Job ID = 14157894 SRX = SRX10040020 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7173756 spots for SRR13642801/SRR13642801.sra Written 7173756 spots for SRR13642801/SRR13642801.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158082 ("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: 00:01:59 7173756 reads; of these: 7173756 (100.00%) were unpaired; of these: 189518 (2.64%) aligned 0 times 5683104 (79.22%) aligned exactly 1 time 1301134 (18.14%) aligned >1 times 97.36% overall alignment rate Time searching: 00:01:59 Overall time: 00:01:59 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] 652199 / 6984238 = 0.0934 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 12:24:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.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 12:24:35: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:24:35: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:24:43: 1000000 INFO @ Wed, 08 Dec 2021 12:24:52: 2000000 INFO @ Wed, 08 Dec 2021 12:25:00: 3000000 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 12:25:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.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 12:25:06: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:25:06: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:25:11: 4000000 INFO @ Wed, 08 Dec 2021 12:25:14: 1000000 INFO @ Wed, 08 Dec 2021 12:25:22: 5000000 INFO @ Wed, 08 Dec 2021 12:25:23: 2000000 INFO @ Wed, 08 Dec 2021 12:25:30: 6000000 INFO @ Wed, 08 Dec 2021 12:25:31: 3000000 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 12:25:34: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:25:34: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:25:34: #1 total tags in treatment: 6332039 INFO @ Wed, 08 Dec 2021 12:25:34: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:25:34: #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 12:25:34: #1 tags after filtering in treatment: 6332039 INFO @ Wed, 08 Dec 2021 12:25:34: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:25:34: #1 finished! INFO @ Wed, 08 Dec 2021 12:25:34: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:25:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:25:34: #2 number of paired peaks: 368 WARNING @ Wed, 08 Dec 2021 12:25:34: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Wed, 08 Dec 2021 12:25:34: start model_add_line... INFO @ Wed, 08 Dec 2021 12:25:34: start X-correlation... INFO @ Wed, 08 Dec 2021 12:25:35: end of X-cor INFO @ Wed, 08 Dec 2021 12:25:35: #2 finished! INFO @ Wed, 08 Dec 2021 12:25:35: #2 predicted fragment length is 52 bps INFO @ Wed, 08 Dec 2021 12:25:35: #2 alternative fragment length(s) may be 4,52,530 bps INFO @ Wed, 08 Dec 2021 12:25:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.05_model.r WARNING @ Wed, 08 Dec 2021 12:25:35: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:25:35: #2 You may need to consider one of the other alternative d(s): 4,52,530 WARNING @ Wed, 08 Dec 2021 12:25:35: #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 12:25:35: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:25:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:25:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.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 12:25:36: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:25:36: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:25:40: 4000000 INFO @ Wed, 08 Dec 2021 12:25:46: 1000000 INFO @ Wed, 08 Dec 2021 12:25:48: 5000000 INFO @ Wed, 08 Dec 2021 12:25:50: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:25:54: 2000000 INFO @ Wed, 08 Dec 2021 12:25:56: 6000000 INFO @ Wed, 08 Dec 2021 12:25:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.05_peaks.xls INFO @ Wed, 08 Dec 2021 12:25:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:25:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.05_summits.bed INFO @ Wed, 08 Dec 2021 12:25:59: Done! INFO @ Wed, 08 Dec 2021 12:26:00: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:26:00: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:26:00: #1 total tags in treatment: 6332039 INFO @ Wed, 08 Dec 2021 12:26:00: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:26:00: #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 12:26:00: #1 tags after filtering in treatment: 6332039 INFO @ Wed, 08 Dec 2021 12:26:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:26:00: #1 finished! INFO @ Wed, 08 Dec 2021 12:26:00: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:26:00: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (6 chroms): 31 millis pass2 - checking and writing primary data (544 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:26:00: #2 number of paired peaks: 368 WARNING @ Wed, 08 Dec 2021 12:26:00: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Wed, 08 Dec 2021 12:26:00: start model_add_line... INFO @ Wed, 08 Dec 2021 12:26:00: start X-correlation... INFO @ Wed, 08 Dec 2021 12:26:00: end of X-cor INFO @ Wed, 08 Dec 2021 12:26:00: #2 finished! INFO @ Wed, 08 Dec 2021 12:26:00: #2 predicted fragment length is 52 bps INFO @ Wed, 08 Dec 2021 12:26:00: #2 alternative fragment length(s) may be 4,52,530 bps INFO @ Wed, 08 Dec 2021 12:26:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.10_model.r WARNING @ Wed, 08 Dec 2021 12:26:00: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:26:00: #2 You may need to consider one of the other alternative d(s): 4,52,530 WARNING @ Wed, 08 Dec 2021 12:26:00: #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 12:26:00: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:26:00: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:26:01: 3000000 INFO @ Wed, 08 Dec 2021 12:26:09: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 12:26:16: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:26:17: 5000000 INFO @ Wed, 08 Dec 2021 12:26:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.10_peaks.xls INFO @ Wed, 08 Dec 2021 12:26:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:26:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.10_summits.bed INFO @ Wed, 08 Dec 2021 12:26:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (320 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:26:24: 6000000 INFO @ Wed, 08 Dec 2021 12:26:27: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:26:27: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:26:27: #1 total tags in treatment: 6332039 INFO @ Wed, 08 Dec 2021 12:26:27: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:26:27: #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 12:26:27: #1 tags after filtering in treatment: 6332039 INFO @ Wed, 08 Dec 2021 12:26:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:26:27: #1 finished! INFO @ Wed, 08 Dec 2021 12:26:27: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:26:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:26:27: #2 number of paired peaks: 368 WARNING @ Wed, 08 Dec 2021 12:26:27: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Wed, 08 Dec 2021 12:26:27: start model_add_line... INFO @ Wed, 08 Dec 2021 12:26:27: start X-correlation... INFO @ Wed, 08 Dec 2021 12:26:27: end of X-cor INFO @ Wed, 08 Dec 2021 12:26:27: #2 finished! INFO @ Wed, 08 Dec 2021 12:26:27: #2 predicted fragment length is 52 bps INFO @ Wed, 08 Dec 2021 12:26:27: #2 alternative fragment length(s) may be 4,52,530 bps INFO @ Wed, 08 Dec 2021 12:26:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.20_model.r WARNING @ Wed, 08 Dec 2021 12:26:27: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:26:27: #2 You may need to consider one of the other alternative d(s): 4,52,530 WARNING @ Wed, 08 Dec 2021 12:26:27: #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 12:26:27: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:26:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 12:26:44: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:26:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.20_peaks.xls INFO @ Wed, 08 Dec 2021 12:26:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:26:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10040020/SRX10040020.20_summits.bed INFO @ Wed, 08 Dec 2021 12:26:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (122 records, 4 fields): 1 millis CompletedMACS2peakCalling