Job ID = 14157857 SRX = SRX7879265 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 31270331 spots for SRR11272880/SRR11272880.sra Written 31270331 spots for SRR11272880/SRR11272880.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158004 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:12 31270331 reads; of these: 31270331 (100.00%) were unpaired; of these: 12115443 (38.74%) aligned 0 times 16035773 (51.28%) aligned exactly 1 time 3119115 (9.97%) aligned >1 times 61.26% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 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_sort_core] merging from 8 files... [bam_rmdupse_core] 13656895 / 19154888 = 0.7130 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 11:46:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.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 11:46:49: #1 read tag files... INFO @ Wed, 08 Dec 2021 11:46:49: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 11:46:55: 1000000 INFO @ Wed, 08 Dec 2021 11:47:01: 2000000 INFO @ Wed, 08 Dec 2021 11:47:07: 3000000 INFO @ Wed, 08 Dec 2021 11:47:14: 4000000 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 11:47:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.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 11:47:18: #1 read tag files... INFO @ Wed, 08 Dec 2021 11:47:18: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 11:47:20: 5000000 INFO @ Wed, 08 Dec 2021 11:47:23: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 11:47:23: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 11:47:23: #1 total tags in treatment: 5497993 INFO @ Wed, 08 Dec 2021 11:47:23: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 11:47:23: #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 11:47:23: #1 tags after filtering in treatment: 5497993 INFO @ Wed, 08 Dec 2021 11:47:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 11:47:23: #1 finished! INFO @ Wed, 08 Dec 2021 11:47:23: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 11:47:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 11:47:24: #2 number of paired peaks: 666 WARNING @ Wed, 08 Dec 2021 11:47:24: Fewer paired peaks (666) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 666 pairs to build model! INFO @ Wed, 08 Dec 2021 11:47:24: start model_add_line... INFO @ Wed, 08 Dec 2021 11:47:24: start X-correlation... INFO @ Wed, 08 Dec 2021 11:47:24: end of X-cor INFO @ Wed, 08 Dec 2021 11:47:24: #2 finished! INFO @ Wed, 08 Dec 2021 11:47:24: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 11:47:24: #2 alternative fragment length(s) may be 3,50,557,562 bps INFO @ Wed, 08 Dec 2021 11:47:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.05_model.r WARNING @ Wed, 08 Dec 2021 11:47:24: #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 11:47:24: #2 You may need to consider one of the other alternative d(s): 3,50,557,562 WARNING @ Wed, 08 Dec 2021 11:47:24: #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 11:47:24: #3 Call peaks... INFO @ Wed, 08 Dec 2021 11:47:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 11:47:25: 1000000 INFO @ Wed, 08 Dec 2021 11:47:31: 2000000 INFO @ Wed, 08 Dec 2021 11:47:36: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 11:47:38: 3000000 INFO @ Wed, 08 Dec 2021 11:47:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.05_peaks.xls INFO @ Wed, 08 Dec 2021 11:47:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 11:47:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.05_summits.bed INFO @ Wed, 08 Dec 2021 11:47:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (789 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 11:47:44: 4000000 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 @ Wed, 08 Dec 2021 11:47:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.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 11:47:48: #1 read tag files... INFO @ Wed, 08 Dec 2021 11:47:48: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 11:47:51: 5000000 INFO @ Wed, 08 Dec 2021 11:47:54: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 11:47:54: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 11:47:54: #1 total tags in treatment: 5497993 INFO @ Wed, 08 Dec 2021 11:47:54: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 11:47:54: #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 11:47:54: #1 tags after filtering in treatment: 5497993 INFO @ Wed, 08 Dec 2021 11:47:54: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 11:47:54: #1 finished! INFO @ Wed, 08 Dec 2021 11:47:54: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 11:47:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 11:47:55: 1000000 INFO @ Wed, 08 Dec 2021 11:47:55: #2 number of paired peaks: 666 WARNING @ Wed, 08 Dec 2021 11:47:55: Fewer paired peaks (666) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 666 pairs to build model! INFO @ Wed, 08 Dec 2021 11:47:55: start model_add_line... INFO @ Wed, 08 Dec 2021 11:47:55: start X-correlation... INFO @ Wed, 08 Dec 2021 11:47:55: end of X-cor INFO @ Wed, 08 Dec 2021 11:47:55: #2 finished! INFO @ Wed, 08 Dec 2021 11:47:55: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 11:47:55: #2 alternative fragment length(s) may be 3,50,557,562 bps INFO @ Wed, 08 Dec 2021 11:47:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.10_model.r WARNING @ Wed, 08 Dec 2021 11:47:55: #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 11:47:55: #2 You may need to consider one of the other alternative d(s): 3,50,557,562 WARNING @ Wed, 08 Dec 2021 11:47:55: #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 11:47:55: #3 Call peaks... INFO @ Wed, 08 Dec 2021 11:47:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 11:48:01: 2000000 INFO @ Wed, 08 Dec 2021 11:48:06: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 11:48:07: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 11:48:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.10_peaks.xls INFO @ Wed, 08 Dec 2021 11:48:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 11:48:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.10_summits.bed INFO @ Wed, 08 Dec 2021 11:48:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (574 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 11:48:13: 4000000 INFO @ Wed, 08 Dec 2021 11:48:19: 5000000 INFO @ Wed, 08 Dec 2021 11:48:22: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 11:48:22: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 11:48:22: #1 total tags in treatment: 5497993 INFO @ Wed, 08 Dec 2021 11:48:22: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 11:48:22: #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 11:48:22: #1 tags after filtering in treatment: 5497993 INFO @ Wed, 08 Dec 2021 11:48:22: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 11:48:22: #1 finished! INFO @ Wed, 08 Dec 2021 11:48:22: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 11:48:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 11:48:23: #2 number of paired peaks: 666 WARNING @ Wed, 08 Dec 2021 11:48:23: Fewer paired peaks (666) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 666 pairs to build model! INFO @ Wed, 08 Dec 2021 11:48:23: start model_add_line... INFO @ Wed, 08 Dec 2021 11:48:23: start X-correlation... INFO @ Wed, 08 Dec 2021 11:48:23: end of X-cor INFO @ Wed, 08 Dec 2021 11:48:23: #2 finished! INFO @ Wed, 08 Dec 2021 11:48:23: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 11:48:23: #2 alternative fragment length(s) may be 3,50,557,562 bps INFO @ Wed, 08 Dec 2021 11:48:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.20_model.r WARNING @ Wed, 08 Dec 2021 11:48:23: #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 11:48:23: #2 You may need to consider one of the other alternative d(s): 3,50,557,562 WARNING @ Wed, 08 Dec 2021 11:48:23: #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 11:48:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 11:48:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 11:48:34: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 11:48:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.20_peaks.xls INFO @ Wed, 08 Dec 2021 11:48:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 11:48:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879265/SRX7879265.20_summits.bed INFO @ Wed, 08 Dec 2021 11:48:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (254 records, 4 fields): 1 millis CompletedMACS2peakCalling