Job ID = 6369035 SRX = SRX982099 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:36:46 prefetch.2.10.7: 1) Downloading 'SRR1956586'... 2020-06-16T00:36:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:38:13 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:38:13 prefetch.2.10.7: 'SRR1956586' is valid 2020-06-16T00:38:13 prefetch.2.10.7: 1) 'SRR1956586' was downloaded successfully Read 11198348 spots for SRR1956586/SRR1956586.sra Written 11198348 spots for SRR1956586/SRR1956586.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: 00:02:34 11198348 reads; of these: 11198348 (100.00%) were unpaired; of these: 94020 (0.84%) aligned 0 times 9240675 (82.52%) aligned exactly 1 time 1863653 (16.64%) aligned >1 times 99.16% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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] 890691 / 11104328 = 0.0802 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 09:44:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.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 09:44:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:36: 1000000 INFO @ Tue, 16 Jun 2020 09:44:41: 2000000 INFO @ Tue, 16 Jun 2020 09:44:46: 3000000 INFO @ Tue, 16 Jun 2020 09:44:52: 4000000 INFO @ Tue, 16 Jun 2020 09:44:57: 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 09:45:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.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 09:45:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:45:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:02: 6000000 INFO @ Tue, 16 Jun 2020 09:45:06: 1000000 INFO @ Tue, 16 Jun 2020 09:45:08: 7000000 INFO @ Tue, 16 Jun 2020 09:45:12: 2000000 INFO @ Tue, 16 Jun 2020 09:45:14: 8000000 INFO @ Tue, 16 Jun 2020 09:45:18: 3000000 INFO @ Tue, 16 Jun 2020 09:45:19: 9000000 INFO @ Tue, 16 Jun 2020 09:45:24: 4000000 INFO @ Tue, 16 Jun 2020 09:45:25: 10000000 INFO @ Tue, 16 Jun 2020 09:45:26: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:45:26: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:45:26: #1 total tags in treatment: 10213637 INFO @ Tue, 16 Jun 2020 09:45:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:26: #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 09:45:27: #1 tags after filtering in treatment: 10213637 INFO @ Tue, 16 Jun 2020 09:45:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:45:27: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:27: #2 number of paired peaks: 320 WARNING @ Tue, 16 Jun 2020 09:45:27: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Tue, 16 Jun 2020 09:45:27: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:27: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:27: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:27: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:27: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:45:27: #2 alternative fragment length(s) may be 2,52 bps INFO @ Tue, 16 Jun 2020 09:45:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.05_model.r WARNING @ Tue, 16 Jun 2020 09:45:27: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:45:27: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Tue, 16 Jun 2020 09:45:27: #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 09:45:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:27: #3 Pre-compute pvalue-qvalue table... 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 09:45:29: 5000000 INFO @ Tue, 16 Jun 2020 09:45:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.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 09:45:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:45:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:35: 6000000 INFO @ Tue, 16 Jun 2020 09:45:38: 1000000 INFO @ Tue, 16 Jun 2020 09:45:41: 7000000 INFO @ Tue, 16 Jun 2020 09:45:45: 2000000 INFO @ Tue, 16 Jun 2020 09:45:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:45:48: 8000000 INFO @ Tue, 16 Jun 2020 09:45:52: 3000000 INFO @ Tue, 16 Jun 2020 09:45:54: 9000000 INFO @ Tue, 16 Jun 2020 09:45:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:45:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:45:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.05_summits.bed INFO @ Tue, 16 Jun 2020 09:45:56: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (613 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:45:59: 4000000 INFO @ Tue, 16 Jun 2020 09:46:00: 10000000 INFO @ Tue, 16 Jun 2020 09:46:01: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:46:01: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:46:01: #1 total tags in treatment: 10213637 INFO @ Tue, 16 Jun 2020 09:46:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:01: #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 09:46:02: #1 tags after filtering in treatment: 10213637 INFO @ Tue, 16 Jun 2020 09:46:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:46:02: #2 number of paired peaks: 320 WARNING @ Tue, 16 Jun 2020 09:46:02: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Tue, 16 Jun 2020 09:46:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:02: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:46:02: #2 alternative fragment length(s) may be 2,52 bps INFO @ Tue, 16 Jun 2020 09:46:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.10_model.r WARNING @ Tue, 16 Jun 2020 09:46:02: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:46:02: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Tue, 16 Jun 2020 09:46:02: #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 09:46:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:46:06: 5000000 INFO @ Tue, 16 Jun 2020 09:46:12: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:46:19: 7000000 INFO @ Tue, 16 Jun 2020 09:46:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:46:26: 8000000 INFO @ Tue, 16 Jun 2020 09:46:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:46:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:46:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.10_summits.bed INFO @ Tue, 16 Jun 2020 09:46:31: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (414 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:46:32: 9000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:46:39: 10000000 INFO @ Tue, 16 Jun 2020 09:46:41: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:46:41: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:46:41: #1 total tags in treatment: 10213637 INFO @ Tue, 16 Jun 2020 09:46:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:41: #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 09:46:41: #1 tags after filtering in treatment: 10213637 INFO @ Tue, 16 Jun 2020 09:46:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:46:41: #2 number of paired peaks: 320 WARNING @ Tue, 16 Jun 2020 09:46:41: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Tue, 16 Jun 2020 09:46:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:41: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:46:41: #2 alternative fragment length(s) may be 2,52 bps INFO @ Tue, 16 Jun 2020 09:46:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.20_model.r WARNING @ Tue, 16 Jun 2020 09:46:41: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:46:41: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Tue, 16 Jun 2020 09:46:41: #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 09:46:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:47:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:47:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982099/SRX982099.20_summits.bed INFO @ Tue, 16 Jun 2020 09:47:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (182 records, 4 fields): 1 millis CompletedMACS2peakCalling