Job ID = 6367922 SRX = SRX4200531 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:50:22 prefetch.2.10.7: 1) Downloading 'SRR7297997'... 2020-06-15T23:50:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:52:18 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:52:19 prefetch.2.10.7: 'SRR7297997' is valid 2020-06-15T23:52:19 prefetch.2.10.7: 1) 'SRR7297997' was downloaded successfully Read 11147180 spots for SRR7297997/SRR7297997.sra Written 11147180 spots for SRR7297997/SRR7297997.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: 00:02:36 11147180 reads; of these: 11147180 (100.00%) were unpaired; of these: 192193 (1.72%) aligned 0 times 8676941 (77.84%) aligned exactly 1 time 2278046 (20.44%) aligned >1 times 98.28% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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] 2859710 / 10954987 = 0.2610 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 08:58:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.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 08:58:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:58:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:58:48: 1000000 INFO @ Tue, 16 Jun 2020 08:58:55: 2000000 INFO @ Tue, 16 Jun 2020 08:59:02: 3000000 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 08:59:10: 4000000 INFO @ Tue, 16 Jun 2020 08:59:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.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 08:59:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:18: 5000000 INFO @ Tue, 16 Jun 2020 08:59:18: 1000000 INFO @ Tue, 16 Jun 2020 08:59:26: 2000000 INFO @ Tue, 16 Jun 2020 08:59:26: 6000000 INFO @ Tue, 16 Jun 2020 08:59:33: 3000000 INFO @ Tue, 16 Jun 2020 08:59:34: 7000000 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 08:59:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.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 08:59:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:41: 4000000 INFO @ Tue, 16 Jun 2020 08:59:42: 8000000 INFO @ Tue, 16 Jun 2020 08:59:43: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:59:43: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:59:43: #1 total tags in treatment: 8095277 INFO @ Tue, 16 Jun 2020 08:59:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:59:43: #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 08:59:43: #1 tags after filtering in treatment: 8095277 INFO @ Tue, 16 Jun 2020 08:59:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:59:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:59:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:59:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:59:43: #2 number of paired peaks: 289 WARNING @ Tue, 16 Jun 2020 08:59:43: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Tue, 16 Jun 2020 08:59:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:59:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:59:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:59:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:59:43: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 08:59:43: #2 alternative fragment length(s) may be 2,44,516,568,580,582,591 bps INFO @ Tue, 16 Jun 2020 08:59:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.05_model.r WARNING @ Tue, 16 Jun 2020 08:59:43: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:59:43: #2 You may need to consider one of the other alternative d(s): 2,44,516,568,580,582,591 WARNING @ Tue, 16 Jun 2020 08:59:43: #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 08:59:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:59:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:59:48: 5000000 INFO @ Tue, 16 Jun 2020 08:59:49: 1000000 INFO @ Tue, 16 Jun 2020 08:59:56: 6000000 INFO @ Tue, 16 Jun 2020 08:59:58: 2000000 INFO @ Tue, 16 Jun 2020 09:00:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:00:03: 7000000 INFO @ Tue, 16 Jun 2020 09:00:07: 3000000 INFO @ Tue, 16 Jun 2020 09:00:11: 8000000 INFO @ Tue, 16 Jun 2020 09:00:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:00:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:00:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.05_summits.bed INFO @ Tue, 16 Jun 2020 09:00:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (413 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:00:12: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:00:12: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:00:12: #1 total tags in treatment: 8095277 INFO @ Tue, 16 Jun 2020 09:00:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:00:12: #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 09:00:12: #1 tags after filtering in treatment: 8095277 INFO @ Tue, 16 Jun 2020 09:00:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:00:12: #1 finished! INFO @ Tue, 16 Jun 2020 09:00:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:00:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:00:13: #2 number of paired peaks: 289 WARNING @ Tue, 16 Jun 2020 09:00:13: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Tue, 16 Jun 2020 09:00:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:00:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:00:13: end of X-cor INFO @ Tue, 16 Jun 2020 09:00:13: #2 finished! INFO @ Tue, 16 Jun 2020 09:00:13: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:00:13: #2 alternative fragment length(s) may be 2,44,516,568,580,582,591 bps INFO @ Tue, 16 Jun 2020 09:00:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.10_model.r WARNING @ Tue, 16 Jun 2020 09:00:13: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:00:13: #2 You may need to consider one of the other alternative d(s): 2,44,516,568,580,582,591 WARNING @ Tue, 16 Jun 2020 09:00:13: #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 09:00:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:00:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:00:15: 4000000 INFO @ Tue, 16 Jun 2020 09:00:23: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:00:31: 6000000 INFO @ Tue, 16 Jun 2020 09:00:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:00:39: 7000000 INFO @ Tue, 16 Jun 2020 09:00:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:00:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:00:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.10_summits.bed INFO @ Tue, 16 Jun 2020 09:00:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (183 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:00:48: 8000000 INFO @ Tue, 16 Jun 2020 09:00:48: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:00:48: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:00:48: #1 total tags in treatment: 8095277 INFO @ Tue, 16 Jun 2020 09:00:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:00:48: #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 09:00:48: #1 tags after filtering in treatment: 8095277 INFO @ Tue, 16 Jun 2020 09:00:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:00:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:00:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:00:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:00:49: #2 number of paired peaks: 289 WARNING @ Tue, 16 Jun 2020 09:00:49: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Tue, 16 Jun 2020 09:00:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:00:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:00:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:00:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:00:49: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:00:49: #2 alternative fragment length(s) may be 2,44,516,568,580,582,591 bps INFO @ Tue, 16 Jun 2020 09:00:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.20_model.r WARNING @ Tue, 16 Jun 2020 09:00:49: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:00:49: #2 You may need to consider one of the other alternative d(s): 2,44,516,568,580,582,591 WARNING @ Tue, 16 Jun 2020 09:00:49: #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 09:00:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:00:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:01:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:01:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:01:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:01:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4200531/SRX4200531.20_summits.bed INFO @ Tue, 16 Jun 2020 09:01:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (44 records, 4 fields): 1 millis CompletedMACS2peakCalling