Job ID = 16434891 SRX = SRX10435504 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:57 28415103 reads; of these: 28415103 (100.00%) were unpaired; of these: 4747709 (16.71%) aligned 0 times 20184833 (71.04%) aligned exactly 1 time 3482561 (12.26%) aligned >1 times 83.29% overall alignment rate Time searching: 00:09:57 Overall time: 00:09:57 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 12 files... [bam_rmdupse_core] 6293004 / 23667394 = 0.2659 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 10:28:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.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 10:28:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:28:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:28:24: 1000000 INFO @ Tue, 02 Aug 2022 10:28:31: 2000000 INFO @ Tue, 02 Aug 2022 10:28:37: 3000000 INFO @ Tue, 02 Aug 2022 10:28:43: 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 10:28:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.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 10:28:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:28:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:28:49: 5000000 INFO @ Tue, 02 Aug 2022 10:28:52: 1000000 INFO @ Tue, 02 Aug 2022 10:28:56: 6000000 INFO @ Tue, 02 Aug 2022 10:28:59: 2000000 INFO @ Tue, 02 Aug 2022 10:29:02: 7000000 INFO @ Tue, 02 Aug 2022 10:29:05: 3000000 INFO @ Tue, 02 Aug 2022 10:29:07: 8000000 INFO @ Tue, 02 Aug 2022 10:29:11: 4000000 INFO @ Tue, 02 Aug 2022 10:29:13: 9000000 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 10:29:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.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 10:29:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:29:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:29:17: 5000000 INFO @ Tue, 02 Aug 2022 10:29:19: 10000000 INFO @ Tue, 02 Aug 2022 10:29:23: 1000000 INFO @ Tue, 02 Aug 2022 10:29:24: 6000000 INFO @ Tue, 02 Aug 2022 10:29:25: 11000000 INFO @ Tue, 02 Aug 2022 10:29:30: 2000000 INFO @ Tue, 02 Aug 2022 10:29:31: 12000000 INFO @ Tue, 02 Aug 2022 10:29:31: 7000000 INFO @ Tue, 02 Aug 2022 10:29:37: 13000000 INFO @ Tue, 02 Aug 2022 10:29:38: 3000000 INFO @ Tue, 02 Aug 2022 10:29:38: 8000000 INFO @ Tue, 02 Aug 2022 10:29:43: 14000000 INFO @ Tue, 02 Aug 2022 10:29:45: 4000000 INFO @ Tue, 02 Aug 2022 10:29:45: 9000000 INFO @ Tue, 02 Aug 2022 10:29:49: 15000000 INFO @ Tue, 02 Aug 2022 10:29:52: 5000000 INFO @ Tue, 02 Aug 2022 10:29:52: 10000000 INFO @ Tue, 02 Aug 2022 10:29:55: 16000000 INFO @ Tue, 02 Aug 2022 10:29:59: 6000000 INFO @ Tue, 02 Aug 2022 10:29:59: 11000000 INFO @ Tue, 02 Aug 2022 10:30:02: 17000000 INFO @ Tue, 02 Aug 2022 10:30:05: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:30:05: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:30:05: #1 total tags in treatment: 17374390 INFO @ Tue, 02 Aug 2022 10:30:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:30:05: #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 10:30:05: #1 tags after filtering in treatment: 17374390 INFO @ Tue, 02 Aug 2022 10:30:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:30:05: #1 finished! INFO @ Tue, 02 Aug 2022 10:30:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:30:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:30:06: 7000000 INFO @ Tue, 02 Aug 2022 10:30:06: #2 number of paired peaks: 292 WARNING @ Tue, 02 Aug 2022 10:30:06: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Tue, 02 Aug 2022 10:30:06: start model_add_line... INFO @ Tue, 02 Aug 2022 10:30:06: start X-correlation... INFO @ Tue, 02 Aug 2022 10:30:06: end of X-cor INFO @ Tue, 02 Aug 2022 10:30:06: #2 finished! INFO @ Tue, 02 Aug 2022 10:30:06: #2 predicted fragment length is 131 bps INFO @ Tue, 02 Aug 2022 10:30:06: #2 alternative fragment length(s) may be 4,131 bps INFO @ Tue, 02 Aug 2022 10:30:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.05_model.r WARNING @ Tue, 02 Aug 2022 10:30:06: #2 Since the d (131) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:30:06: #2 You may need to consider one of the other alternative d(s): 4,131 WARNING @ Tue, 02 Aug 2022 10:30:06: #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 10:30:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:30:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:30:06: 12000000 INFO @ Tue, 02 Aug 2022 10:30:13: 8000000 INFO @ Tue, 02 Aug 2022 10:30:13: 13000000 INFO @ Tue, 02 Aug 2022 10:30:20: 9000000 INFO @ Tue, 02 Aug 2022 10:30:21: 14000000 INFO @ Tue, 02 Aug 2022 10:30:27: 10000000 INFO @ Tue, 02 Aug 2022 10:30:27: 15000000 INFO @ Tue, 02 Aug 2022 10:30:34: 11000000 INFO @ Tue, 02 Aug 2022 10:30:34: 16000000 INFO @ Tue, 02 Aug 2022 10:30:38: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:30:41: 12000000 INFO @ Tue, 02 Aug 2022 10:30:41: 17000000 INFO @ Tue, 02 Aug 2022 10:30:44: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:30:44: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:30:44: #1 total tags in treatment: 17374390 INFO @ Tue, 02 Aug 2022 10:30:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:30:44: #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 10:30:44: #1 tags after filtering in treatment: 17374390 INFO @ Tue, 02 Aug 2022 10:30:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:30:44: #1 finished! INFO @ Tue, 02 Aug 2022 10:30:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:30:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:30:46: #2 number of paired peaks: 292 WARNING @ Tue, 02 Aug 2022 10:30:46: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Tue, 02 Aug 2022 10:30:46: start model_add_line... INFO @ Tue, 02 Aug 2022 10:30:46: start X-correlation... INFO @ Tue, 02 Aug 2022 10:30:46: end of X-cor INFO @ Tue, 02 Aug 2022 10:30:46: #2 finished! INFO @ Tue, 02 Aug 2022 10:30:46: #2 predicted fragment length is 131 bps INFO @ Tue, 02 Aug 2022 10:30:46: #2 alternative fragment length(s) may be 4,131 bps INFO @ Tue, 02 Aug 2022 10:30:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.10_model.r WARNING @ Tue, 02 Aug 2022 10:30:46: #2 Since the d (131) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:30:46: #2 You may need to consider one of the other alternative d(s): 4,131 WARNING @ Tue, 02 Aug 2022 10:30:46: #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 10:30:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:30:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:30:48: 13000000 INFO @ Tue, 02 Aug 2022 10:30:57: 14000000 INFO @ Tue, 02 Aug 2022 10:30:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:30:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:30:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.05_summits.bed INFO @ Tue, 02 Aug 2022 10:30:58: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (2398 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:31:05: 15000000 INFO @ Tue, 02 Aug 2022 10:31:13: 16000000 INFO @ Tue, 02 Aug 2022 10:31:21: 17000000 INFO @ Tue, 02 Aug 2022 10:31:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:31:24: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:31:24: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:31:24: #1 total tags in treatment: 17374390 INFO @ Tue, 02 Aug 2022 10:31:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:31:24: #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 10:31:24: #1 tags after filtering in treatment: 17374390 INFO @ Tue, 02 Aug 2022 10:31:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:31:24: #1 finished! INFO @ Tue, 02 Aug 2022 10:31:24: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:31:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:31:25: #2 number of paired peaks: 292 WARNING @ Tue, 02 Aug 2022 10:31:25: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Tue, 02 Aug 2022 10:31:25: start model_add_line... INFO @ Tue, 02 Aug 2022 10:31:25: start X-correlation... INFO @ Tue, 02 Aug 2022 10:31:25: end of X-cor INFO @ Tue, 02 Aug 2022 10:31:25: #2 finished! INFO @ Tue, 02 Aug 2022 10:31:25: #2 predicted fragment length is 131 bps INFO @ Tue, 02 Aug 2022 10:31:25: #2 alternative fragment length(s) may be 4,131 bps INFO @ Tue, 02 Aug 2022 10:31:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.20_model.r WARNING @ Tue, 02 Aug 2022 10:31:25: #2 Since the d (131) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:31:25: #2 You may need to consider one of the other alternative d(s): 4,131 WARNING @ Tue, 02 Aug 2022 10:31:25: #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 10:31:25: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:31:25: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:31:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:31:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:31:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.10_summits.bed INFO @ Tue, 02 Aug 2022 10:31:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1498 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:32:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:32:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:32:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:32:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435504/SRX10435504.20_summits.bed INFO @ Tue, 02 Aug 2022 10:32:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (838 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。