Job ID = 16434926 SRX = SRX11633396 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14804697 spots for SRR15329104/SRR15329104.sra Written 14804697 spots for SRR15329104/SRR15329104.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434989 ("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: 00:05:51 14804697 reads; of these: 14804697 (100.00%) were unpaired; of these: 1059914 (7.16%) aligned 0 times 11594748 (78.32%) aligned exactly 1 time 2150035 (14.52%) aligned >1 times 92.84% overall alignment rate Time searching: 00:05:51 Overall time: 00:05:51 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] 1276935 / 13744783 = 0.0929 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 10:30:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.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 10:30:32: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:30:32: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:30:41: 1000000 INFO @ Tue, 02 Aug 2022 10:30:49: 2000000 INFO @ Tue, 02 Aug 2022 10:30:58: 3000000 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 10:31:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.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 10:31:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:31:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:31:06: 4000000 INFO @ Tue, 02 Aug 2022 10:31:12: 1000000 INFO @ Tue, 02 Aug 2022 10:31:15: 5000000 INFO @ Tue, 02 Aug 2022 10:31:22: 2000000 INFO @ Tue, 02 Aug 2022 10:31:23: 6000000 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 10:31:31: 3000000 INFO @ Tue, 02 Aug 2022 10:31:32: 7000000 INFO @ Tue, 02 Aug 2022 10:31:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.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 10:31:32: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:31:32: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:31:41: 8000000 INFO @ Tue, 02 Aug 2022 10:31:43: 4000000 INFO @ Tue, 02 Aug 2022 10:31:44: 1000000 INFO @ Tue, 02 Aug 2022 10:31:50: 9000000 INFO @ Tue, 02 Aug 2022 10:31:54: 5000000 INFO @ Tue, 02 Aug 2022 10:31:55: 2000000 INFO @ Tue, 02 Aug 2022 10:32:00: 10000000 INFO @ Tue, 02 Aug 2022 10:32:06: 6000000 INFO @ Tue, 02 Aug 2022 10:32:06: 3000000 INFO @ Tue, 02 Aug 2022 10:32:10: 11000000 INFO @ Tue, 02 Aug 2022 10:32:16: 4000000 INFO @ Tue, 02 Aug 2022 10:32:18: 7000000 INFO @ Tue, 02 Aug 2022 10:32:20: 12000000 INFO @ Tue, 02 Aug 2022 10:32:26: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:32:26: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:32:26: #1 total tags in treatment: 12467848 INFO @ Tue, 02 Aug 2022 10:32:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:32:26: #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 10:32:27: #1 tags after filtering in treatment: 12467848 INFO @ Tue, 02 Aug 2022 10:32:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:32:27: #1 finished! INFO @ Tue, 02 Aug 2022 10:32:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:32:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:32:28: #2 number of paired peaks: 276 WARNING @ Tue, 02 Aug 2022 10:32:28: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Tue, 02 Aug 2022 10:32:28: start model_add_line... INFO @ Tue, 02 Aug 2022 10:32:28: start X-correlation... INFO @ Tue, 02 Aug 2022 10:32:28: end of X-cor INFO @ Tue, 02 Aug 2022 10:32:28: #2 finished! INFO @ Tue, 02 Aug 2022 10:32:28: #2 predicted fragment length is 66 bps INFO @ Tue, 02 Aug 2022 10:32:28: #2 alternative fragment length(s) may be 4,66 bps INFO @ Tue, 02 Aug 2022 10:32:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.05_model.r WARNING @ Tue, 02 Aug 2022 10:32:28: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:32:28: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Tue, 02 Aug 2022 10:32:28: #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 10:32:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:32:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:32:30: 5000000 INFO @ Tue, 02 Aug 2022 10:32:32: 8000000 INFO @ Tue, 02 Aug 2022 10:32:42: 6000000 INFO @ Tue, 02 Aug 2022 10:32:42: 9000000 INFO @ Tue, 02 Aug 2022 10:32:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:32:54: 10000000 INFO @ Tue, 02 Aug 2022 10:32:54: 7000000 INFO @ Tue, 02 Aug 2022 10:33:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:33:05: 11000000 INFO @ Tue, 02 Aug 2022 10:33:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:33:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.05_summits.bed INFO @ Tue, 02 Aug 2022 10:33:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (734 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:33:06: 8000000 INFO @ Tue, 02 Aug 2022 10:33:14: 12000000 INFO @ Tue, 02 Aug 2022 10:33:17: 9000000 INFO @ Tue, 02 Aug 2022 10:33:19: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:33:19: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:33:19: #1 total tags in treatment: 12467848 INFO @ Tue, 02 Aug 2022 10:33:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:33:19: #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 10:33:19: #1 tags after filtering in treatment: 12467848 INFO @ Tue, 02 Aug 2022 10:33:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:33:19: #1 finished! INFO @ Tue, 02 Aug 2022 10:33:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:33:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:33:20: #2 number of paired peaks: 276 WARNING @ Tue, 02 Aug 2022 10:33:20: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Tue, 02 Aug 2022 10:33:20: start model_add_line... INFO @ Tue, 02 Aug 2022 10:33:20: start X-correlation... INFO @ Tue, 02 Aug 2022 10:33:20: end of X-cor INFO @ Tue, 02 Aug 2022 10:33:20: #2 finished! INFO @ Tue, 02 Aug 2022 10:33:20: #2 predicted fragment length is 66 bps INFO @ Tue, 02 Aug 2022 10:33:20: #2 alternative fragment length(s) may be 4,66 bps INFO @ Tue, 02 Aug 2022 10:33:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.10_model.r WARNING @ Tue, 02 Aug 2022 10:33:20: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:33:20: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Tue, 02 Aug 2022 10:33:20: #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 10:33:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:33:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:33:27: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:33:37: 11000000 INFO @ Tue, 02 Aug 2022 10:33:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:33:48: 12000000 INFO @ Tue, 02 Aug 2022 10:33:53: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:33:53: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:33:53: #1 total tags in treatment: 12467848 INFO @ Tue, 02 Aug 2022 10:33:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:33:53: #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 10:33:53: #1 tags after filtering in treatment: 12467848 INFO @ Tue, 02 Aug 2022 10:33:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:33:53: #1 finished! INFO @ Tue, 02 Aug 2022 10:33:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:33:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:33:54: #2 number of paired peaks: 276 WARNING @ Tue, 02 Aug 2022 10:33:54: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Tue, 02 Aug 2022 10:33:54: start model_add_line... INFO @ Tue, 02 Aug 2022 10:33:54: start X-correlation... INFO @ Tue, 02 Aug 2022 10:33:54: end of X-cor INFO @ Tue, 02 Aug 2022 10:33:54: #2 finished! INFO @ Tue, 02 Aug 2022 10:33:54: #2 predicted fragment length is 66 bps INFO @ Tue, 02 Aug 2022 10:33:54: #2 alternative fragment length(s) may be 4,66 bps INFO @ Tue, 02 Aug 2022 10:33:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.20_model.r WARNING @ Tue, 02 Aug 2022 10:33:54: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:33:54: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Tue, 02 Aug 2022 10:33:54: #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 10:33:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:33:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:33:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:33:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:33:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.10_summits.bed INFO @ Tue, 02 Aug 2022 10:33:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (364 records, 4 fields): 26 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:34:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:34:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:34:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:34:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633396/SRX11633396.20_summits.bed INFO @ Tue, 02 Aug 2022 10:34:29: Done! pass1 - making usageList (6 chroms): 12 millis pass2 - checking and writing primary data (174 records, 4 fields): 30 millis CompletedMACS2peakCalling