Job ID = 6626380 SRX = SRX7262217 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5940876 spots for SRR10581840/SRR10581840.sra Written 5940876 spots for SRR10581840/SRR10581840.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626452 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:39 5940876 reads; of these: 5940876 (100.00%) were unpaired; of these: 147701 (2.49%) aligned 0 times 4470274 (75.25%) aligned exactly 1 time 1322901 (22.27%) aligned >1 times 97.51% overall alignment rate Time searching: 00:01:39 Overall time: 00:01:39 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] 523013 / 5793175 = 0.0903 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, 14 Jul 2020 07:00:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.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, 14 Jul 2020 07:00:15: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:00:15: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:00:20: 1000000 INFO @ Tue, 14 Jul 2020 07:00:25: 2000000 INFO @ Tue, 14 Jul 2020 07:00:30: 3000000 INFO @ Tue, 14 Jul 2020 07:00:35: 4000000 INFO @ Tue, 14 Jul 2020 07:00:39: 5000000 INFO @ Tue, 14 Jul 2020 07:00:41: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:00:41: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:00:41: #1 total tags in treatment: 5270162 INFO @ Tue, 14 Jul 2020 07:00:41: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:00:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:00:41: #1 tags after filtering in treatment: 5270162 INFO @ Tue, 14 Jul 2020 07:00:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:00:41: #1 finished! INFO @ Tue, 14 Jul 2020 07:00:41: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:00:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:00:41: #2 number of paired peaks: 518 WARNING @ Tue, 14 Jul 2020 07:00:41: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Tue, 14 Jul 2020 07:00:41: start model_add_line... INFO @ Tue, 14 Jul 2020 07:00:41: start X-correlation... INFO @ Tue, 14 Jul 2020 07:00:41: end of X-cor INFO @ Tue, 14 Jul 2020 07:00:41: #2 finished! INFO @ Tue, 14 Jul 2020 07:00:41: #2 predicted fragment length is 51 bps INFO @ Tue, 14 Jul 2020 07:00:41: #2 alternative fragment length(s) may be 4,51 bps INFO @ Tue, 14 Jul 2020 07:00:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.05_model.r WARNING @ Tue, 14 Jul 2020 07:00:41: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:00:41: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Tue, 14 Jul 2020 07:00:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:00:41: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:00:41: #3 Pre-compute pvalue-qvalue table... 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, 14 Jul 2020 07:00:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.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, 14 Jul 2020 07:00:45: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:00:45: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:00:50: 1000000 INFO @ Tue, 14 Jul 2020 07:00:52: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:00:55: 2000000 INFO @ Tue, 14 Jul 2020 07:00:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:00:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:00:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.05_summits.bed INFO @ Tue, 14 Jul 2020 07:00:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (576 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:00:59: 3000000 INFO @ Tue, 14 Jul 2020 07:01:04: 4000000 INFO @ Tue, 14 Jul 2020 07:01:09: 5000000 INFO @ Tue, 14 Jul 2020 07:01:10: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:01:10: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:01:10: #1 total tags in treatment: 5270162 INFO @ Tue, 14 Jul 2020 07:01:10: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:01:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:01:10: #1 tags after filtering in treatment: 5270162 INFO @ Tue, 14 Jul 2020 07:01:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:01:10: #1 finished! INFO @ Tue, 14 Jul 2020 07:01:10: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:01:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:01:10: #2 number of paired peaks: 518 WARNING @ Tue, 14 Jul 2020 07:01:10: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Tue, 14 Jul 2020 07:01:10: start model_add_line... INFO @ Tue, 14 Jul 2020 07:01:10: start X-correlation... INFO @ Tue, 14 Jul 2020 07:01:10: end of X-cor INFO @ Tue, 14 Jul 2020 07:01:10: #2 finished! INFO @ Tue, 14 Jul 2020 07:01:10: #2 predicted fragment length is 51 bps INFO @ Tue, 14 Jul 2020 07:01:10: #2 alternative fragment length(s) may be 4,51 bps INFO @ Tue, 14 Jul 2020 07:01:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.10_model.r WARNING @ Tue, 14 Jul 2020 07:01:11: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:01:11: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Tue, 14 Jul 2020 07:01:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:01:11: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:01:11: #3 Pre-compute pvalue-qvalue table... 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, 14 Jul 2020 07:01:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.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, 14 Jul 2020 07:01:15: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:01:15: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:01:21: 1000000 INFO @ Tue, 14 Jul 2020 07:01:22: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:01:26: 2000000 INFO @ Tue, 14 Jul 2020 07:01:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:01:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:01:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.10_summits.bed INFO @ Tue, 14 Jul 2020 07:01:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (382 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:01:32: 3000000 INFO @ Tue, 14 Jul 2020 07:01:38: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:01:43: 5000000 INFO @ Tue, 14 Jul 2020 07:01:45: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:01:45: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:01:45: #1 total tags in treatment: 5270162 INFO @ Tue, 14 Jul 2020 07:01:45: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:01:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:01:45: #1 tags after filtering in treatment: 5270162 INFO @ Tue, 14 Jul 2020 07:01:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:01:45: #1 finished! INFO @ Tue, 14 Jul 2020 07:01:45: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:01:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:01:45: #2 number of paired peaks: 518 WARNING @ Tue, 14 Jul 2020 07:01:45: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Tue, 14 Jul 2020 07:01:45: start model_add_line... INFO @ Tue, 14 Jul 2020 07:01:45: start X-correlation... INFO @ Tue, 14 Jul 2020 07:01:45: end of X-cor INFO @ Tue, 14 Jul 2020 07:01:45: #2 finished! INFO @ Tue, 14 Jul 2020 07:01:45: #2 predicted fragment length is 51 bps INFO @ Tue, 14 Jul 2020 07:01:45: #2 alternative fragment length(s) may be 4,51 bps INFO @ Tue, 14 Jul 2020 07:01:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.20_model.r WARNING @ Tue, 14 Jul 2020 07:01:46: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:01:46: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Tue, 14 Jul 2020 07:01:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:01:46: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:01:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:01:57: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:02:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:02:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:02:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262217/SRX7262217.20_summits.bed INFO @ Tue, 14 Jul 2020 07:02:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (158 records, 4 fields): 16 millis CompletedMACS2peakCalling