Job ID = 6367472 SRX = SRX331229 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:29:05 prefetch.2.10.7: 1) Downloading 'SRR947461'... 2020-06-15T23:29:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:29:56 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:29:57 prefetch.2.10.7: 'SRR947461' is valid 2020-06-15T23:29:57 prefetch.2.10.7: 1) 'SRR947461' was downloaded successfully Read 6513257 spots for SRR947461/SRR947461.sra Written 6513257 spots for SRR947461/SRR947461.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: 00:00:58 6513257 reads; of these: 6513257 (100.00%) were unpaired; of these: 50009 (0.77%) aligned 0 times 5457757 (83.79%) aligned exactly 1 time 1005491 (15.44%) aligned >1 times 99.23% overall alignment rate Time searching: 00:00:59 Overall time: 00:00:59 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] 491141 / 6463248 = 0.0760 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 08:32:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.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 08:32:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:02: 1000000 INFO @ Tue, 16 Jun 2020 08:33:07: 2000000 INFO @ Tue, 16 Jun 2020 08:33:13: 3000000 INFO @ Tue, 16 Jun 2020 08:33:18: 4000000 INFO @ Tue, 16 Jun 2020 08:33:23: 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 08:33:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.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 08:33:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:29: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:33:29: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:33:29: #1 total tags in treatment: 5972107 INFO @ Tue, 16 Jun 2020 08:33:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:29: #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 08:33:29: #1 tags after filtering in treatment: 5972107 INFO @ Tue, 16 Jun 2020 08:33:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:29: #2 number of paired peaks: 393 WARNING @ Tue, 16 Jun 2020 08:33:29: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:29: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:33:29: #2 alternative fragment length(s) may be 3,31,70,101,122,516,598 bps INFO @ Tue, 16 Jun 2020 08:33:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.05_model.r WARNING @ Tue, 16 Jun 2020 08:33:29: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:33:29: #2 You may need to consider one of the other alternative d(s): 3,31,70,101,122,516,598 WARNING @ Tue, 16 Jun 2020 08:33:29: #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 08:33:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:33:31: 1000000 INFO @ Tue, 16 Jun 2020 08:33:36: 2000000 INFO @ Tue, 16 Jun 2020 08:33:41: 3000000 INFO @ Tue, 16 Jun 2020 08:33:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:45: 4000000 INFO @ Tue, 16 Jun 2020 08:33:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.05_summits.bed INFO @ Tue, 16 Jun 2020 08:33:48: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (432 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:33:50: 5000000 INFO @ Tue, 16 Jun 2020 08:33:55: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:33:55: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:33:55: #1 total tags in treatment: 5972107 INFO @ Tue, 16 Jun 2020 08:33:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:55: #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 08:33:55: #1 tags after filtering in treatment: 5972107 INFO @ Tue, 16 Jun 2020 08:33:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:55: #2 looking for paired plus/minus strand peaks... 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 08:33:55: #2 number of paired peaks: 393 WARNING @ Tue, 16 Jun 2020 08:33:55: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:55: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:33:55: #2 alternative fragment length(s) may be 3,31,70,101,122,516,598 bps INFO @ Tue, 16 Jun 2020 08:33:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.10_model.r WARNING @ Tue, 16 Jun 2020 08:33:55: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:33:55: #2 You may need to consider one of the other alternative d(s): 3,31,70,101,122,516,598 WARNING @ Tue, 16 Jun 2020 08:33:55: #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 08:33:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:33:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.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 08:33:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:01: 1000000 INFO @ Tue, 16 Jun 2020 08:34:06: 2000000 INFO @ Tue, 16 Jun 2020 08:34:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:10: 3000000 INFO @ Tue, 16 Jun 2020 08:34:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.10_summits.bed INFO @ Tue, 16 Jun 2020 08:34:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (175 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:34:15: 4000000 INFO @ Tue, 16 Jun 2020 08:34:19: 5000000 INFO @ Tue, 16 Jun 2020 08:34:24: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:34:24: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:34:24: #1 total tags in treatment: 5972107 INFO @ Tue, 16 Jun 2020 08:34:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:24: #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 08:34:24: #1 tags after filtering in treatment: 5972107 INFO @ Tue, 16 Jun 2020 08:34:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:24: #2 number of paired peaks: 393 WARNING @ Tue, 16 Jun 2020 08:34:24: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:24: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:34:24: #2 alternative fragment length(s) may be 3,31,70,101,122,516,598 bps INFO @ Tue, 16 Jun 2020 08:34:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.20_model.r WARNING @ Tue, 16 Jun 2020 08:34:24: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:34:24: #2 You may need to consider one of the other alternative d(s): 3,31,70,101,122,516,598 WARNING @ Tue, 16 Jun 2020 08:34:24: #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 08:34:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:24: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:34:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:34:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331229/SRX331229.20_summits.bed INFO @ Tue, 16 Jun 2020 08:34:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (36 records, 4 fields): 0 millis CompletedMACS2peakCalling