Job ID = 16434927 SRX = SRX11633397 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14135109 spots for SRR15329105/SRR15329105.sra Written 14135109 spots for SRR15329105/SRR15329105.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434988 ("srTce11") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:29 14135109 reads; of these: 14135109 (100.00%) were unpaired; of these: 1332105 (9.42%) aligned 0 times 11037179 (78.08%) aligned exactly 1 time 1765825 (12.49%) aligned >1 times 90.58% overall alignment rate Time searching: 00:05:30 Overall time: 00:05:30 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] 739282 / 12803004 = 0.0577 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 10:30:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.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 10:30:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:30:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:30:56: 1000000 INFO @ Tue, 02 Aug 2022 10:31:05: 2000000 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 10:31:14: 3000000 INFO @ Tue, 02 Aug 2022 10:31:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.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 10:31:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:31:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:31:23: 4000000 INFO @ Tue, 02 Aug 2022 10:31:25: 1000000 INFO @ Tue, 02 Aug 2022 10:31:32: 5000000 INFO @ Tue, 02 Aug 2022 10:31:34: 2000000 INFO @ Tue, 02 Aug 2022 10:31:41: 6000000 INFO @ Tue, 02 Aug 2022 10:31:43: 3000000 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 10:31:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.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 10:31:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:31:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:31:51: 7000000 INFO @ Tue, 02 Aug 2022 10:31:53: 4000000 INFO @ Tue, 02 Aug 2022 10:31:55: 1000000 INFO @ Tue, 02 Aug 2022 10:32:00: 8000000 INFO @ Tue, 02 Aug 2022 10:32:02: 5000000 INFO @ Tue, 02 Aug 2022 10:32:05: 2000000 INFO @ Tue, 02 Aug 2022 10:32:09: 9000000 INFO @ Tue, 02 Aug 2022 10:32:11: 6000000 INFO @ Tue, 02 Aug 2022 10:32:14: 3000000 INFO @ Tue, 02 Aug 2022 10:32:18: 10000000 INFO @ Tue, 02 Aug 2022 10:32:21: 7000000 INFO @ Tue, 02 Aug 2022 10:32:24: 4000000 INFO @ Tue, 02 Aug 2022 10:32:27: 11000000 INFO @ Tue, 02 Aug 2022 10:32:30: 8000000 INFO @ Tue, 02 Aug 2022 10:32:34: 5000000 INFO @ Tue, 02 Aug 2022 10:32:37: 12000000 INFO @ Tue, 02 Aug 2022 10:32:37: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:32:37: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:32:37: #1 total tags in treatment: 12063722 INFO @ Tue, 02 Aug 2022 10:32:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:32:37: #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 10:32:38: #1 tags after filtering in treatment: 12063722 INFO @ Tue, 02 Aug 2022 10:32:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:32:38: #1 finished! INFO @ Tue, 02 Aug 2022 10:32:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:32:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:32:38: #2 number of paired peaks: 198 WARNING @ Tue, 02 Aug 2022 10:32:38: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Tue, 02 Aug 2022 10:32:38: start model_add_line... INFO @ Tue, 02 Aug 2022 10:32:38: start X-correlation... INFO @ Tue, 02 Aug 2022 10:32:39: end of X-cor INFO @ Tue, 02 Aug 2022 10:32:39: #2 finished! INFO @ Tue, 02 Aug 2022 10:32:39: #2 predicted fragment length is 69 bps INFO @ Tue, 02 Aug 2022 10:32:39: #2 alternative fragment length(s) may be 3,69,598 bps INFO @ Tue, 02 Aug 2022 10:32:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.05_model.r WARNING @ Tue, 02 Aug 2022 10:32:39: #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 10:32:39: #2 You may need to consider one of the other alternative d(s): 3,69,598 WARNING @ Tue, 02 Aug 2022 10:32:39: #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 10:32:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:32:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:32:39: 9000000 INFO @ Tue, 02 Aug 2022 10:32:43: 6000000 INFO @ Tue, 02 Aug 2022 10:32:48: 10000000 INFO @ Tue, 02 Aug 2022 10:32:52: 7000000 INFO @ Tue, 02 Aug 2022 10:32:57: 11000000 INFO @ Tue, 02 Aug 2022 10:32:59: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:33:01: 8000000 INFO @ Tue, 02 Aug 2022 10:33:06: 12000000 INFO @ Tue, 02 Aug 2022 10:33:07: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:33:07: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:33:07: #1 total tags in treatment: 12063722 INFO @ Tue, 02 Aug 2022 10:33:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:33:07: #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 10:33:07: #1 tags after filtering in treatment: 12063722 INFO @ Tue, 02 Aug 2022 10:33:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:33:07: #1 finished! INFO @ Tue, 02 Aug 2022 10:33:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:33:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:33:08: #2 number of paired peaks: 198 WARNING @ Tue, 02 Aug 2022 10:33:08: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Tue, 02 Aug 2022 10:33:08: start model_add_line... INFO @ Tue, 02 Aug 2022 10:33:08: start X-correlation... INFO @ Tue, 02 Aug 2022 10:33:08: end of X-cor INFO @ Tue, 02 Aug 2022 10:33:08: #2 finished! INFO @ Tue, 02 Aug 2022 10:33:08: #2 predicted fragment length is 69 bps INFO @ Tue, 02 Aug 2022 10:33:08: #2 alternative fragment length(s) may be 3,69,598 bps INFO @ Tue, 02 Aug 2022 10:33:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.10_model.r WARNING @ Tue, 02 Aug 2022 10:33:08: #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 10:33:08: #2 You may need to consider one of the other alternative d(s): 3,69,598 WARNING @ Tue, 02 Aug 2022 10:33:08: #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 10:33:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:33:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:33:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:33:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:33:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.05_summits.bed INFO @ Tue, 02 Aug 2022 10:33:10: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (455 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:33:10: 9000000 INFO @ Tue, 02 Aug 2022 10:33:19: 10000000 INFO @ Tue, 02 Aug 2022 10:33:28: 11000000 INFO @ Tue, 02 Aug 2022 10:33:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:33:37: 12000000 INFO @ Tue, 02 Aug 2022 10:33:38: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:33:38: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:33:38: #1 total tags in treatment: 12063722 INFO @ Tue, 02 Aug 2022 10:33:38: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:33:38: #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 10:33:38: #1 tags after filtering in treatment: 12063722 INFO @ Tue, 02 Aug 2022 10:33:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:33:38: #1 finished! INFO @ Tue, 02 Aug 2022 10:33:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:33:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:33:39: #2 number of paired peaks: 198 WARNING @ Tue, 02 Aug 2022 10:33:39: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Tue, 02 Aug 2022 10:33:39: start model_add_line... INFO @ Tue, 02 Aug 2022 10:33:39: start X-correlation... INFO @ Tue, 02 Aug 2022 10:33:39: end of X-cor INFO @ Tue, 02 Aug 2022 10:33:39: #2 finished! INFO @ Tue, 02 Aug 2022 10:33:39: #2 predicted fragment length is 69 bps INFO @ Tue, 02 Aug 2022 10:33:39: #2 alternative fragment length(s) may be 3,69,598 bps INFO @ Tue, 02 Aug 2022 10:33:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.20_model.r WARNING @ Tue, 02 Aug 2022 10:33:39: #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 10:33:39: #2 You may need to consider one of the other alternative d(s): 3,69,598 WARNING @ Tue, 02 Aug 2022 10:33:39: #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 10:33:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:33:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:33:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:33:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:33:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.10_summits.bed INFO @ Tue, 02 Aug 2022 10:33:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (294 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:33:59: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:34:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:34:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:34:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633397/SRX11633397.20_summits.bed INFO @ Tue, 02 Aug 2022 10:34:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (166 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。