2020 09:39:19: 7000000 INFO @ Tue, 16 Jun 2020 09:39:23: 13000000 INFO @ Tue, 16 Jun 2020 09:39:26: 8000000 INFO @ Tue, 16 Jun 2020 09:39:30: 14000000 INFO @ Tue, 16 Jun 2020 09:39:33: 9000000 INFO @ Tue, 16 Jun 2020 09:39:37: 15000000 INFO @ Tue, 16 Jun 2020 09:39:41: 10000000 INFO @ Tue, 16 Jun 2020 09:39:43: 16000000 INFO @ Tue, 16 Jun 2020 09:39:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:39:48: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:39:50: 17000000 INFO @ Tue, 16 Jun 2020 09:39:52: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:39:52: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:39:52: #1 total tags in treatment: 17241582 INFO @ Tue, 16 Jun 2020 09:39:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:52: #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 09:39:52: #1 tags after filtering in treatment: 17241582 INFO @ Tue, 16 Jun 2020 09:39:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:53: #2 number of paired peaks: 202 WARNING @ Tue, 16 Jun 2020 09:39:53: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:53: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:39:53: #2 alternative fragment length(s) may be 1,32 bps INFO @ Tue, 16 Jun 2020 09:39:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.10_model.r WARNING @ Tue, 16 Jun 2020 09:39:53: #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 09:39:53: #2 You may need to consider one of the other alternative d(s): 1,32 WARNING @ Tue, 16 Jun 2020 09:39:53: #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 09:39:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:39:55: 12000000 INFO @ Tue, 16 Jun 2020 09:39:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:39:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:39:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.05_summits.bed INFO @ Tue, 16 Jun 2020 09:39:59: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:40:02: 13000000 INFO @ Tue, 16 Jun 2020 09:40:08: 14000000 INFO @ Tue, 16 Jun 2020 09:40:15: 15000000 INFO @ Tue, 16 Jun 2020 09:40:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:21: 16000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:40:28: 17000000 INFO @ Tue, 16 Jun 2020 09:40:29: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:40:29: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:40:29: #1 total tags in treatment: 17241582 INFO @ Tue, 16 Jun 2020 09:40:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:29: #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 09:40:30: #1 tags after filtering in treatment: 17241582 INFO @ Tue, 16 Jun 2020 09:40:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:30: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:31: #2 number of paired peaks: 202 WARNING @ Tue, 16 Jun 2020 09:40:31: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:31: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:40:31: #2 alternative fragment length(s) may be 1,32 bps INFO @ Tue, 16 Jun 2020 09:40:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.20_model.r WARNING @ Tue, 16 Jun 2020 09:40:31: #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 09:40:31: #2 You may need to consider one of the other alternative d(s): 1,32 WARNING @ Tue, 16 Jun 2020 09:40:31: #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 09:40:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.10_summits.bed INFO @ Tue, 16 Jun 2020 09:40:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:40:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529213/SRX529213.20_summits.bed INFO @ Tue, 16 Jun 2020 09:41:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling