Job ID = 14159601 SRX = SRX3180779 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17772057 spots for SRR6030430/SRR6030430.sra Written 17772057 spots for SRR6030430/SRR6030430.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160109 ("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: 00:03:46 17772057 reads; of these: 17772057 (100.00%) were unpaired; of these: 488852 (2.75%) aligned 0 times 14359633 (80.80%) aligned exactly 1 time 2923572 (16.45%) aligned >1 times 97.25% overall alignment rate Time searching: 00:03:46 Overall time: 00:03:46 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] 2839635 / 17283205 = 0.1643 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 23:22:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.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 @ Wed, 08 Dec 2021 23:22:55: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:22:55: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:23:00: 1000000 INFO @ Wed, 08 Dec 2021 23:23:05: 2000000 INFO @ Wed, 08 Dec 2021 23:23:10: 3000000 INFO @ Wed, 08 Dec 2021 23:23:15: 4000000 INFO @ Wed, 08 Dec 2021 23:23:20: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 23:23:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.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 @ Wed, 08 Dec 2021 23:23:25: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:23:25: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:23:25: 6000000 INFO @ Wed, 08 Dec 2021 23:23:30: 1000000 INFO @ Wed, 08 Dec 2021 23:23:30: 7000000 INFO @ Wed, 08 Dec 2021 23:23:36: 2000000 INFO @ Wed, 08 Dec 2021 23:23:36: 8000000 INFO @ Wed, 08 Dec 2021 23:23:41: 3000000 INFO @ Wed, 08 Dec 2021 23:23:41: 9000000 INFO @ Wed, 08 Dec 2021 23:23:46: 4000000 INFO @ Wed, 08 Dec 2021 23:23:46: 10000000 INFO @ Wed, 08 Dec 2021 23:23:52: 5000000 INFO @ Wed, 08 Dec 2021 23:23:52: 11000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 23:23:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.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 @ Wed, 08 Dec 2021 23:23:55: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:23:55: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:23:57: 6000000 INFO @ Wed, 08 Dec 2021 23:23:57: 12000000 INFO @ Wed, 08 Dec 2021 23:24:01: 1000000 INFO @ Wed, 08 Dec 2021 23:24:03: 7000000 INFO @ Wed, 08 Dec 2021 23:24:03: 13000000 INFO @ Wed, 08 Dec 2021 23:24:07: 2000000 INFO @ Wed, 08 Dec 2021 23:24:09: 8000000 INFO @ Wed, 08 Dec 2021 23:24:09: 14000000 INFO @ Wed, 08 Dec 2021 23:24:11: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:24:11: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:24:11: #1 total tags in treatment: 14443570 INFO @ Wed, 08 Dec 2021 23:24:11: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:24:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 23:24:12: #1 tags after filtering in treatment: 14443570 INFO @ Wed, 08 Dec 2021 23:24:12: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:24:12: #1 finished! INFO @ Wed, 08 Dec 2021 23:24:12: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:24:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:24:13: #2 number of paired peaks: 318 WARNING @ Wed, 08 Dec 2021 23:24:13: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Wed, 08 Dec 2021 23:24:13: start model_add_line... INFO @ Wed, 08 Dec 2021 23:24:13: start X-correlation... INFO @ Wed, 08 Dec 2021 23:24:13: end of X-cor INFO @ Wed, 08 Dec 2021 23:24:13: #2 finished! INFO @ Wed, 08 Dec 2021 23:24:13: #2 predicted fragment length is 46 bps INFO @ Wed, 08 Dec 2021 23:24:13: #2 alternative fragment length(s) may be 2,46 bps INFO @ Wed, 08 Dec 2021 23:24:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.05_model.r WARNING @ Wed, 08 Dec 2021 23:24:13: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:24:13: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Wed, 08 Dec 2021 23:24:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 23:24:13: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:24:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:24:13: 3000000 INFO @ Wed, 08 Dec 2021 23:24:14: 9000000 INFO @ Wed, 08 Dec 2021 23:24:19: 4000000 INFO @ Wed, 08 Dec 2021 23:24:20: 10000000 INFO @ Wed, 08 Dec 2021 23:24:26: 5000000 INFO @ Wed, 08 Dec 2021 23:24:26: 11000000 INFO @ Wed, 08 Dec 2021 23:24:31: 12000000 INFO @ Wed, 08 Dec 2021 23:24:32: 6000000 INFO @ Wed, 08 Dec 2021 23:24:37: 13000000 INFO @ Wed, 08 Dec 2021 23:24:38: 7000000 INFO @ Wed, 08 Dec 2021 23:24:39: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:24:43: 14000000 INFO @ Wed, 08 Dec 2021 23:24:44: 8000000 INFO @ Wed, 08 Dec 2021 23:24:45: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:24:45: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:24:45: #1 total tags in treatment: 14443570 INFO @ Wed, 08 Dec 2021 23:24:45: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:24:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 23:24:46: #1 tags after filtering in treatment: 14443570 INFO @ Wed, 08 Dec 2021 23:24:46: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:24:46: #1 finished! INFO @ Wed, 08 Dec 2021 23:24:46: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:24:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:24:47: #2 number of paired peaks: 318 WARNING @ Wed, 08 Dec 2021 23:24:47: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Wed, 08 Dec 2021 23:24:47: start model_add_line... INFO @ Wed, 08 Dec 2021 23:24:47: start X-correlation... INFO @ Wed, 08 Dec 2021 23:24:47: end of X-cor INFO @ Wed, 08 Dec 2021 23:24:47: #2 finished! INFO @ Wed, 08 Dec 2021 23:24:47: #2 predicted fragment length is 46 bps INFO @ Wed, 08 Dec 2021 23:24:47: #2 alternative fragment length(s) may be 2,46 bps INFO @ Wed, 08 Dec 2021 23:24:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.10_model.r WARNING @ Wed, 08 Dec 2021 23:24:47: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:24:47: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Wed, 08 Dec 2021 23:24:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 23:24:47: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:24:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:24:50: 9000000 INFO @ Wed, 08 Dec 2021 23:24:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:24:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:24:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.05_summits.bed INFO @ Wed, 08 Dec 2021 23:24:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (711 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:24:56: 10000000 INFO @ Wed, 08 Dec 2021 23:25:02: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:25:08: 12000000 INFO @ Wed, 08 Dec 2021 23:25:12: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:25:13: 13000000 INFO @ Wed, 08 Dec 2021 23:25:19: 14000000 INFO @ Wed, 08 Dec 2021 23:25:22: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:25:22: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:25:22: #1 total tags in treatment: 14443570 INFO @ Wed, 08 Dec 2021 23:25:22: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:25:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 23:25:22: #1 tags after filtering in treatment: 14443570 INFO @ Wed, 08 Dec 2021 23:25:22: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:25:22: #1 finished! INFO @ Wed, 08 Dec 2021 23:25:22: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:25:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:25:23: #2 number of paired peaks: 318 WARNING @ Wed, 08 Dec 2021 23:25:23: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Wed, 08 Dec 2021 23:25:23: start model_add_line... INFO @ Wed, 08 Dec 2021 23:25:23: start X-correlation... INFO @ Wed, 08 Dec 2021 23:25:23: end of X-cor INFO @ Wed, 08 Dec 2021 23:25:23: #2 finished! INFO @ Wed, 08 Dec 2021 23:25:23: #2 predicted fragment length is 46 bps INFO @ Wed, 08 Dec 2021 23:25:23: #2 alternative fragment length(s) may be 2,46 bps INFO @ Wed, 08 Dec 2021 23:25:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.20_model.r WARNING @ Wed, 08 Dec 2021 23:25:23: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:25:23: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Wed, 08 Dec 2021 23:25:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 23:25:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:25:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:25:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:25:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:25:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.10_summits.bed INFO @ Wed, 08 Dec 2021 23:25:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (461 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:25:48: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:26:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:26:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:26:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180779/SRX3180779.20_summits.bed INFO @ Wed, 08 Dec 2021 23:26:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 1 millis CompletedMACS2peakCalling