Job ID = 14159449 SRX = SRX3180805 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:10 16493597 reads; of these: 16493597 (100.00%) were unpaired; of these: 11770266 (71.36%) aligned 0 times 3967861 (24.06%) aligned exactly 1 time 755470 (4.58%) aligned >1 times 28.64% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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] 3335116 / 4723331 = 0.7061 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 22:03:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.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 22:03:47: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:03:47: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:03:53: 1000000 INFO @ Wed, 08 Dec 2021 22:03:56: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:03:56: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:03:56: #1 total tags in treatment: 1388215 INFO @ Wed, 08 Dec 2021 22:03:56: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:03:56: #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 22:03:56: #1 tags after filtering in treatment: 1388215 INFO @ Wed, 08 Dec 2021 22:03:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:03:56: #1 finished! INFO @ Wed, 08 Dec 2021 22:03:56: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:03:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:03:56: #2 number of paired peaks: 791 WARNING @ Wed, 08 Dec 2021 22:03:56: Fewer paired peaks (791) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 791 pairs to build model! INFO @ Wed, 08 Dec 2021 22:03:56: start model_add_line... INFO @ Wed, 08 Dec 2021 22:03:56: start X-correlation... INFO @ Wed, 08 Dec 2021 22:03:56: end of X-cor INFO @ Wed, 08 Dec 2021 22:03:56: #2 finished! INFO @ Wed, 08 Dec 2021 22:03:56: #2 predicted fragment length is 51 bps INFO @ Wed, 08 Dec 2021 22:03:56: #2 alternative fragment length(s) may be 51 bps INFO @ Wed, 08 Dec 2021 22:03:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.05_model.r WARNING @ Wed, 08 Dec 2021 22:03:56: #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 22:03:56: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Wed, 08 Dec 2021 22:03:56: #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 22:03:56: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:03:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:03:59: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:04:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:04:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:04:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.05_summits.bed INFO @ Wed, 08 Dec 2021 22:04:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (462 records, 4 fields): 2 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 22:04:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.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 22:04:17: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:04:17: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:04:24: 1000000 INFO @ Wed, 08 Dec 2021 22:04:26: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:04:26: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:04:26: #1 total tags in treatment: 1388215 INFO @ Wed, 08 Dec 2021 22:04:26: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:04:26: #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 22:04:26: #1 tags after filtering in treatment: 1388215 INFO @ Wed, 08 Dec 2021 22:04:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:04:26: #1 finished! INFO @ Wed, 08 Dec 2021 22:04:26: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:04:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:04:26: #2 number of paired peaks: 791 WARNING @ Wed, 08 Dec 2021 22:04:26: Fewer paired peaks (791) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 791 pairs to build model! INFO @ Wed, 08 Dec 2021 22:04:26: start model_add_line... INFO @ Wed, 08 Dec 2021 22:04:26: start X-correlation... INFO @ Wed, 08 Dec 2021 22:04:26: end of X-cor INFO @ Wed, 08 Dec 2021 22:04:26: #2 finished! INFO @ Wed, 08 Dec 2021 22:04:26: #2 predicted fragment length is 51 bps INFO @ Wed, 08 Dec 2021 22:04:26: #2 alternative fragment length(s) may be 51 bps INFO @ Wed, 08 Dec 2021 22:04:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.10_model.r WARNING @ Wed, 08 Dec 2021 22:04:26: #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 22:04:26: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Wed, 08 Dec 2021 22:04:26: #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 22:04:26: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:04:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:04:29: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:04:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:04:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:04:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.10_summits.bed INFO @ Wed, 08 Dec 2021 22:04:31: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (248 records, 4 fields): 2 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 22:04:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.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 22:04:47: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:04:47: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:04:54: 1000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:04:56: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:04:56: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:04:56: #1 total tags in treatment: 1388215 INFO @ Wed, 08 Dec 2021 22:04:56: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:04:56: #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 22:04:56: #1 tags after filtering in treatment: 1388215 INFO @ Wed, 08 Dec 2021 22:04:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:04:56: #1 finished! INFO @ Wed, 08 Dec 2021 22:04:56: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:04:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:04:56: #2 number of paired peaks: 791 WARNING @ Wed, 08 Dec 2021 22:04:56: Fewer paired peaks (791) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 791 pairs to build model! INFO @ Wed, 08 Dec 2021 22:04:56: start model_add_line... INFO @ Wed, 08 Dec 2021 22:04:56: start X-correlation... INFO @ Wed, 08 Dec 2021 22:04:56: end of X-cor INFO @ Wed, 08 Dec 2021 22:04:56: #2 finished! INFO @ Wed, 08 Dec 2021 22:04:56: #2 predicted fragment length is 51 bps INFO @ Wed, 08 Dec 2021 22:04:56: #2 alternative fragment length(s) may be 51 bps INFO @ Wed, 08 Dec 2021 22:04:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.20_model.r WARNING @ Wed, 08 Dec 2021 22:04:56: #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 22:04:56: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Wed, 08 Dec 2021 22:04:56: #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 22:04:56: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:04:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:04:59: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:05:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:05:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:05:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180805/SRX3180805.20_summits.bed INFO @ Wed, 08 Dec 2021 22:05:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (84 records, 4 fields): 1 millis CompletedMACS2peakCalling