Job ID = 14159309 SRX = SRX3180823 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9583300 spots for SRR6030474/SRR6030474.sra Written 9583300 spots for SRR6030474/SRR6030474.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159509 ("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: 00:01:27 9583300 reads; of these: 9583300 (100.00%) were unpaired; of these: 4762146 (49.69%) aligned 0 times 4058009 (42.34%) aligned exactly 1 time 763145 (7.96%) aligned >1 times 50.31% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 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] 1830873 / 4821154 = 0.3798 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 20:53:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.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 20:53:03: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:53:03: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:53:08: 1000000 INFO @ Wed, 08 Dec 2021 20:53:14: 2000000 INFO @ Wed, 08 Dec 2021 20:53:20: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:53:20: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:53:20: #1 total tags in treatment: 2990281 INFO @ Wed, 08 Dec 2021 20:53:20: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:53:20: #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 20:53:20: #1 tags after filtering in treatment: 2990281 INFO @ Wed, 08 Dec 2021 20:53:20: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:53:20: #1 finished! INFO @ Wed, 08 Dec 2021 20:53:20: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:53:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:53:20: #2 number of paired peaks: 477 WARNING @ Wed, 08 Dec 2021 20:53:20: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Wed, 08 Dec 2021 20:53:20: start model_add_line... INFO @ Wed, 08 Dec 2021 20:53:20: start X-correlation... INFO @ Wed, 08 Dec 2021 20:53:20: end of X-cor INFO @ Wed, 08 Dec 2021 20:53:20: #2 finished! INFO @ Wed, 08 Dec 2021 20:53:20: #2 predicted fragment length is 51 bps INFO @ Wed, 08 Dec 2021 20:53:20: #2 alternative fragment length(s) may be 51,570 bps INFO @ Wed, 08 Dec 2021 20:53:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.05_model.r WARNING @ Wed, 08 Dec 2021 20:53:20: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:53:20: #2 You may need to consider one of the other alternative d(s): 51,570 WARNING @ Wed, 08 Dec 2021 20:53:20: #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 20:53:20: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:53:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:53:26: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:53:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:53:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:53:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.05_summits.bed INFO @ Wed, 08 Dec 2021 20:53:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (485 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 20:53:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.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 20:53:33: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:53:33: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:53:38: 1000000 INFO @ Wed, 08 Dec 2021 20:53:44: 2000000 INFO @ Wed, 08 Dec 2021 20:53:50: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:53:50: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:53:50: #1 total tags in treatment: 2990281 INFO @ Wed, 08 Dec 2021 20:53:50: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:53:50: #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 20:53:50: #1 tags after filtering in treatment: 2990281 INFO @ Wed, 08 Dec 2021 20:53:50: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:53:50: #1 finished! INFO @ Wed, 08 Dec 2021 20:53:50: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:53:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:53:50: #2 number of paired peaks: 477 WARNING @ Wed, 08 Dec 2021 20:53:50: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Wed, 08 Dec 2021 20:53:50: start model_add_line... INFO @ Wed, 08 Dec 2021 20:53:50: start X-correlation... INFO @ Wed, 08 Dec 2021 20:53:50: end of X-cor INFO @ Wed, 08 Dec 2021 20:53:50: #2 finished! INFO @ Wed, 08 Dec 2021 20:53:50: #2 predicted fragment length is 51 bps INFO @ Wed, 08 Dec 2021 20:53:50: #2 alternative fragment length(s) may be 51,570 bps INFO @ Wed, 08 Dec 2021 20:53:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.10_model.r WARNING @ Wed, 08 Dec 2021 20:53:50: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:53:50: #2 You may need to consider one of the other alternative d(s): 51,570 WARNING @ Wed, 08 Dec 2021 20:53:50: #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 20:53:50: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:53:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:53:56: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:53:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:53:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:53:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.10_summits.bed INFO @ Wed, 08 Dec 2021 20:53:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 20:54:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.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 20:54:03: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:54:03: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:54:08: 1000000 INFO @ Wed, 08 Dec 2021 20:54:14: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:54:20: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:54:20: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:54:20: #1 total tags in treatment: 2990281 INFO @ Wed, 08 Dec 2021 20:54:20: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:54:20: #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 20:54:20: #1 tags after filtering in treatment: 2990281 INFO @ Wed, 08 Dec 2021 20:54:20: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:54:20: #1 finished! INFO @ Wed, 08 Dec 2021 20:54:20: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:54:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:54:20: #2 number of paired peaks: 477 WARNING @ Wed, 08 Dec 2021 20:54:20: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Wed, 08 Dec 2021 20:54:20: start model_add_line... INFO @ Wed, 08 Dec 2021 20:54:20: start X-correlation... INFO @ Wed, 08 Dec 2021 20:54:20: end of X-cor INFO @ Wed, 08 Dec 2021 20:54:20: #2 finished! INFO @ Wed, 08 Dec 2021 20:54:20: #2 predicted fragment length is 51 bps INFO @ Wed, 08 Dec 2021 20:54:20: #2 alternative fragment length(s) may be 51,570 bps INFO @ Wed, 08 Dec 2021 20:54:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.20_model.r WARNING @ Wed, 08 Dec 2021 20:54:20: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:54:20: #2 You may need to consider one of the other alternative d(s): 51,570 WARNING @ Wed, 08 Dec 2021 20:54:20: #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 20:54:20: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:54:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:54:26: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:54:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:54:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:54:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180823/SRX3180823.20_summits.bed INFO @ Wed, 08 Dec 2021 20:54:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (111 records, 4 fields): 2 millis CompletedMACS2peakCalling