Job ID = 14157856 SRX = SRX7879264 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 30577070 spots for SRR11272879/SRR11272879.sra Written 30577070 spots for SRR11272879/SRR11272879.sra fastq に変換しました。 bowtie でマッピング中... Your job 14157998 ("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: 00:02:45 30577070 reads; of these: 30577070 (100.00%) were unpaired; of these: 30273207 (99.01%) aligned 0 times 244068 (0.80%) aligned exactly 1 time 59795 (0.20%) aligned >1 times 0.99% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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] 23196 / 303863 = 0.0763 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 @ Wed, 08 Dec 2021 11:41:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.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 @ Wed, 08 Dec 2021 11:41:19: #1 read tag files... INFO @ Wed, 08 Dec 2021 11:41:19: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 11:41:20: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 11:41:20: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 11:41:20: #1 total tags in treatment: 280667 INFO @ Wed, 08 Dec 2021 11:41:20: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 11:41:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 11:41:20: #1 tags after filtering in treatment: 280667 INFO @ Wed, 08 Dec 2021 11:41:20: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 11:41:20: #1 finished! INFO @ Wed, 08 Dec 2021 11:41:20: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 11:41:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 11:41:20: #2 number of paired peaks: 421 WARNING @ Wed, 08 Dec 2021 11:41:20: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Wed, 08 Dec 2021 11:41:20: start model_add_line... INFO @ Wed, 08 Dec 2021 11:41:20: start X-correlation... INFO @ Wed, 08 Dec 2021 11:41:20: end of X-cor INFO @ Wed, 08 Dec 2021 11:41:20: #2 finished! INFO @ Wed, 08 Dec 2021 11:41:20: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 11:41:20: #2 alternative fragment length(s) may be 50,207,233,278,354,408,448,461,507,543 bps INFO @ Wed, 08 Dec 2021 11:41:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.05_model.r WARNING @ Wed, 08 Dec 2021 11:41:20: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 11:41:20: #2 You may need to consider one of the other alternative d(s): 50,207,233,278,354,408,448,461,507,543 WARNING @ Wed, 08 Dec 2021 11:41:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 11:41:20: #3 Call peaks... INFO @ Wed, 08 Dec 2021 11:41:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 11:41:21: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 11:41:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.05_peaks.xls INFO @ Wed, 08 Dec 2021 11:41:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 11:41:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.05_summits.bed INFO @ Wed, 08 Dec 2021 11:41:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (194 records, 4 fields): 2 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 @ Wed, 08 Dec 2021 11:41:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.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 @ Wed, 08 Dec 2021 11:41:49: #1 read tag files... INFO @ Wed, 08 Dec 2021 11:41:49: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 11:41:51: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 11:41:51: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 11:41:51: #1 total tags in treatment: 280667 INFO @ Wed, 08 Dec 2021 11:41:51: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 11:41:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 11:41:51: #1 tags after filtering in treatment: 280667 INFO @ Wed, 08 Dec 2021 11:41:51: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 11:41:51: #1 finished! INFO @ Wed, 08 Dec 2021 11:41:51: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 11:41:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 11:41:51: #2 number of paired peaks: 421 WARNING @ Wed, 08 Dec 2021 11:41:51: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Wed, 08 Dec 2021 11:41:51: start model_add_line... INFO @ Wed, 08 Dec 2021 11:41:51: start X-correlation... INFO @ Wed, 08 Dec 2021 11:41:51: end of X-cor INFO @ Wed, 08 Dec 2021 11:41:51: #2 finished! INFO @ Wed, 08 Dec 2021 11:41:51: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 11:41:51: #2 alternative fragment length(s) may be 50,207,233,278,354,408,448,461,507,543 bps INFO @ Wed, 08 Dec 2021 11:41:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.10_model.r WARNING @ Wed, 08 Dec 2021 11:41:51: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 11:41:51: #2 You may need to consider one of the other alternative d(s): 50,207,233,278,354,408,448,461,507,543 WARNING @ Wed, 08 Dec 2021 11:41:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 11:41:51: #3 Call peaks... INFO @ Wed, 08 Dec 2021 11:41:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 11:41:51: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 11:41:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.10_peaks.xls INFO @ Wed, 08 Dec 2021 11:41:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 11:41:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.10_summits.bed INFO @ Wed, 08 Dec 2021 11:41:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (101 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 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 11:42:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.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 @ Wed, 08 Dec 2021 11:42:19: #1 read tag files... INFO @ Wed, 08 Dec 2021 11:42:19: #1 read treatment tags... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 11:42:20: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 11:42:20: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 11:42:20: #1 total tags in treatment: 280667 INFO @ Wed, 08 Dec 2021 11:42:20: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 11:42:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 11:42:20: #1 tags after filtering in treatment: 280667 INFO @ Wed, 08 Dec 2021 11:42:20: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 11:42:20: #1 finished! INFO @ Wed, 08 Dec 2021 11:42:20: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 11:42:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 11:42:21: #2 number of paired peaks: 421 WARNING @ Wed, 08 Dec 2021 11:42:21: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Wed, 08 Dec 2021 11:42:21: start model_add_line... INFO @ Wed, 08 Dec 2021 11:42:21: start X-correlation... INFO @ Wed, 08 Dec 2021 11:42:21: end of X-cor INFO @ Wed, 08 Dec 2021 11:42:21: #2 finished! INFO @ Wed, 08 Dec 2021 11:42:21: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 11:42:21: #2 alternative fragment length(s) may be 50,207,233,278,354,408,448,461,507,543 bps INFO @ Wed, 08 Dec 2021 11:42:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.20_model.r WARNING @ Wed, 08 Dec 2021 11:42:21: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 11:42:21: #2 You may need to consider one of the other alternative d(s): 50,207,233,278,354,408,448,461,507,543 WARNING @ Wed, 08 Dec 2021 11:42:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 11:42:21: #3 Call peaks... INFO @ Wed, 08 Dec 2021 11:42:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 11:42:21: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 11:42:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.20_peaks.xls INFO @ Wed, 08 Dec 2021 11:42:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 11:42:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879264/SRX7879264.20_summits.bed INFO @ Wed, 08 Dec 2021 11:42:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (61 records, 4 fields): 13 millis CompletedMACS2peakCalling