Job ID = 16434834 SRX = SRX10435509 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21224863 spots for SRR14060941/SRR14060941.sra Written 21224863 spots for SRR14060941/SRR14060941.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434878 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:41 21224863 reads; of these: 21224863 (100.00%) were unpaired; of these: 7926539 (37.35%) aligned 0 times 11002259 (51.84%) aligned exactly 1 time 2296065 (10.82%) aligned >1 times 62.65% overall alignment rate Time searching: 00:06:42 Overall time: 00:06:42 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] 2003057 / 13298324 = 0.1506 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 10:08:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.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 10:08:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:08:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:08:54: 1000000 INFO @ Tue, 02 Aug 2022 10:09:01: 2000000 INFO @ Tue, 02 Aug 2022 10:09:08: 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 10:09:15: 4000000 INFO @ Tue, 02 Aug 2022 10:09:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.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 10:09:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:09:17: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:09:23: 5000000 INFO @ Tue, 02 Aug 2022 10:09:24: 1000000 INFO @ Tue, 02 Aug 2022 10:09:31: 6000000 INFO @ Tue, 02 Aug 2022 10:09:32: 2000000 INFO @ Tue, 02 Aug 2022 10:09:39: 7000000 INFO @ Tue, 02 Aug 2022 10:09:39: 3000000 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 10:09:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.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 10:09:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:09:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:09:47: 4000000 INFO @ Tue, 02 Aug 2022 10:09:47: 8000000 INFO @ Tue, 02 Aug 2022 10:09:54: 5000000 INFO @ Tue, 02 Aug 2022 10:09:55: 1000000 INFO @ Tue, 02 Aug 2022 10:09:55: 9000000 INFO @ Tue, 02 Aug 2022 10:10:02: 6000000 INFO @ Tue, 02 Aug 2022 10:10:03: 2000000 INFO @ Tue, 02 Aug 2022 10:10:04: 10000000 INFO @ Tue, 02 Aug 2022 10:10:09: 7000000 INFO @ Tue, 02 Aug 2022 10:10:11: 3000000 INFO @ Tue, 02 Aug 2022 10:10:12: 11000000 INFO @ Tue, 02 Aug 2022 10:10:14: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:10:14: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:10:14: #1 total tags in treatment: 11295267 INFO @ Tue, 02 Aug 2022 10:10:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:10:14: #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 10:10:15: #1 tags after filtering in treatment: 11295267 INFO @ Tue, 02 Aug 2022 10:10:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:10:15: #1 finished! INFO @ Tue, 02 Aug 2022 10:10:15: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:10:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:10:15: #2 number of paired peaks: 371 WARNING @ Tue, 02 Aug 2022 10:10:15: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Tue, 02 Aug 2022 10:10:15: start model_add_line... INFO @ Tue, 02 Aug 2022 10:10:15: start X-correlation... INFO @ Tue, 02 Aug 2022 10:10:15: end of X-cor INFO @ Tue, 02 Aug 2022 10:10:15: #2 finished! INFO @ Tue, 02 Aug 2022 10:10:15: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 10:10:15: #2 alternative fragment length(s) may be 4,76 bps INFO @ Tue, 02 Aug 2022 10:10:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.05_model.r WARNING @ Tue, 02 Aug 2022 10:10:16: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:10:16: #2 You may need to consider one of the other alternative d(s): 4,76 WARNING @ Tue, 02 Aug 2022 10:10:16: #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 10:10:16: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:10:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:10:17: 8000000 INFO @ Tue, 02 Aug 2022 10:10:18: 4000000 INFO @ Tue, 02 Aug 2022 10:10:24: 9000000 INFO @ Tue, 02 Aug 2022 10:10:26: 5000000 INFO @ Tue, 02 Aug 2022 10:10:31: 10000000 INFO @ Tue, 02 Aug 2022 10:10:34: 6000000 INFO @ Tue, 02 Aug 2022 10:10:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:10:39: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:10:41: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:10:41: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:10:41: #1 total tags in treatment: 11295267 INFO @ Tue, 02 Aug 2022 10:10:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:10:41: #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 10:10:41: #1 tags after filtering in treatment: 11295267 INFO @ Tue, 02 Aug 2022 10:10:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:10:41: #1 finished! INFO @ Tue, 02 Aug 2022 10:10:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:10:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:10:42: #2 number of paired peaks: 371 WARNING @ Tue, 02 Aug 2022 10:10:42: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Tue, 02 Aug 2022 10:10:42: start model_add_line... INFO @ Tue, 02 Aug 2022 10:10:42: start X-correlation... INFO @ Tue, 02 Aug 2022 10:10:42: end of X-cor INFO @ Tue, 02 Aug 2022 10:10:42: #2 finished! INFO @ Tue, 02 Aug 2022 10:10:42: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 10:10:42: #2 alternative fragment length(s) may be 4,76 bps INFO @ Tue, 02 Aug 2022 10:10:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.10_model.r WARNING @ Tue, 02 Aug 2022 10:10:42: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:10:42: #2 You may need to consider one of the other alternative d(s): 4,76 WARNING @ Tue, 02 Aug 2022 10:10:42: #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 10:10:42: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:10:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:10:42: 7000000 INFO @ Tue, 02 Aug 2022 10:10:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:10:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:10:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.05_summits.bed INFO @ Tue, 02 Aug 2022 10:10:48: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (847 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:10:49: 8000000 INFO @ Tue, 02 Aug 2022 10:10:56: 9000000 INFO @ Tue, 02 Aug 2022 10:11:03: 10000000 INFO @ Tue, 02 Aug 2022 10:11:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:11:09: 11000000 INFO @ Tue, 02 Aug 2022 10:11:11: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:11:11: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:11:11: #1 total tags in treatment: 11295267 INFO @ Tue, 02 Aug 2022 10:11:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:11:11: #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 10:11:11: #1 tags after filtering in treatment: 11295267 INFO @ Tue, 02 Aug 2022 10:11:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:11:11: #1 finished! INFO @ Tue, 02 Aug 2022 10:11:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:11:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:11:12: #2 number of paired peaks: 371 WARNING @ Tue, 02 Aug 2022 10:11:12: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Tue, 02 Aug 2022 10:11:12: start model_add_line... INFO @ Tue, 02 Aug 2022 10:11:12: start X-correlation... INFO @ Tue, 02 Aug 2022 10:11:12: end of X-cor INFO @ Tue, 02 Aug 2022 10:11:12: #2 finished! INFO @ Tue, 02 Aug 2022 10:11:12: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 10:11:12: #2 alternative fragment length(s) may be 4,76 bps INFO @ Tue, 02 Aug 2022 10:11:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.20_model.r WARNING @ Tue, 02 Aug 2022 10:11:12: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:11:12: #2 You may need to consider one of the other alternative d(s): 4,76 WARNING @ Tue, 02 Aug 2022 10:11:12: #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 10:11:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:11:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:11:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:11:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:11:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.10_summits.bed INFO @ Tue, 02 Aug 2022 10:11:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (511 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:11:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:11:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:11:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:11:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435509/SRX10435509.20_summits.bed INFO @ Tue, 02 Aug 2022 10:11:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (279 records, 4 fields): 25 millis CompletedMACS2peakCalling