Job ID = 6369006 SRX = SRX982072 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:40:59 prefetch.2.10.7: 1) Downloading 'SRR1956550'... 2020-06-16T00:40:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:42:43 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:42:43 prefetch.2.10.7: 'SRR1956550' is valid 2020-06-16T00:42:43 prefetch.2.10.7: 1) 'SRR1956550' was downloaded successfully Read 11041327 spots for SRR1956550/SRR1956550.sra Written 11041327 spots for SRR1956550/SRR1956550.sra 2020-06-16T00:43:27 prefetch.2.10.7: 1) Downloading 'SRR1956551'... 2020-06-16T00:43:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:46:18 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:46:19 prefetch.2.10.7: 'SRR1956551' is valid 2020-06-16T00:46:19 prefetch.2.10.7: 1) 'SRR1956551' was downloaded successfully Read 13062468 spots for SRR1956551/SRR1956551.sra Written 13062468 spots for SRR1956551/SRR1956551.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: 00:05:41 24103795 reads; of these: 24103795 (100.00%) were unpaired; of these: 565820 (2.35%) aligned 0 times 18984465 (78.76%) aligned exactly 1 time 4553510 (18.89%) aligned >1 times 97.65% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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] 4249809 / 23537975 = 0.1806 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 09:59:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.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 09:59:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:59:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:59:28: 1000000 INFO @ Tue, 16 Jun 2020 09:59:34: 2000000 INFO @ Tue, 16 Jun 2020 09:59:40: 3000000 INFO @ Tue, 16 Jun 2020 09:59:45: 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 09:59:51: 5000000 INFO @ Tue, 16 Jun 2020 09:59:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.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 09:59:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:59:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:59:57: 6000000 INFO @ Tue, 16 Jun 2020 09:59:58: 1000000 INFO @ Tue, 16 Jun 2020 10:00:03: 2000000 INFO @ Tue, 16 Jun 2020 10:00:03: 7000000 INFO @ Tue, 16 Jun 2020 10:00:09: 3000000 INFO @ Tue, 16 Jun 2020 10:00:09: 8000000 INFO @ Tue, 16 Jun 2020 10:00:15: 4000000 INFO @ Tue, 16 Jun 2020 10:00:15: 9000000 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 10:00:21: 5000000 INFO @ Tue, 16 Jun 2020 10:00:22: 10000000 INFO @ Tue, 16 Jun 2020 10:00:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.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 10:00:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:00:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:00:26: 6000000 INFO @ Tue, 16 Jun 2020 10:00:28: 11000000 INFO @ Tue, 16 Jun 2020 10:00:28: 1000000 INFO @ Tue, 16 Jun 2020 10:00:32: 7000000 INFO @ Tue, 16 Jun 2020 10:00:34: 12000000 INFO @ Tue, 16 Jun 2020 10:00:34: 2000000 INFO @ Tue, 16 Jun 2020 10:00:37: 8000000 INFO @ Tue, 16 Jun 2020 10:00:40: 13000000 INFO @ Tue, 16 Jun 2020 10:00:40: 3000000 INFO @ Tue, 16 Jun 2020 10:00:43: 9000000 INFO @ Tue, 16 Jun 2020 10:00:46: 14000000 INFO @ Tue, 16 Jun 2020 10:00:47: 4000000 INFO @ Tue, 16 Jun 2020 10:00:49: 10000000 INFO @ Tue, 16 Jun 2020 10:00:52: 15000000 INFO @ Tue, 16 Jun 2020 10:00:53: 5000000 INFO @ Tue, 16 Jun 2020 10:00:54: 11000000 INFO @ Tue, 16 Jun 2020 10:00:58: 16000000 INFO @ Tue, 16 Jun 2020 10:00:59: 6000000 INFO @ Tue, 16 Jun 2020 10:01:00: 12000000 INFO @ Tue, 16 Jun 2020 10:01:04: 17000000 INFO @ Tue, 16 Jun 2020 10:01:05: 7000000 INFO @ Tue, 16 Jun 2020 10:01:06: 13000000 INFO @ Tue, 16 Jun 2020 10:01:10: 18000000 INFO @ Tue, 16 Jun 2020 10:01:11: 14000000 INFO @ Tue, 16 Jun 2020 10:01:11: 8000000 INFO @ Tue, 16 Jun 2020 10:01:16: 19000000 INFO @ Tue, 16 Jun 2020 10:01:17: 15000000 INFO @ Tue, 16 Jun 2020 10:01:18: 9000000 INFO @ Tue, 16 Jun 2020 10:01:18: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:01:18: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:01:18: #1 total tags in treatment: 19288166 INFO @ Tue, 16 Jun 2020 10:01:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:01:18: #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 10:01:18: #1 tags after filtering in treatment: 19288166 INFO @ Tue, 16 Jun 2020 10:01:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:01:18: #1 finished! INFO @ Tue, 16 Jun 2020 10:01:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:01:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:01:19: #2 number of paired peaks: 292 WARNING @ Tue, 16 Jun 2020 10:01:19: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Tue, 16 Jun 2020 10:01:19: start model_add_line... INFO @ Tue, 16 Jun 2020 10:01:20: start X-correlation... INFO @ Tue, 16 Jun 2020 10:01:20: end of X-cor INFO @ Tue, 16 Jun 2020 10:01:20: #2 finished! INFO @ Tue, 16 Jun 2020 10:01:20: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 10:01:20: #2 alternative fragment length(s) may be 2,48,578 bps INFO @ Tue, 16 Jun 2020 10:01:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.05_model.r WARNING @ Tue, 16 Jun 2020 10:01:20: #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 10:01:20: #2 You may need to consider one of the other alternative d(s): 2,48,578 WARNING @ Tue, 16 Jun 2020 10:01:20: #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 10:01:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:01:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:01:22: 16000000 INFO @ Tue, 16 Jun 2020 10:01:24: 10000000 INFO @ Tue, 16 Jun 2020 10:01:28: 17000000 INFO @ Tue, 16 Jun 2020 10:01:30: 11000000 INFO @ Tue, 16 Jun 2020 10:01:33: 18000000 INFO @ Tue, 16 Jun 2020 10:01:36: 12000000 INFO @ Tue, 16 Jun 2020 10:01:39: 19000000 INFO @ Tue, 16 Jun 2020 10:01:41: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:01:41: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:01:41: #1 total tags in treatment: 19288166 INFO @ Tue, 16 Jun 2020 10:01:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:01:41: #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 10:01:41: #1 tags after filtering in treatment: 19288166 INFO @ Tue, 16 Jun 2020 10:01:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:01:41: #1 finished! INFO @ Tue, 16 Jun 2020 10:01:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:01:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:01:42: #2 number of paired peaks: 292 WARNING @ Tue, 16 Jun 2020 10:01:42: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Tue, 16 Jun 2020 10:01:42: start model_add_line... INFO @ Tue, 16 Jun 2020 10:01:42: 13000000 INFO @ Tue, 16 Jun 2020 10:01:42: start X-correlation... INFO @ Tue, 16 Jun 2020 10:01:43: end of X-cor INFO @ Tue, 16 Jun 2020 10:01:43: #2 finished! INFO @ Tue, 16 Jun 2020 10:01:43: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 10:01:43: #2 alternative fragment length(s) may be 2,48,578 bps INFO @ Tue, 16 Jun 2020 10:01:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.10_model.r WARNING @ Tue, 16 Jun 2020 10:01:43: #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 10:01:43: #2 You may need to consider one of the other alternative d(s): 2,48,578 WARNING @ Tue, 16 Jun 2020 10:01:43: #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 10:01:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:01:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:01:48: 14000000 INFO @ Tue, 16 Jun 2020 10:01:54: 15000000 INFO @ Tue, 16 Jun 2020 10:01:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:02:00: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:02:06: 17000000 INFO @ Tue, 16 Jun 2020 10:02:12: 18000000 INFO @ Tue, 16 Jun 2020 10:02:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:02:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:02:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.05_summits.bed INFO @ Tue, 16 Jun 2020 10:02:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2445 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:02:18: 19000000 INFO @ Tue, 16 Jun 2020 10:02:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:02:20: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:02:20: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:02:20: #1 total tags in treatment: 19288166 INFO @ Tue, 16 Jun 2020 10:02:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:02:20: #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 10:02:20: #1 tags after filtering in treatment: 19288166 INFO @ Tue, 16 Jun 2020 10:02:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:02:20: #1 finished! INFO @ Tue, 16 Jun 2020 10:02:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:02:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:02:22: #2 number of paired peaks: 292 WARNING @ Tue, 16 Jun 2020 10:02:22: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Tue, 16 Jun 2020 10:02:22: start model_add_line... INFO @ Tue, 16 Jun 2020 10:02:22: start X-correlation... INFO @ Tue, 16 Jun 2020 10:02:22: end of X-cor INFO @ Tue, 16 Jun 2020 10:02:22: #2 finished! INFO @ Tue, 16 Jun 2020 10:02:22: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 10:02:22: #2 alternative fragment length(s) may be 2,48,578 bps INFO @ Tue, 16 Jun 2020 10:02:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.20_model.r WARNING @ Tue, 16 Jun 2020 10:02:22: #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 10:02:22: #2 You may need to consider one of the other alternative d(s): 2,48,578 WARNING @ Tue, 16 Jun 2020 10:02:22: #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 10:02:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:02:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:02:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:02:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:02:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.10_summits.bed INFO @ Tue, 16 Jun 2020 10:02:37: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (642 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:02:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:03:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:03:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:03:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982072/SRX982072.20_summits.bed INFO @ Tue, 16 Jun 2020 10:03:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (156 records, 4 fields): 2 millis CompletedMACS2peakCalling