Job ID = 14158109 SRX = SRX7739514 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12520761 spots for SRR11100918/SRR11100918.sra Written 12520761 spots for SRR11100918/SRR11100918.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158342 ("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: 00:02:38 12520761 reads; of these: 12520761 (100.00%) were unpaired; of these: 900428 (7.19%) aligned 0 times 9730770 (77.72%) aligned exactly 1 time 1889563 (15.09%) aligned >1 times 92.81% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 5239930 / 11620333 = 0.4509 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 14:30:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.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 14:30:16: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:30:16: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:30:20: 1000000 INFO @ Wed, 08 Dec 2021 14:30:25: 2000000 INFO @ Wed, 08 Dec 2021 14:30:29: 3000000 INFO @ Wed, 08 Dec 2021 14:30:33: 4000000 INFO @ Wed, 08 Dec 2021 14:30:38: 5000000 INFO @ Wed, 08 Dec 2021 14:30:42: 6000000 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 14:30:44: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:30:44: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:30:44: #1 total tags in treatment: 6380403 INFO @ Wed, 08 Dec 2021 14:30:44: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:30:44: #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 14:30:44: #1 tags after filtering in treatment: 6380403 INFO @ Wed, 08 Dec 2021 14:30:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:30:44: #1 finished! INFO @ Wed, 08 Dec 2021 14:30:44: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:30:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:30:45: #2 number of paired peaks: 519 WARNING @ Wed, 08 Dec 2021 14:30:45: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Wed, 08 Dec 2021 14:30:45: start model_add_line... INFO @ Wed, 08 Dec 2021 14:30:45: start X-correlation... INFO @ Wed, 08 Dec 2021 14:30:45: end of X-cor INFO @ Wed, 08 Dec 2021 14:30:45: #2 finished! INFO @ Wed, 08 Dec 2021 14:30:45: #2 predicted fragment length is 53 bps INFO @ Wed, 08 Dec 2021 14:30:45: #2 alternative fragment length(s) may be 4,53 bps INFO @ Wed, 08 Dec 2021 14:30:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.05_model.r WARNING @ Wed, 08 Dec 2021 14:30:45: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:30:45: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Wed, 08 Dec 2021 14:30:45: #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 14:30:45: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:30:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:30:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.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 14:30:46: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:30:46: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:30:50: 1000000 INFO @ Wed, 08 Dec 2021 14:30:55: 2000000 INFO @ Wed, 08 Dec 2021 14:30:58: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:30:59: 3000000 INFO @ Wed, 08 Dec 2021 14:31:04: 4000000 INFO @ Wed, 08 Dec 2021 14:31:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:31:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:31:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.05_summits.bed INFO @ Wed, 08 Dec 2021 14:31:04: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (741 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:31:08: 5000000 INFO @ Wed, 08 Dec 2021 14:31:13: 6000000 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 14:31:14: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:31:14: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:31:14: #1 total tags in treatment: 6380403 INFO @ Wed, 08 Dec 2021 14:31:14: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:31:14: #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 14:31:14: #1 tags after filtering in treatment: 6380403 INFO @ Wed, 08 Dec 2021 14:31:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:31:14: #1 finished! INFO @ Wed, 08 Dec 2021 14:31:14: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:31:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:31:15: #2 number of paired peaks: 519 WARNING @ Wed, 08 Dec 2021 14:31:15: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Wed, 08 Dec 2021 14:31:15: start model_add_line... INFO @ Wed, 08 Dec 2021 14:31:15: start X-correlation... INFO @ Wed, 08 Dec 2021 14:31:15: end of X-cor INFO @ Wed, 08 Dec 2021 14:31:15: #2 finished! INFO @ Wed, 08 Dec 2021 14:31:15: #2 predicted fragment length is 53 bps INFO @ Wed, 08 Dec 2021 14:31:15: #2 alternative fragment length(s) may be 4,53 bps INFO @ Wed, 08 Dec 2021 14:31:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.10_model.r WARNING @ Wed, 08 Dec 2021 14:31:15: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:31:15: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Wed, 08 Dec 2021 14:31:15: #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 14:31:15: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:31:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:31:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.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 14:31:16: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:31:16: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:31:20: 1000000 INFO @ Wed, 08 Dec 2021 14:31:25: 2000000 INFO @ Wed, 08 Dec 2021 14:31:27: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:31:29: 3000000 INFO @ Wed, 08 Dec 2021 14:31:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:31:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:31:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.10_summits.bed INFO @ Wed, 08 Dec 2021 14:31:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (490 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:31:34: 4000000 INFO @ Wed, 08 Dec 2021 14:31:38: 5000000 INFO @ Wed, 08 Dec 2021 14:31:43: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:31:44: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:31:44: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:31:44: #1 total tags in treatment: 6380403 INFO @ Wed, 08 Dec 2021 14:31:44: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:31:44: #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 14:31:44: #1 tags after filtering in treatment: 6380403 INFO @ Wed, 08 Dec 2021 14:31:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:31:44: #1 finished! INFO @ Wed, 08 Dec 2021 14:31:44: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:31:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:31:45: #2 number of paired peaks: 519 WARNING @ Wed, 08 Dec 2021 14:31:45: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Wed, 08 Dec 2021 14:31:45: start model_add_line... INFO @ Wed, 08 Dec 2021 14:31:45: start X-correlation... INFO @ Wed, 08 Dec 2021 14:31:45: end of X-cor INFO @ Wed, 08 Dec 2021 14:31:45: #2 finished! INFO @ Wed, 08 Dec 2021 14:31:45: #2 predicted fragment length is 53 bps INFO @ Wed, 08 Dec 2021 14:31:45: #2 alternative fragment length(s) may be 4,53 bps INFO @ Wed, 08 Dec 2021 14:31:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.20_model.r WARNING @ Wed, 08 Dec 2021 14:31:45: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:31:45: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Wed, 08 Dec 2021 14:31:45: #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 14:31:45: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:31:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:31:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:32:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:32:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:32:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7739514/SRX7739514.20_summits.bed INFO @ Wed, 08 Dec 2021 14:32:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (207 records, 4 fields): 4 millis CompletedMACS2peakCalling