Job ID = 14159678 SRX = SRX3180797 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17796426 spots for SRR6030448/SRR6030448.sra Written 17796426 spots for SRR6030448/SRR6030448.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160284 ("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: 00:01:59 17796426 reads; of these: 17796426 (100.00%) were unpaired; of these: 14601841 (82.05%) aligned 0 times 2634295 (14.80%) aligned exactly 1 time 560290 (3.15%) aligned >1 times 17.95% overall alignment rate Time searching: 00:01:59 Overall time: 00:01:59 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] 2571362 / 3194585 = 0.8049 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 00:19:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.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 @ Thu, 09 Dec 2021 00:19:39: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:19:39: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:19:42: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 00:19:42: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 00:19:42: #1 total tags in treatment: 623223 INFO @ Thu, 09 Dec 2021 00:19:42: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:19:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:19:42: #1 tags after filtering in treatment: 623223 INFO @ Thu, 09 Dec 2021 00:19:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:19:42: #1 finished! INFO @ Thu, 09 Dec 2021 00:19:42: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:19:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:19:42: #2 number of paired peaks: 996 WARNING @ Thu, 09 Dec 2021 00:19:42: Fewer paired peaks (996) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 996 pairs to build model! INFO @ Thu, 09 Dec 2021 00:19:42: start model_add_line... INFO @ Thu, 09 Dec 2021 00:19:42: start X-correlation... INFO @ Thu, 09 Dec 2021 00:19:42: end of X-cor INFO @ Thu, 09 Dec 2021 00:19:42: #2 finished! INFO @ Thu, 09 Dec 2021 00:19:42: #2 predicted fragment length is 49 bps INFO @ Thu, 09 Dec 2021 00:19:42: #2 alternative fragment length(s) may be 49,539 bps INFO @ Thu, 09 Dec 2021 00:19:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.05_model.r WARNING @ Thu, 09 Dec 2021 00:19:42: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:19:42: #2 You may need to consider one of the other alternative d(s): 49,539 WARNING @ Thu, 09 Dec 2021 00:19:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 00:19:42: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:19:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:19:43: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:19:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:19:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:19:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.05_summits.bed INFO @ Thu, 09 Dec 2021 00:19:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (377 records, 4 fields): 1 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 00:20:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.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 @ Thu, 09 Dec 2021 00:20:09: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:20:09: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:20:12: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 00:20:12: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 00:20:12: #1 total tags in treatment: 623223 INFO @ Thu, 09 Dec 2021 00:20:12: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:20:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:20:12: #1 tags after filtering in treatment: 623223 INFO @ Thu, 09 Dec 2021 00:20:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:20:12: #1 finished! INFO @ Thu, 09 Dec 2021 00:20:12: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:20:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:20:12: #2 number of paired peaks: 996 WARNING @ Thu, 09 Dec 2021 00:20:12: Fewer paired peaks (996) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 996 pairs to build model! INFO @ Thu, 09 Dec 2021 00:20:12: start model_add_line... INFO @ Thu, 09 Dec 2021 00:20:12: start X-correlation... INFO @ Thu, 09 Dec 2021 00:20:12: end of X-cor INFO @ Thu, 09 Dec 2021 00:20:12: #2 finished! INFO @ Thu, 09 Dec 2021 00:20:12: #2 predicted fragment length is 49 bps INFO @ Thu, 09 Dec 2021 00:20:12: #2 alternative fragment length(s) may be 49,539 bps INFO @ Thu, 09 Dec 2021 00:20:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.10_model.r WARNING @ Thu, 09 Dec 2021 00:20:12: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:20:12: #2 You may need to consider one of the other alternative d(s): 49,539 WARNING @ Thu, 09 Dec 2021 00:20:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 00:20:12: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:20:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:20:13: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:20:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:20:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:20:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.10_summits.bed INFO @ Thu, 09 Dec 2021 00:20:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (183 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 00:20:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.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 @ Thu, 09 Dec 2021 00:20:39: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:20:39: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:20:42: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 00:20:42: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 00:20:42: #1 total tags in treatment: 623223 INFO @ Thu, 09 Dec 2021 00:20:42: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:20:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:20:42: #1 tags after filtering in treatment: 623223 INFO @ Thu, 09 Dec 2021 00:20:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:20:42: #1 finished! INFO @ Thu, 09 Dec 2021 00:20:42: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:20:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:20:42: #2 number of paired peaks: 996 WARNING @ Thu, 09 Dec 2021 00:20:42: Fewer paired peaks (996) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 996 pairs to build model! INFO @ Thu, 09 Dec 2021 00:20:42: start model_add_line... INFO @ Thu, 09 Dec 2021 00:20:42: start X-correlation... INFO @ Thu, 09 Dec 2021 00:20:42: end of X-cor INFO @ Thu, 09 Dec 2021 00:20:42: #2 finished! INFO @ Thu, 09 Dec 2021 00:20:42: #2 predicted fragment length is 49 bps INFO @ Thu, 09 Dec 2021 00:20:42: #2 alternative fragment length(s) may be 49,539 bps INFO @ Thu, 09 Dec 2021 00:20:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.20_model.r WARNING @ Thu, 09 Dec 2021 00:20:42: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:20:42: #2 You may need to consider one of the other alternative d(s): 49,539 WARNING @ Thu, 09 Dec 2021 00:20:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 00:20:42: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:20:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:20:43: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:20:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:20:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:20:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180797/SRX3180797.20_summits.bed INFO @ Thu, 09 Dec 2021 00:20:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (47 records, 4 fields): 1 millis CompletedMACS2peakCalling