Job ID = 6366910 SRX = SRX257655 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:07:53 prefetch.2.10.7: 1) Downloading 'SRR800666'... 2020-06-15T23:07:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:09:09 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:09:10 prefetch.2.10.7: 'SRR800666' is valid 2020-06-15T23:09:10 prefetch.2.10.7: 1) 'SRR800666' was downloaded successfully Read 8743647 spots for SRR800666/SRR800666.sra Written 8743647 spots for SRR800666/SRR800666.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: 00:02:07 8743647 reads; of these: 8743647 (100.00%) were unpaired; of these: 367773 (4.21%) aligned 0 times 6880832 (78.70%) aligned exactly 1 time 1495042 (17.10%) aligned >1 times 95.79% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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] 675003 / 8375874 = 0.0806 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 08:14:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.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 08:14:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:32: 1000000 INFO @ Tue, 16 Jun 2020 08:14:38: 2000000 INFO @ Tue, 16 Jun 2020 08:14:44: 3000000 INFO @ Tue, 16 Jun 2020 08:14:49: 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 08:14:55: 5000000 INFO @ Tue, 16 Jun 2020 08:14:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.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 08:14:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:01: 6000000 INFO @ Tue, 16 Jun 2020 08:15:03: 1000000 INFO @ Tue, 16 Jun 2020 08:15:08: 7000000 INFO @ Tue, 16 Jun 2020 08:15:09: 2000000 INFO @ Tue, 16 Jun 2020 08:15:12: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:15:12: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:15:12: #1 total tags in treatment: 7700871 INFO @ Tue, 16 Jun 2020 08:15:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:12: #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 08:15:12: #1 tags after filtering in treatment: 7700871 INFO @ Tue, 16 Jun 2020 08:15:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:13: #2 number of paired peaks: 386 WARNING @ Tue, 16 Jun 2020 08:15:13: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:13: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:15:13: #2 alternative fragment length(s) may be 4,52,533 bps INFO @ Tue, 16 Jun 2020 08:15:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.05_model.r WARNING @ Tue, 16 Jun 2020 08:15:13: #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 08:15:13: #2 You may need to consider one of the other alternative d(s): 4,52,533 WARNING @ Tue, 16 Jun 2020 08:15:13: #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 08:15:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:15: 3000000 INFO @ Tue, 16 Jun 2020 08:15:21: 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 08:15:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.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 08:15:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:27: 5000000 INFO @ Tue, 16 Jun 2020 08:15:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:33: 1000000 INFO @ Tue, 16 Jun 2020 08:15:34: 6000000 INFO @ Tue, 16 Jun 2020 08:15:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.05_summits.bed INFO @ Tue, 16 Jun 2020 08:15:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (653 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:15:40: 2000000 INFO @ Tue, 16 Jun 2020 08:15:40: 7000000 INFO @ Tue, 16 Jun 2020 08:15:45: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:15:45: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:15:45: #1 total tags in treatment: 7700871 INFO @ Tue, 16 Jun 2020 08:15:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:45: #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 08:15:45: #1 tags after filtering in treatment: 7700871 INFO @ Tue, 16 Jun 2020 08:15:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:45: #2 number of paired peaks: 386 WARNING @ Tue, 16 Jun 2020 08:15:45: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:45: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:15:45: #2 alternative fragment length(s) may be 4,52,533 bps INFO @ Tue, 16 Jun 2020 08:15:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.10_model.r WARNING @ Tue, 16 Jun 2020 08:15:46: #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 08:15:46: #2 You may need to consider one of the other alternative d(s): 4,52,533 WARNING @ Tue, 16 Jun 2020 08:15:46: #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 08:15:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:46: 3000000 INFO @ Tue, 16 Jun 2020 08:15:52: 4000000 INFO @ Tue, 16 Jun 2020 08:15:58: 5000000 INFO @ Tue, 16 Jun 2020 08:16:02: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:16:04: 6000000 INFO @ Tue, 16 Jun 2020 08:16:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.10_summits.bed INFO @ Tue, 16 Jun 2020 08:16:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (421 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:16:10: 7000000 INFO @ Tue, 16 Jun 2020 08:16:14: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:16:14: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:16:14: #1 total tags in treatment: 7700871 INFO @ Tue, 16 Jun 2020 08:16:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:14: #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 08:16:14: #1 tags after filtering in treatment: 7700871 INFO @ Tue, 16 Jun 2020 08:16:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:14: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:15: #2 number of paired peaks: 386 WARNING @ Tue, 16 Jun 2020 08:16:15: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:15: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:16:15: #2 alternative fragment length(s) may be 4,52,533 bps INFO @ Tue, 16 Jun 2020 08:16:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.20_model.r WARNING @ Tue, 16 Jun 2020 08:16:15: #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 08:16:15: #2 You may need to consider one of the other alternative d(s): 4,52,533 WARNING @ Tue, 16 Jun 2020 08:16:15: #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 08:16:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:16:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257655/SRX257655.20_summits.bed INFO @ Tue, 16 Jun 2020 08:16:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (202 records, 4 fields): 1 millis CompletedMACS2peakCalling