Job ID = 6369044 SRX = SRX982108 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:41:43 prefetch.2.10.7: 1) Downloading 'SRR1956598'... 2020-06-16T00:41:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:45:19 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:45:20 prefetch.2.10.7: 'SRR1956598' is valid 2020-06-16T00:45:20 prefetch.2.10.7: 1) 'SRR1956598' was downloaded successfully Read 15198859 spots for SRR1956598/SRR1956598.sra Written 15198859 spots for SRR1956598/SRR1956598.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: 00:03:18 15198859 reads; of these: 15198859 (100.00%) were unpaired; of these: 1340911 (8.82%) aligned 0 times 11521337 (75.80%) aligned exactly 1 time 2336611 (15.37%) aligned >1 times 91.18% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 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] 1139680 / 13857948 = 0.0822 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 09:53:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.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 09:53:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:07: 1000000 INFO @ Tue, 16 Jun 2020 09:53:12: 2000000 INFO @ Tue, 16 Jun 2020 09:53:17: 3000000 INFO @ Tue, 16 Jun 2020 09:53:22: 4000000 INFO @ Tue, 16 Jun 2020 09:53:28: 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 09:53:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.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 09:53:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:33: 6000000 INFO @ Tue, 16 Jun 2020 09:53:38: 1000000 INFO @ Tue, 16 Jun 2020 09:53:38: 7000000 INFO @ Tue, 16 Jun 2020 09:53:43: 8000000 INFO @ Tue, 16 Jun 2020 09:53:44: 2000000 INFO @ Tue, 16 Jun 2020 09:53:49: 9000000 INFO @ Tue, 16 Jun 2020 09:53:49: 3000000 INFO @ Tue, 16 Jun 2020 09:53:54: 10000000 INFO @ Tue, 16 Jun 2020 09:53:55: 4000000 INFO @ Tue, 16 Jun 2020 09:53:59: 11000000 INFO @ Tue, 16 Jun 2020 09:54:00: 5000000 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 09:54:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.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 09:54:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:54:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:54:05: 12000000 INFO @ Tue, 16 Jun 2020 09:54:06: 6000000 INFO @ Tue, 16 Jun 2020 09:54:08: 1000000 INFO @ Tue, 16 Jun 2020 09:54:09: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:54:09: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:54:09: #1 total tags in treatment: 12718268 INFO @ Tue, 16 Jun 2020 09:54:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:09: #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 09:54:09: #1 tags after filtering in treatment: 12718268 INFO @ Tue, 16 Jun 2020 09:54:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:09: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:10: #2 number of paired peaks: 301 WARNING @ Tue, 16 Jun 2020 09:54:10: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Tue, 16 Jun 2020 09:54:10: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:10: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:10: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:10: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:10: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:54:10: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 09:54:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.05_model.r WARNING @ Tue, 16 Jun 2020 09:54:10: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:54:10: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 09:54:10: #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 09:54:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:11: 7000000 INFO @ Tue, 16 Jun 2020 09:54:13: 2000000 INFO @ Tue, 16 Jun 2020 09:54:17: 8000000 INFO @ Tue, 16 Jun 2020 09:54:19: 3000000 INFO @ Tue, 16 Jun 2020 09:54:22: 9000000 INFO @ Tue, 16 Jun 2020 09:54:24: 4000000 INFO @ Tue, 16 Jun 2020 09:54:27: 10000000 INFO @ Tue, 16 Jun 2020 09:54:30: 5000000 INFO @ Tue, 16 Jun 2020 09:54:33: 11000000 INFO @ Tue, 16 Jun 2020 09:54:35: 6000000 INFO @ Tue, 16 Jun 2020 09:54:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:54:38: 12000000 INFO @ Tue, 16 Jun 2020 09:54:40: 7000000 INFO @ Tue, 16 Jun 2020 09:54:41: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:54:41: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:54:41: #1 total tags in treatment: 12718268 INFO @ Tue, 16 Jun 2020 09:54:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:41: #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 09:54:42: #1 tags after filtering in treatment: 12718268 INFO @ Tue, 16 Jun 2020 09:54:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:43: #2 number of paired peaks: 301 WARNING @ Tue, 16 Jun 2020 09:54:43: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Tue, 16 Jun 2020 09:54:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:43: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:54:43: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 09:54:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.10_model.r WARNING @ Tue, 16 Jun 2020 09:54:43: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:54:43: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 09:54:43: #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 09:54:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:45: 8000000 INFO @ Tue, 16 Jun 2020 09:54:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.05_summits.bed INFO @ Tue, 16 Jun 2020 09:54:48: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (646 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:54:51: 9000000 INFO @ Tue, 16 Jun 2020 09:54:56: 10000000 INFO @ Tue, 16 Jun 2020 09:55:01: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:55:06: 12000000 INFO @ Tue, 16 Jun 2020 09:55:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:55:09: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:55:09: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:55:09: #1 total tags in treatment: 12718268 INFO @ Tue, 16 Jun 2020 09:55:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:55:09: #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 09:55:10: #1 tags after filtering in treatment: 12718268 INFO @ Tue, 16 Jun 2020 09:55:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:55:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:55:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:55:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:55:11: #2 number of paired peaks: 301 WARNING @ Tue, 16 Jun 2020 09:55:11: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Tue, 16 Jun 2020 09:55:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:55:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:55:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:55:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:55:11: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:55:11: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 09:55:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.20_model.r WARNING @ Tue, 16 Jun 2020 09:55:11: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:55:11: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 09:55:11: #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 09:55:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:55:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:55:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:55:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:55:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.10_summits.bed INFO @ Tue, 16 Jun 2020 09:55:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (425 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:55:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:55:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:55:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:55:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982108/SRX982108.20_summits.bed INFO @ Tue, 16 Jun 2020 09:55:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (169 records, 4 fields): 1 millis CompletedMACS2peakCalling