Job ID = 6369017 SRX = SRX982083 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:38:46 prefetch.2.10.7: 1) Downloading 'SRR1956569'... 2020-06-16T00:38:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:39:35 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:39:35 prefetch.2.10.7: 'SRR1956569' is valid 2020-06-16T00:39:35 prefetch.2.10.7: 1) 'SRR1956569' was downloaded successfully Read 4408512 spots for SRR1956569/SRR1956569.sra Written 4408512 spots for SRR1956569/SRR1956569.sra 2020-06-16T00:40:01 prefetch.2.10.7: 1) Downloading 'SRR1956570'... 2020-06-16T00:40:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:40:42 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:40:42 prefetch.2.10.7: 'SRR1956570' is valid 2020-06-16T00:40:42 prefetch.2.10.7: 1) 'SRR1956570' was downloaded successfully Read 4925522 spots for SRR1956570/SRR1956570.sra Written 4925522 spots for SRR1956570/SRR1956570.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: 00:01:59 9334034 reads; of these: 9334034 (100.00%) were unpaired; of these: 360338 (3.86%) aligned 0 times 7405897 (79.34%) aligned exactly 1 time 1567799 (16.80%) aligned >1 times 96.14% overall alignment rate Time searching: 00:01:59 Overall time: 00:01:59 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_rmdupse_core] 605836 / 8973696 = 0.0675 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 09:46:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.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 09:46:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:56: 1000000 INFO @ Tue, 16 Jun 2020 09:47:02: 2000000 INFO @ Tue, 16 Jun 2020 09:47:08: 3000000 INFO @ Tue, 16 Jun 2020 09:47:14: 4000000 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 09:47:20: 5000000 INFO @ Tue, 16 Jun 2020 09:47:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.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 09:47:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:26: 6000000 INFO @ Tue, 16 Jun 2020 09:47:27: 1000000 INFO @ Tue, 16 Jun 2020 09:47:32: 7000000 INFO @ Tue, 16 Jun 2020 09:47:34: 2000000 INFO @ Tue, 16 Jun 2020 09:47:38: 8000000 INFO @ Tue, 16 Jun 2020 09:47:40: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:47:40: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:47:40: #1 total tags in treatment: 8367860 INFO @ Tue, 16 Jun 2020 09:47:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:47:40: #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 09:47:41: #1 tags after filtering in treatment: 8367860 INFO @ Tue, 16 Jun 2020 09:47:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:47:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:47:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:47:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:47:41: 3000000 INFO @ Tue, 16 Jun 2020 09:47:41: #2 number of paired peaks: 334 WARNING @ Tue, 16 Jun 2020 09:47:41: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Tue, 16 Jun 2020 09:47:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:47:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:47:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:47:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:47:41: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:47:41: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 16 Jun 2020 09:47:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.05_model.r WARNING @ Tue, 16 Jun 2020 09:47:41: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:47:41: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 16 Jun 2020 09:47:41: #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 09:47:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:47:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:47:47: 4000000 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 09:47:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.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 09:47:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:54: 5000000 INFO @ Tue, 16 Jun 2020 09:47:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:47:58: 1000000 INFO @ Tue, 16 Jun 2020 09:48:02: 6000000 INFO @ Tue, 16 Jun 2020 09:48:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:48:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:48:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.05_summits.bed INFO @ Tue, 16 Jun 2020 09:48:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (625 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:48:05: 2000000 INFO @ Tue, 16 Jun 2020 09:48:09: 7000000 INFO @ Tue, 16 Jun 2020 09:48:13: 3000000 INFO @ Tue, 16 Jun 2020 09:48:16: 8000000 INFO @ Tue, 16 Jun 2020 09:48:18: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:48:18: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:48:18: #1 total tags in treatment: 8367860 INFO @ Tue, 16 Jun 2020 09:48:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:18: #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 09:48:19: #1 tags after filtering in treatment: 8367860 INFO @ Tue, 16 Jun 2020 09:48:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:48:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:48:19: #2 number of paired peaks: 334 WARNING @ Tue, 16 Jun 2020 09:48:19: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Tue, 16 Jun 2020 09:48:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:19: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:48:19: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 16 Jun 2020 09:48:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.10_model.r WARNING @ Tue, 16 Jun 2020 09:48:19: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:48:19: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 16 Jun 2020 09:48:19: #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 09:48:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:48:20: 4000000 INFO @ Tue, 16 Jun 2020 09:48:26: 5000000 INFO @ Tue, 16 Jun 2020 09:48:33: 6000000 INFO @ Tue, 16 Jun 2020 09:48:35: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:48:40: 7000000 INFO @ Tue, 16 Jun 2020 09:48:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:48:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:48:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.10_summits.bed INFO @ Tue, 16 Jun 2020 09:48:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (351 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:48:46: 8000000 INFO @ Tue, 16 Jun 2020 09:48:49: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:48:49: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:48:49: #1 total tags in treatment: 8367860 INFO @ Tue, 16 Jun 2020 09:48:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:49: #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 09:48:49: #1 tags after filtering in treatment: 8367860 INFO @ Tue, 16 Jun 2020 09:48:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:48:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:48:49: #2 number of paired peaks: 334 WARNING @ Tue, 16 Jun 2020 09:48:49: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Tue, 16 Jun 2020 09:48:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:49: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:48:49: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 16 Jun 2020 09:48:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.20_model.r WARNING @ Tue, 16 Jun 2020 09:48:49: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:48:49: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 16 Jun 2020 09:48:49: #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 09:48:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:49:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982083/SRX982083.20_summits.bed INFO @ Tue, 16 Jun 2020 09:49:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (147 records, 4 fields): 2 millis CompletedMACS2peakCalling