Job ID = 14160287 SRX = SRX3180798 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: 00:01:59 16767409 reads; of these: 16767409 (100.00%) were unpaired; of these: 11659873 (69.54%) aligned 0 times 4282628 (25.54%) aligned exactly 1 time 824908 (4.92%) aligned >1 times 30.46% 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] 4365493 / 5107536 = 0.8547 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 @ Thu, 09 Dec 2021 01:16:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.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 @ Thu, 09 Dec 2021 01:16:39: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:16:39: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:16:44: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:16:44: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:16:44: #1 total tags in treatment: 742043 INFO @ Thu, 09 Dec 2021 01:16:44: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:16:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:16:44: #1 tags after filtering in treatment: 742043 INFO @ Thu, 09 Dec 2021 01:16:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 01:16:44: #1 finished! INFO @ Thu, 09 Dec 2021 01:16:44: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:16:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:16:44: #2 number of paired peaks: 1102 INFO @ Thu, 09 Dec 2021 01:16:44: start model_add_line... INFO @ Thu, 09 Dec 2021 01:16:44: start X-correlation... INFO @ Thu, 09 Dec 2021 01:16:44: end of X-cor INFO @ Thu, 09 Dec 2021 01:16:44: #2 finished! INFO @ Thu, 09 Dec 2021 01:16:44: #2 predicted fragment length is 54 bps INFO @ Thu, 09 Dec 2021 01:16:44: #2 alternative fragment length(s) may be 54,208,543,568 bps INFO @ Thu, 09 Dec 2021 01:16:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.05_model.r WARNING @ Thu, 09 Dec 2021 01:16:44: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:16:44: #2 You may need to consider one of the other alternative d(s): 54,208,543,568 WARNING @ Thu, 09 Dec 2021 01:16:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 01:16:44: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:16:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:16:45: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:16:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.05_peaks.xls INFO @ Thu, 09 Dec 2021 01:16:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:16:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.05_summits.bed INFO @ Thu, 09 Dec 2021 01:16:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (435 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 @ Thu, 09 Dec 2021 01:17:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.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 @ Thu, 09 Dec 2021 01:17:09: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:17:09: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:17:13: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:17:13: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:17:13: #1 total tags in treatment: 742043 INFO @ Thu, 09 Dec 2021 01:17:13: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:17:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:17:13: #1 tags after filtering in treatment: 742043 INFO @ Thu, 09 Dec 2021 01:17:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 01:17:13: #1 finished! INFO @ Thu, 09 Dec 2021 01:17:13: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:17:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:17:14: #2 number of paired peaks: 1102 INFO @ Thu, 09 Dec 2021 01:17:14: start model_add_line... INFO @ Thu, 09 Dec 2021 01:17:14: start X-correlation... INFO @ Thu, 09 Dec 2021 01:17:14: end of X-cor INFO @ Thu, 09 Dec 2021 01:17:14: #2 finished! INFO @ Thu, 09 Dec 2021 01:17:14: #2 predicted fragment length is 54 bps INFO @ Thu, 09 Dec 2021 01:17:14: #2 alternative fragment length(s) may be 54,208,543,568 bps INFO @ Thu, 09 Dec 2021 01:17:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.10_model.r WARNING @ Thu, 09 Dec 2021 01:17:14: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:17:14: #2 You may need to consider one of the other alternative d(s): 54,208,543,568 WARNING @ Thu, 09 Dec 2021 01:17:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 01:17:14: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:17:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:17:15: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:17:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.10_peaks.xls INFO @ Thu, 09 Dec 2021 01:17:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:17:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.10_summits.bed INFO @ Thu, 09 Dec 2021 01:17:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (245 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 @ Thu, 09 Dec 2021 01:17:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.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 @ Thu, 09 Dec 2021 01:17:39: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:17:39: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 01:17:43: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:17:43: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:17:43: #1 total tags in treatment: 742043 INFO @ Thu, 09 Dec 2021 01:17:43: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:17:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:17:43: #1 tags after filtering in treatment: 742043 INFO @ Thu, 09 Dec 2021 01:17:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 01:17:43: #1 finished! INFO @ Thu, 09 Dec 2021 01:17:43: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:17:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:17:43: #2 number of paired peaks: 1102 INFO @ Thu, 09 Dec 2021 01:17:43: start model_add_line... INFO @ Thu, 09 Dec 2021 01:17:43: start X-correlation... INFO @ Thu, 09 Dec 2021 01:17:43: end of X-cor INFO @ Thu, 09 Dec 2021 01:17:43: #2 finished! INFO @ Thu, 09 Dec 2021 01:17:43: #2 predicted fragment length is 54 bps INFO @ Thu, 09 Dec 2021 01:17:43: #2 alternative fragment length(s) may be 54,208,543,568 bps INFO @ Thu, 09 Dec 2021 01:17:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.20_model.r WARNING @ Thu, 09 Dec 2021 01:17:43: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:17:43: #2 You may need to consider one of the other alternative d(s): 54,208,543,568 WARNING @ Thu, 09 Dec 2021 01:17:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 01:17:43: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:17:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:17:45: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:17:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.20_peaks.xls INFO @ Thu, 09 Dec 2021 01:17:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:17:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180798/SRX3180798.20_summits.bed INFO @ Thu, 09 Dec 2021 01:17:46: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (70 records, 4 fields): 1 millis CompletedMACS2peakCalling