Job ID = 16434864 SRX = SRX10435526 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 26895587 spots for SRR14060926/SRR14060926.sra Written 26895587 spots for SRR14060926/SRR14060926.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434941 ("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: 00:07:52 26895587 reads; of these: 26895587 (100.00%) were unpaired; of these: 4497131 (16.72%) aligned 0 times 18784586 (69.84%) aligned exactly 1 time 3613870 (13.44%) aligned >1 times 83.28% overall alignment rate Time searching: 00:07:52 Overall time: 00:07:52 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] 5334692 / 22398456 = 0.2382 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 10:18:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.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 10:18:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:18:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:18:32: 1000000 INFO @ Tue, 02 Aug 2022 10:18:38: 2000000 INFO @ Tue, 02 Aug 2022 10:18:44: 3000000 INFO @ Tue, 02 Aug 2022 10:18:50: 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 10:18:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.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 10:18:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:18:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:18:56: 5000000 INFO @ Tue, 02 Aug 2022 10:19:02: 1000000 INFO @ Tue, 02 Aug 2022 10:19:02: 6000000 INFO @ Tue, 02 Aug 2022 10:19:08: 7000000 INFO @ Tue, 02 Aug 2022 10:19:09: 2000000 INFO @ Tue, 02 Aug 2022 10:19:14: 8000000 INFO @ Tue, 02 Aug 2022 10:19:15: 3000000 INFO @ Tue, 02 Aug 2022 10:19:20: 9000000 INFO @ Tue, 02 Aug 2022 10:19:22: 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 10:19:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.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 10:19:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:19:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:19:26: 10000000 INFO @ Tue, 02 Aug 2022 10:19:29: 5000000 INFO @ Tue, 02 Aug 2022 10:19:31: 1000000 INFO @ Tue, 02 Aug 2022 10:19:32: 11000000 INFO @ Tue, 02 Aug 2022 10:19:36: 6000000 INFO @ Tue, 02 Aug 2022 10:19:38: 2000000 INFO @ Tue, 02 Aug 2022 10:19:39: 12000000 INFO @ Tue, 02 Aug 2022 10:19:43: 7000000 INFO @ Tue, 02 Aug 2022 10:19:44: 3000000 INFO @ Tue, 02 Aug 2022 10:19:45: 13000000 INFO @ Tue, 02 Aug 2022 10:19:50: 8000000 INFO @ Tue, 02 Aug 2022 10:19:50: 4000000 INFO @ Tue, 02 Aug 2022 10:19:51: 14000000 INFO @ Tue, 02 Aug 2022 10:19:56: 5000000 INFO @ Tue, 02 Aug 2022 10:19:56: 9000000 INFO @ Tue, 02 Aug 2022 10:19:57: 15000000 INFO @ Tue, 02 Aug 2022 10:20:02: 6000000 INFO @ Tue, 02 Aug 2022 10:20:02: 16000000 INFO @ Tue, 02 Aug 2022 10:20:03: 10000000 INFO @ Tue, 02 Aug 2022 10:20:08: 7000000 INFO @ Tue, 02 Aug 2022 10:20:08: 17000000 INFO @ Tue, 02 Aug 2022 10:20:08: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:20:08: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:20:08: #1 total tags in treatment: 17063764 INFO @ Tue, 02 Aug 2022 10:20:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:20:08: #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 10:20:09: #1 tags after filtering in treatment: 17063764 INFO @ Tue, 02 Aug 2022 10:20:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:20:09: #1 finished! INFO @ Tue, 02 Aug 2022 10:20:09: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:20:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:20:10: #2 number of paired peaks: 289 WARNING @ Tue, 02 Aug 2022 10:20:10: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Tue, 02 Aug 2022 10:20:10: start model_add_line... INFO @ Tue, 02 Aug 2022 10:20:10: start X-correlation... INFO @ Tue, 02 Aug 2022 10:20:10: end of X-cor INFO @ Tue, 02 Aug 2022 10:20:10: #2 finished! INFO @ Tue, 02 Aug 2022 10:20:10: #2 predicted fragment length is 96 bps INFO @ Tue, 02 Aug 2022 10:20:10: #2 alternative fragment length(s) may be 4,96,595 bps INFO @ Tue, 02 Aug 2022 10:20:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.05_model.r WARNING @ Tue, 02 Aug 2022 10:20:10: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:20:10: #2 You may need to consider one of the other alternative d(s): 4,96,595 WARNING @ Tue, 02 Aug 2022 10:20:10: #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 10:20:10: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:20:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:20:10: 11000000 INFO @ Tue, 02 Aug 2022 10:20:14: 8000000 INFO @ Tue, 02 Aug 2022 10:20:17: 12000000 INFO @ Tue, 02 Aug 2022 10:20:20: 9000000 INFO @ Tue, 02 Aug 2022 10:20:24: 13000000 INFO @ Tue, 02 Aug 2022 10:20:26: 10000000 INFO @ Tue, 02 Aug 2022 10:20:31: 14000000 INFO @ Tue, 02 Aug 2022 10:20:32: 11000000 INFO @ Tue, 02 Aug 2022 10:20:37: 15000000 INFO @ Tue, 02 Aug 2022 10:20:38: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:20:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:20:43: 13000000 INFO @ Tue, 02 Aug 2022 10:20:44: 16000000 INFO @ Tue, 02 Aug 2022 10:20:49: 14000000 INFO @ Tue, 02 Aug 2022 10:20:51: 17000000 INFO @ Tue, 02 Aug 2022 10:20:51: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:20:51: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:20:51: #1 total tags in treatment: 17063764 INFO @ Tue, 02 Aug 2022 10:20:51: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:20:51: #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 10:20:51: #1 tags after filtering in treatment: 17063764 INFO @ Tue, 02 Aug 2022 10:20:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:20:51: #1 finished! INFO @ Tue, 02 Aug 2022 10:20:51: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:20:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:20:52: #2 number of paired peaks: 289 WARNING @ Tue, 02 Aug 2022 10:20:52: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Tue, 02 Aug 2022 10:20:52: start model_add_line... INFO @ Tue, 02 Aug 2022 10:20:53: start X-correlation... INFO @ Tue, 02 Aug 2022 10:20:53: end of X-cor INFO @ Tue, 02 Aug 2022 10:20:53: #2 finished! INFO @ Tue, 02 Aug 2022 10:20:53: #2 predicted fragment length is 96 bps INFO @ Tue, 02 Aug 2022 10:20:53: #2 alternative fragment length(s) may be 4,96,595 bps INFO @ Tue, 02 Aug 2022 10:20:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.10_model.r WARNING @ Tue, 02 Aug 2022 10:20:53: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:20:53: #2 You may need to consider one of the other alternative d(s): 4,96,595 WARNING @ Tue, 02 Aug 2022 10:20:53: #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 10:20:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:20:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:20:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:20:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:20:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.05_summits.bed INFO @ Tue, 02 Aug 2022 10:20:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1256 records, 4 fields): 53 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:20:55: 15000000 INFO @ Tue, 02 Aug 2022 10:21:01: 16000000 INFO @ Tue, 02 Aug 2022 10:21:06: 17000000 INFO @ Tue, 02 Aug 2022 10:21:07: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:21:07: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:21:07: #1 total tags in treatment: 17063764 INFO @ Tue, 02 Aug 2022 10:21:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:21:07: #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 10:21:07: #1 tags after filtering in treatment: 17063764 INFO @ Tue, 02 Aug 2022 10:21:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:21:07: #1 finished! INFO @ Tue, 02 Aug 2022 10:21:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:21:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:21:08: #2 number of paired peaks: 289 WARNING @ Tue, 02 Aug 2022 10:21:08: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Tue, 02 Aug 2022 10:21:08: start model_add_line... INFO @ Tue, 02 Aug 2022 10:21:08: start X-correlation... INFO @ Tue, 02 Aug 2022 10:21:08: end of X-cor INFO @ Tue, 02 Aug 2022 10:21:08: #2 finished! INFO @ Tue, 02 Aug 2022 10:21:08: #2 predicted fragment length is 96 bps INFO @ Tue, 02 Aug 2022 10:21:08: #2 alternative fragment length(s) may be 4,96,595 bps INFO @ Tue, 02 Aug 2022 10:21:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.20_model.r WARNING @ Tue, 02 Aug 2022 10:21:08: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:21:08: #2 You may need to consider one of the other alternative d(s): 4,96,595 WARNING @ Tue, 02 Aug 2022 10:21:08: #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 10:21:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:21:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:21:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:21:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:21:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:21:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.10_summits.bed INFO @ Tue, 02 Aug 2022 10:21:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (780 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:21:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:21:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:21:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:21:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435526/SRX10435526.20_summits.bed INFO @ Tue, 02 Aug 2022 10:21:51: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (418 records, 4 fields): 34 millis CompletedMACS2peakCalling