Job ID = 16434844 SRX = SRX10435517 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17361112 spots for SRR14060949/SRR14060949.sra Written 17361112 spots for SRR14060949/SRR14060949.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434888 ("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: 00:04:58 17361112 reads; of these: 17361112 (100.00%) were unpaired; of these: 2648001 (15.25%) aligned 0 times 12428178 (71.59%) aligned exactly 1 time 2284933 (13.16%) aligned >1 times 84.75% overall alignment rate Time searching: 00:04:58 Overall time: 00:04:58 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] 1540738 / 14713111 = 0.1047 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 10:09:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.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 10:09:31: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:09:31: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:09:38: 1000000 INFO @ Tue, 02 Aug 2022 10:09:44: 2000000 INFO @ Tue, 02 Aug 2022 10:09:50: 3000000 INFO @ Tue, 02 Aug 2022 10:09:56: 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 10:10:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.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 10:10:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:10:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:10:03: 5000000 INFO @ Tue, 02 Aug 2022 10:10:09: 1000000 INFO @ Tue, 02 Aug 2022 10:10:11: 6000000 INFO @ Tue, 02 Aug 2022 10:10:18: 2000000 INFO @ Tue, 02 Aug 2022 10:10:18: 7000000 INFO @ Tue, 02 Aug 2022 10:10:25: 8000000 INFO @ Tue, 02 Aug 2022 10:10:26: 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 10:10:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.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 10:10:31: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:10:31: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:10:32: 9000000 INFO @ Tue, 02 Aug 2022 10:10:34: 4000000 INFO @ Tue, 02 Aug 2022 10:10:39: 1000000 INFO @ Tue, 02 Aug 2022 10:10:40: 10000000 INFO @ Tue, 02 Aug 2022 10:10:42: 5000000 INFO @ Tue, 02 Aug 2022 10:10:46: 2000000 INFO @ Tue, 02 Aug 2022 10:10:47: 11000000 INFO @ Tue, 02 Aug 2022 10:10:51: 6000000 INFO @ Tue, 02 Aug 2022 10:10:54: 3000000 INFO @ Tue, 02 Aug 2022 10:10:55: 12000000 INFO @ Tue, 02 Aug 2022 10:10:59: 7000000 INFO @ Tue, 02 Aug 2022 10:11:01: 4000000 INFO @ Tue, 02 Aug 2022 10:11:02: 13000000 INFO @ Tue, 02 Aug 2022 10:11:03: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:11:03: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:11:03: #1 total tags in treatment: 13172373 INFO @ Tue, 02 Aug 2022 10:11:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:11:03: #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 10:11:03: #1 tags after filtering in treatment: 13172373 INFO @ Tue, 02 Aug 2022 10:11:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:11:03: #1 finished! INFO @ Tue, 02 Aug 2022 10:11:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:11:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:11:04: #2 number of paired peaks: 226 WARNING @ Tue, 02 Aug 2022 10:11:04: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Tue, 02 Aug 2022 10:11:04: start model_add_line... INFO @ Tue, 02 Aug 2022 10:11:04: start X-correlation... INFO @ Tue, 02 Aug 2022 10:11:04: end of X-cor INFO @ Tue, 02 Aug 2022 10:11:04: #2 finished! INFO @ Tue, 02 Aug 2022 10:11:04: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 10:11:04: #2 alternative fragment length(s) may be 3,72 bps INFO @ Tue, 02 Aug 2022 10:11:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.05_model.r WARNING @ Tue, 02 Aug 2022 10:11:04: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:11:04: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Tue, 02 Aug 2022 10:11:04: #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 10:11:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:11:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:11:07: 8000000 INFO @ Tue, 02 Aug 2022 10:11:09: 5000000 INFO @ Tue, 02 Aug 2022 10:11:14: 9000000 INFO @ Tue, 02 Aug 2022 10:11:16: 6000000 INFO @ Tue, 02 Aug 2022 10:11:22: 10000000 INFO @ Tue, 02 Aug 2022 10:11:23: 7000000 INFO @ Tue, 02 Aug 2022 10:11:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:11:29: 11000000 INFO @ Tue, 02 Aug 2022 10:11:30: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:11:36: 12000000 INFO @ Tue, 02 Aug 2022 10:11:38: 9000000 INFO @ Tue, 02 Aug 2022 10:11:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:11:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:11:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.05_summits.bed INFO @ Tue, 02 Aug 2022 10:11:41: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (659 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:11:44: 13000000 INFO @ Tue, 02 Aug 2022 10:11:45: 10000000 INFO @ Tue, 02 Aug 2022 10:11:45: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:11:45: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:11:45: #1 total tags in treatment: 13172373 INFO @ Tue, 02 Aug 2022 10:11:45: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:11:45: #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 10:11:45: #1 tags after filtering in treatment: 13172373 INFO @ Tue, 02 Aug 2022 10:11:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:11:45: #1 finished! INFO @ Tue, 02 Aug 2022 10:11:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:11:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:11:46: #2 number of paired peaks: 226 WARNING @ Tue, 02 Aug 2022 10:11:46: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Tue, 02 Aug 2022 10:11:46: start model_add_line... INFO @ Tue, 02 Aug 2022 10:11:46: start X-correlation... INFO @ Tue, 02 Aug 2022 10:11:46: end of X-cor INFO @ Tue, 02 Aug 2022 10:11:46: #2 finished! INFO @ Tue, 02 Aug 2022 10:11:46: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 10:11:46: #2 alternative fragment length(s) may be 3,72 bps INFO @ Tue, 02 Aug 2022 10:11:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.10_model.r WARNING @ Tue, 02 Aug 2022 10:11:46: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:11:46: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Tue, 02 Aug 2022 10:11:46: #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 10:11:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:11:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:11:51: 11000000 INFO @ Tue, 02 Aug 2022 10:11:57: 12000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:12:03: 13000000 INFO @ Tue, 02 Aug 2022 10:12:04: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:12:04: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:12:04: #1 total tags in treatment: 13172373 INFO @ Tue, 02 Aug 2022 10:12:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:12:04: #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 10:12:04: #1 tags after filtering in treatment: 13172373 INFO @ Tue, 02 Aug 2022 10:12:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:12:04: #1 finished! INFO @ Tue, 02 Aug 2022 10:12:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:12:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:12:05: #2 number of paired peaks: 226 WARNING @ Tue, 02 Aug 2022 10:12:05: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Tue, 02 Aug 2022 10:12:05: start model_add_line... INFO @ Tue, 02 Aug 2022 10:12:05: start X-correlation... INFO @ Tue, 02 Aug 2022 10:12:06: end of X-cor INFO @ Tue, 02 Aug 2022 10:12:06: #2 finished! INFO @ Tue, 02 Aug 2022 10:12:06: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 10:12:06: #2 alternative fragment length(s) may be 3,72 bps INFO @ Tue, 02 Aug 2022 10:12:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.20_model.r WARNING @ Tue, 02 Aug 2022 10:12:06: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:12:06: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Tue, 02 Aug 2022 10:12:06: #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 10:12:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:12:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:12:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:12:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:12:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:12:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.10_summits.bed INFO @ Tue, 02 Aug 2022 10:12:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (392 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:12:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:12:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:12:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:12:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435517/SRX10435517.20_summits.bed INFO @ Tue, 02 Aug 2022 10:12:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (215 records, 4 fields): 32 millis CompletedMACS2peakCalling