Job ID = 16434875 SRX = SRX10435529 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21391298 spots for SRR14060929/SRR14060929.sra Written 21391298 spots for SRR14060929/SRR14060929.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434948 ("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: 00:06:02 21391298 reads; of these: 21391298 (100.00%) were unpaired; of these: 4749762 (22.20%) aligned 0 times 14174828 (66.26%) aligned exactly 1 time 2466708 (11.53%) aligned >1 times 77.80% overall alignment rate Time searching: 00:06:03 Overall time: 00:06:03 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] 2081834 / 16641536 = 0.1251 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 10:19:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.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 10:19:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:19:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:19:34: 1000000 INFO @ Tue, 02 Aug 2022 10:19:40: 2000000 INFO @ Tue, 02 Aug 2022 10:19:46: 3000000 INFO @ Tue, 02 Aug 2022 10:19:51: 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 10:19:57: 5000000 INFO @ Tue, 02 Aug 2022 10:19:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.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 10:19:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:19:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:20:03: 6000000 INFO @ Tue, 02 Aug 2022 10:20:05: 1000000 INFO @ Tue, 02 Aug 2022 10:20:09: 7000000 INFO @ Tue, 02 Aug 2022 10:20:12: 2000000 INFO @ Tue, 02 Aug 2022 10:20:16: 8000000 INFO @ Tue, 02 Aug 2022 10:20:18: 3000000 INFO @ Tue, 02 Aug 2022 10:20:22: 9000000 INFO @ Tue, 02 Aug 2022 10:20:25: 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 10:20:28: 10000000 INFO @ Tue, 02 Aug 2022 10:20:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.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 10:20:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:20:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:20:31: 5000000 INFO @ Tue, 02 Aug 2022 10:20:35: 11000000 INFO @ Tue, 02 Aug 2022 10:20:35: 1000000 INFO @ Tue, 02 Aug 2022 10:20:38: 6000000 INFO @ Tue, 02 Aug 2022 10:20:42: 12000000 INFO @ Tue, 02 Aug 2022 10:20:42: 2000000 INFO @ Tue, 02 Aug 2022 10:20:44: 7000000 INFO @ Tue, 02 Aug 2022 10:20:48: 13000000 INFO @ Tue, 02 Aug 2022 10:20:49: 3000000 INFO @ Tue, 02 Aug 2022 10:20:51: 8000000 INFO @ Tue, 02 Aug 2022 10:20:55: 14000000 INFO @ Tue, 02 Aug 2022 10:20:55: 4000000 INFO @ Tue, 02 Aug 2022 10:20:57: 9000000 INFO @ Tue, 02 Aug 2022 10:20:58: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:20:58: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:20:58: #1 total tags in treatment: 14559702 INFO @ Tue, 02 Aug 2022 10:20:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:20:58: #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 10:20:59: #1 tags after filtering in treatment: 14559702 INFO @ Tue, 02 Aug 2022 10:20:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:20:59: #1 finished! INFO @ Tue, 02 Aug 2022 10:20:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:20:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:20:59: #2 number of paired peaks: 386 WARNING @ Tue, 02 Aug 2022 10:20:59: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Tue, 02 Aug 2022 10:20:59: start model_add_line... INFO @ Tue, 02 Aug 2022 10:21:00: start X-correlation... INFO @ Tue, 02 Aug 2022 10:21:00: end of X-cor INFO @ Tue, 02 Aug 2022 10:21:00: #2 finished! INFO @ Tue, 02 Aug 2022 10:21:00: #2 predicted fragment length is 120 bps INFO @ Tue, 02 Aug 2022 10:21:00: #2 alternative fragment length(s) may be 120 bps INFO @ Tue, 02 Aug 2022 10:21:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.05_model.r WARNING @ Tue, 02 Aug 2022 10:21:00: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:21:00: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Tue, 02 Aug 2022 10:21:00: #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 10:21:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:21:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:21:01: 5000000 INFO @ Tue, 02 Aug 2022 10:21:03: 10000000 INFO @ Tue, 02 Aug 2022 10:21:08: 6000000 INFO @ Tue, 02 Aug 2022 10:21:10: 11000000 INFO @ Tue, 02 Aug 2022 10:21:14: 7000000 INFO @ Tue, 02 Aug 2022 10:21:16: 12000000 INFO @ Tue, 02 Aug 2022 10:21:20: 8000000 INFO @ Tue, 02 Aug 2022 10:21:22: 13000000 INFO @ Tue, 02 Aug 2022 10:21:27: 9000000 INFO @ Tue, 02 Aug 2022 10:21:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:21:29: 14000000 INFO @ Tue, 02 Aug 2022 10:21:32: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:21:32: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:21:32: #1 total tags in treatment: 14559702 INFO @ Tue, 02 Aug 2022 10:21:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:21:32: #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 10:21:32: #1 tags after filtering in treatment: 14559702 INFO @ Tue, 02 Aug 2022 10:21:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:21:32: #1 finished! INFO @ Tue, 02 Aug 2022 10:21:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:21:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:21:33: 10000000 INFO @ Tue, 02 Aug 2022 10:21:33: #2 number of paired peaks: 386 WARNING @ Tue, 02 Aug 2022 10:21:33: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Tue, 02 Aug 2022 10:21:33: start model_add_line... INFO @ Tue, 02 Aug 2022 10:21:33: start X-correlation... INFO @ Tue, 02 Aug 2022 10:21:33: end of X-cor INFO @ Tue, 02 Aug 2022 10:21:33: #2 finished! INFO @ Tue, 02 Aug 2022 10:21:33: #2 predicted fragment length is 120 bps INFO @ Tue, 02 Aug 2022 10:21:33: #2 alternative fragment length(s) may be 120 bps INFO @ Tue, 02 Aug 2022 10:21:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.10_model.r WARNING @ Tue, 02 Aug 2022 10:21:33: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:21:33: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Tue, 02 Aug 2022 10:21:33: #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 10:21:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:21:33: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:21:39: 11000000 INFO @ Tue, 02 Aug 2022 10:21:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:21:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:21:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.05_summits.bed INFO @ Tue, 02 Aug 2022 10:21:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2147 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:21:45: 12000000 INFO @ Tue, 02 Aug 2022 10:21:50: 13000000 INFO @ Tue, 02 Aug 2022 10:21:56: 14000000 INFO @ Tue, 02 Aug 2022 10:21:59: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:21:59: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:21:59: #1 total tags in treatment: 14559702 INFO @ Tue, 02 Aug 2022 10:21:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:21:59: #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 10:21:59: #1 tags after filtering in treatment: 14559702 INFO @ Tue, 02 Aug 2022 10:21:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:21:59: #1 finished! INFO @ Tue, 02 Aug 2022 10:21:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:21:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:22:00: #2 number of paired peaks: 386 WARNING @ Tue, 02 Aug 2022 10:22:00: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Tue, 02 Aug 2022 10:22:00: start model_add_line... INFO @ Tue, 02 Aug 2022 10:22:00: start X-correlation... INFO @ Tue, 02 Aug 2022 10:22:00: end of X-cor INFO @ Tue, 02 Aug 2022 10:22:00: #2 finished! INFO @ Tue, 02 Aug 2022 10:22:00: #2 predicted fragment length is 120 bps INFO @ Tue, 02 Aug 2022 10:22:00: #2 alternative fragment length(s) may be 120 bps INFO @ Tue, 02 Aug 2022 10:22:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.20_model.r WARNING @ Tue, 02 Aug 2022 10:22:00: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:22:00: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Tue, 02 Aug 2022 10:22:00: #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 10:22:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:22:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:22:02: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:22:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:22:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:22:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.10_summits.bed INFO @ Tue, 02 Aug 2022 10:22:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1395 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:22:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:22:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:22:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:22:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435529/SRX10435529.20_summits.bed INFO @ Tue, 02 Aug 2022 10:22:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (790 records, 4 fields): 16 millis CompletedMACS2peakCalling