Job ID = 16434899 SRX = SRX11633392 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 11159475 spots for SRR15329100/SRR15329100.sra Written 11159475 spots for SRR15329100/SRR15329100.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434970 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:22 11159475 reads; of these: 11159475 (100.00%) were unpaired; of these: 2119476 (18.99%) aligned 0 times 7660614 (68.65%) aligned exactly 1 time 1379385 (12.36%) aligned >1 times 81.01% overall alignment rate Time searching: 00:03:23 Overall time: 00:03:23 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] 3931733 / 9039999 = 0.4349 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:20:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.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, 02 Aug 2022 10:20:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:20:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:20:37: 1000000 INFO @ Tue, 02 Aug 2022 10:20:43: 2000000 INFO @ Tue, 02 Aug 2022 10:20:50: 3000000 INFO @ Tue, 02 Aug 2022 10:20:56: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:21:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.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, 02 Aug 2022 10:21:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:21:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:21:03: 5000000 INFO @ Tue, 02 Aug 2022 10:21:04: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:21:04: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:21:04: #1 total tags in treatment: 5108266 INFO @ Tue, 02 Aug 2022 10:21:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:21:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:21:04: #1 tags after filtering in treatment: 5108266 INFO @ Tue, 02 Aug 2022 10:21:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:21:04: #1 finished! INFO @ Tue, 02 Aug 2022 10:21:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:21:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:21:04: #2 number of paired peaks: 391 WARNING @ Tue, 02 Aug 2022 10:21:04: Fewer paired peaks (391) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 391 pairs to build model! INFO @ Tue, 02 Aug 2022 10:21:04: start model_add_line... INFO @ Tue, 02 Aug 2022 10:21:04: start X-correlation... INFO @ Tue, 02 Aug 2022 10:21:04: end of X-cor INFO @ Tue, 02 Aug 2022 10:21:04: #2 finished! INFO @ Tue, 02 Aug 2022 10:21:04: #2 predicted fragment length is 69 bps INFO @ Tue, 02 Aug 2022 10:21:04: #2 alternative fragment length(s) may be 69,550,577 bps INFO @ Tue, 02 Aug 2022 10:21:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.05_model.r WARNING @ Tue, 02 Aug 2022 10:21:04: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:21:04: #2 You may need to consider one of the other alternative d(s): 69,550,577 WARNING @ Tue, 02 Aug 2022 10:21:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:21:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:21:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:21:07: 1000000 INFO @ Tue, 02 Aug 2022 10:21:13: 2000000 INFO @ Tue, 02 Aug 2022 10:21:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:21:20: 3000000 INFO @ Tue, 02 Aug 2022 10:21:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:21:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:21:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.05_summits.bed INFO @ Tue, 02 Aug 2022 10:21:20: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (522 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:21:26: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:21:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.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, 02 Aug 2022 10:21:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:21:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:21:33: 5000000 INFO @ Tue, 02 Aug 2022 10:21:33: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:21:33: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:21:33: #1 total tags in treatment: 5108266 INFO @ Tue, 02 Aug 2022 10:21:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:21:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:21:33: #1 tags after filtering in treatment: 5108266 INFO @ Tue, 02 Aug 2022 10:21:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:21:33: #1 finished! INFO @ Tue, 02 Aug 2022 10:21:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:21:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:21:34: #2 number of paired peaks: 391 WARNING @ Tue, 02 Aug 2022 10:21:34: Fewer paired peaks (391) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 391 pairs to build model! INFO @ Tue, 02 Aug 2022 10:21:34: start model_add_line... INFO @ Tue, 02 Aug 2022 10:21:34: start X-correlation... INFO @ Tue, 02 Aug 2022 10:21:34: end of X-cor INFO @ Tue, 02 Aug 2022 10:21:34: #2 finished! INFO @ Tue, 02 Aug 2022 10:21:34: #2 predicted fragment length is 69 bps INFO @ Tue, 02 Aug 2022 10:21:34: #2 alternative fragment length(s) may be 69,550,577 bps INFO @ Tue, 02 Aug 2022 10:21:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.10_model.r WARNING @ Tue, 02 Aug 2022 10:21:34: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:21:34: #2 You may need to consider one of the other alternative d(s): 69,550,577 WARNING @ Tue, 02 Aug 2022 10:21:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:21:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:21:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:21:37: 1000000 INFO @ Tue, 02 Aug 2022 10:21:43: 2000000 INFO @ Tue, 02 Aug 2022 10:21:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:21:49: 3000000 INFO @ Tue, 02 Aug 2022 10:21:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:21:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:21:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.10_summits.bed INFO @ Tue, 02 Aug 2022 10:21:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (297 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:21:56: 4000000 INFO @ Tue, 02 Aug 2022 10:22:02: 5000000 INFO @ Tue, 02 Aug 2022 10:22:03: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:22:03: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:22:03: #1 total tags in treatment: 5108266 INFO @ Tue, 02 Aug 2022 10:22:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:22:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:22:03: #1 tags after filtering in treatment: 5108266 INFO @ Tue, 02 Aug 2022 10:22:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:22:03: #1 finished! INFO @ Tue, 02 Aug 2022 10:22:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:22:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:22:03: #2 number of paired peaks: 391 WARNING @ Tue, 02 Aug 2022 10:22:03: Fewer paired peaks (391) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 391 pairs to build model! INFO @ Tue, 02 Aug 2022 10:22:03: start model_add_line... INFO @ Tue, 02 Aug 2022 10:22:03: start X-correlation... INFO @ Tue, 02 Aug 2022 10:22:03: end of X-cor INFO @ Tue, 02 Aug 2022 10:22:03: #2 finished! INFO @ Tue, 02 Aug 2022 10:22:03: #2 predicted fragment length is 69 bps INFO @ Tue, 02 Aug 2022 10:22:03: #2 alternative fragment length(s) may be 69,550,577 bps INFO @ Tue, 02 Aug 2022 10:22:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.20_model.r WARNING @ Tue, 02 Aug 2022 10:22:03: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:22:03: #2 You may need to consider one of the other alternative d(s): 69,550,577 WARNING @ Tue, 02 Aug 2022 10:22:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:22:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:22:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:22:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:22:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:22:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:22:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633392/SRX11633392.20_summits.bed INFO @ Tue, 02 Aug 2022 10:22:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (150 records, 4 fields): 15 millis CompletedMACS2peakCalling