Job ID = 6368083 SRX = SRX466546 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:58:50 prefetch.2.10.7: 1) Downloading 'SRR1163612'... 2020-06-15T23:58:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:00:11 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:00:12 prefetch.2.10.7: 'SRR1163612' is valid 2020-06-16T00:00:12 prefetch.2.10.7: 1) 'SRR1163612' was downloaded successfully Read 8486964 spots for SRR1163612/SRR1163612.sra Written 8486964 spots for SRR1163612/SRR1163612.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: 00:00:01 Multiseed full-index search: 00:01:32 8486964 reads; of these: 8486964 (100.00%) were unpaired; of these: 851535 (10.03%) aligned 0 times 6355465 (74.89%) aligned exactly 1 time 1279964 (15.08%) aligned >1 times 89.97% overall alignment rate Time searching: 00:01:33 Overall time: 00:01:33 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] 1758368 / 7635429 = 0.2303 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 09:04:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.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 09:04:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:04:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:04:24: 1000000 INFO @ Tue, 16 Jun 2020 09:04:31: 2000000 INFO @ Tue, 16 Jun 2020 09:04:38: 3000000 INFO @ Tue, 16 Jun 2020 09:04:45: 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 09:04:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.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 09:04:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:04:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:04:53: 5000000 INFO @ Tue, 16 Jun 2020 09:04:55: 1000000 INFO @ Tue, 16 Jun 2020 09:04:59: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:04:59: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:04:59: #1 total tags in treatment: 5877061 INFO @ Tue, 16 Jun 2020 09:04:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:04:59: #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 09:05:00: #1 tags after filtering in treatment: 5877061 INFO @ Tue, 16 Jun 2020 09:05:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:05:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:05:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:05:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:05:00: #2 number of paired peaks: 303 WARNING @ Tue, 16 Jun 2020 09:05:00: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Tue, 16 Jun 2020 09:05:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:05:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:05:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:05:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:05:00: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 09:05:00: #2 alternative fragment length(s) may be 41,483,555 bps INFO @ Tue, 16 Jun 2020 09:05:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.05_model.r WARNING @ Tue, 16 Jun 2020 09:05:00: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:05:00: #2 You may need to consider one of the other alternative d(s): 41,483,555 WARNING @ Tue, 16 Jun 2020 09:05:00: #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 09:05:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:05:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:05:02: 2000000 INFO @ Tue, 16 Jun 2020 09:05:09: 3000000 INFO @ Tue, 16 Jun 2020 09:05:12: #3 Call peaks for each chromosome... 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 09:05:17: 4000000 INFO @ Tue, 16 Jun 2020 09:05:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.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 09:05:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:05:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:05:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.05_summits.bed INFO @ Tue, 16 Jun 2020 09:05:19: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (443 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:05:24: 5000000 INFO @ Tue, 16 Jun 2020 09:05:24: 1000000 INFO @ Tue, 16 Jun 2020 09:05:30: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:05:30: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:05:30: #1 total tags in treatment: 5877061 INFO @ Tue, 16 Jun 2020 09:05:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:05:30: #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 09:05:31: #1 tags after filtering in treatment: 5877061 INFO @ Tue, 16 Jun 2020 09:05:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:05:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:05:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:05:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:05:31: #2 number of paired peaks: 303 WARNING @ Tue, 16 Jun 2020 09:05:31: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Tue, 16 Jun 2020 09:05:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:05:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:05:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:05:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:05:31: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 09:05:31: #2 alternative fragment length(s) may be 41,483,555 bps INFO @ Tue, 16 Jun 2020 09:05:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.10_model.r WARNING @ Tue, 16 Jun 2020 09:05:31: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:05:31: #2 You may need to consider one of the other alternative d(s): 41,483,555 WARNING @ Tue, 16 Jun 2020 09:05:31: #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 09:05:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:05:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:05:32: 2000000 INFO @ Tue, 16 Jun 2020 09:05:38: 3000000 INFO @ Tue, 16 Jun 2020 09:05:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:05:44: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:05:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:05:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:05:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.10_summits.bed INFO @ Tue, 16 Jun 2020 09:05:50: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (233 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:05:50: 5000000 INFO @ Tue, 16 Jun 2020 09:05:56: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:05:56: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:05:56: #1 total tags in treatment: 5877061 INFO @ Tue, 16 Jun 2020 09:05:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:05:56: #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 09:05:56: #1 tags after filtering in treatment: 5877061 INFO @ Tue, 16 Jun 2020 09:05:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:05:56: #1 finished! INFO @ Tue, 16 Jun 2020 09:05:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:05:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:05:56: #2 number of paired peaks: 303 WARNING @ Tue, 16 Jun 2020 09:05:56: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Tue, 16 Jun 2020 09:05:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:05:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:05:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:05:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:05:56: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 09:05:56: #2 alternative fragment length(s) may be 41,483,555 bps INFO @ Tue, 16 Jun 2020 09:05:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.20_model.r WARNING @ Tue, 16 Jun 2020 09:05:56: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:05:56: #2 You may need to consider one of the other alternative d(s): 41,483,555 WARNING @ Tue, 16 Jun 2020 09:05:56: #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 09:05:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:05:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:06:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:06:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:06:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:06:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466546/SRX466546.20_summits.bed INFO @ Tue, 16 Jun 2020 09:06:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (85 records, 4 fields): 1 millis CompletedMACS2peakCalling