Job ID = 16435030 SRX = SRX13110319 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:33:02 prefetch.2.10.7: 1) Downloading 'SRR16917989'... 2022-08-02T01:33:02 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:33:32 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:33:32 prefetch.2.10.7: 'SRR16917989' is valid 2022-08-02T01:33:32 prefetch.2.10.7: 1) 'SRR16917989' was downloaded successfully 2022-08-02T01:33:32 prefetch.2.10.7: 'SRR16917989' has 0 unresolved dependencies Read 16705645 spots for SRR16917989/SRR16917989.sra Written 16705645 spots for SRR16917989/SRR16917989.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435491 ("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 16705645 reads; of these: 16705645 (100.00%) were unpaired; of these: 7480753 (44.78%) aligned 0 times 7806639 (46.73%) aligned exactly 1 time 1418253 (8.49%) aligned >1 times 55.22% 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_rmdupse_core] 793204 / 9224892 = 0.0860 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 10:40:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.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 10:40:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:40:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:40:57: 1000000 INFO @ Tue, 02 Aug 2022 10:41:02: 2000000 INFO @ Tue, 02 Aug 2022 10:41:08: 3000000 INFO @ Tue, 02 Aug 2022 10:41:13: 4000000 INFO @ Tue, 02 Aug 2022 10:41:18: 5000000 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 10:41:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.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 10:41:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:41:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:41:24: 6000000 INFO @ Tue, 02 Aug 2022 10:41:28: 1000000 INFO @ Tue, 02 Aug 2022 10:41:30: 7000000 INFO @ Tue, 02 Aug 2022 10:41:35: 2000000 INFO @ Tue, 02 Aug 2022 10:41:36: 8000000 INFO @ Tue, 02 Aug 2022 10:41:39: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:41:39: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:41:39: #1 total tags in treatment: 8431688 INFO @ Tue, 02 Aug 2022 10:41:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:41:39: #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 10:41:39: #1 tags after filtering in treatment: 8431688 INFO @ Tue, 02 Aug 2022 10:41:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:41:39: #1 finished! INFO @ Tue, 02 Aug 2022 10:41:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:41:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:41:39: #2 number of paired peaks: 318 WARNING @ Tue, 02 Aug 2022 10:41:39: 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 @ Tue, 02 Aug 2022 10:41:39: start model_add_line... INFO @ Tue, 02 Aug 2022 10:41:39: start X-correlation... INFO @ Tue, 02 Aug 2022 10:41:39: end of X-cor INFO @ Tue, 02 Aug 2022 10:41:39: #2 finished! INFO @ Tue, 02 Aug 2022 10:41:39: #2 predicted fragment length is 86 bps INFO @ Tue, 02 Aug 2022 10:41:39: #2 alternative fragment length(s) may be 86 bps INFO @ Tue, 02 Aug 2022 10:41:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.05_model.r WARNING @ Tue, 02 Aug 2022 10:41:39: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:41:39: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Tue, 02 Aug 2022 10:41:39: #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 10:41:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:41:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:41:42: 3000000 INFO @ Tue, 02 Aug 2022 10:41:48: 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 10:41:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.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 10:41:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:41:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:41:55: 5000000 INFO @ Tue, 02 Aug 2022 10:41:56: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:41:58: 1000000 INFO @ Tue, 02 Aug 2022 10:42:02: 6000000 INFO @ Tue, 02 Aug 2022 10:42:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:42:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:42:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.05_summits.bed INFO @ Tue, 02 Aug 2022 10:42:05: Done! INFO @ Tue, 02 Aug 2022 10:42:05: 2000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1346 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:42:08: 7000000 INFO @ Tue, 02 Aug 2022 10:42:12: 3000000 INFO @ Tue, 02 Aug 2022 10:42:15: 8000000 INFO @ Tue, 02 Aug 2022 10:42:18: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:42:18: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:42:18: #1 total tags in treatment: 8431688 INFO @ Tue, 02 Aug 2022 10:42:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:42:18: #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 10:42:18: #1 tags after filtering in treatment: 8431688 INFO @ Tue, 02 Aug 2022 10:42:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:42:18: #1 finished! INFO @ Tue, 02 Aug 2022 10:42:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:42:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:42:18: 4000000 INFO @ Tue, 02 Aug 2022 10:42:19: #2 number of paired peaks: 318 WARNING @ Tue, 02 Aug 2022 10:42:19: 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 @ Tue, 02 Aug 2022 10:42:19: start model_add_line... INFO @ Tue, 02 Aug 2022 10:42:19: start X-correlation... INFO @ Tue, 02 Aug 2022 10:42:19: end of X-cor INFO @ Tue, 02 Aug 2022 10:42:19: #2 finished! INFO @ Tue, 02 Aug 2022 10:42:19: #2 predicted fragment length is 86 bps INFO @ Tue, 02 Aug 2022 10:42:19: #2 alternative fragment length(s) may be 86 bps INFO @ Tue, 02 Aug 2022 10:42:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.10_model.r WARNING @ Tue, 02 Aug 2022 10:42:19: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:42:19: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Tue, 02 Aug 2022 10:42:19: #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 10:42:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:42:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:42:25: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:42:31: 6000000 INFO @ Tue, 02 Aug 2022 10:42:35: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:42:38: 7000000 INFO @ Tue, 02 Aug 2022 10:42:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:42:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:42:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.10_summits.bed INFO @ Tue, 02 Aug 2022 10:42:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (646 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:42:44: 8000000 INFO @ Tue, 02 Aug 2022 10:42:47: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:42:47: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:42:47: #1 total tags in treatment: 8431688 INFO @ Tue, 02 Aug 2022 10:42:47: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:42:47: #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 10:42:47: #1 tags after filtering in treatment: 8431688 INFO @ Tue, 02 Aug 2022 10:42:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:42:47: #1 finished! INFO @ Tue, 02 Aug 2022 10:42:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:42:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:42:47: #2 number of paired peaks: 318 WARNING @ Tue, 02 Aug 2022 10:42:47: 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 @ Tue, 02 Aug 2022 10:42:47: start model_add_line... INFO @ Tue, 02 Aug 2022 10:42:47: start X-correlation... INFO @ Tue, 02 Aug 2022 10:42:47: end of X-cor INFO @ Tue, 02 Aug 2022 10:42:47: #2 finished! INFO @ Tue, 02 Aug 2022 10:42:47: #2 predicted fragment length is 86 bps INFO @ Tue, 02 Aug 2022 10:42:47: #2 alternative fragment length(s) may be 86 bps INFO @ Tue, 02 Aug 2022 10:42:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.20_model.r WARNING @ Tue, 02 Aug 2022 10:42:47: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:42:47: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Tue, 02 Aug 2022 10:42:47: #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 10:42:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:42:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:43:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:43:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:43:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:43:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110319/SRX13110319.20_summits.bed INFO @ Tue, 02 Aug 2022 10:43:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (275 records, 4 fields): 205 millis CompletedMACS2peakCalling