Job ID = 14160850 SRX = SRX10569207 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: 00:03:35 16009808 reads; of these: 16009808 (100.00%) were unpaired; of these: 9258526 (57.83%) aligned 0 times 5265439 (32.89%) aligned exactly 1 time 1485843 (9.28%) aligned >1 times 42.17% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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] 1369645 / 6751282 = 0.2029 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 04:40:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.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 04:40:43: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:40:43: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:40:49: 1000000 INFO @ Thu, 09 Dec 2021 04:40:55: 2000000 INFO @ Thu, 09 Dec 2021 04:41:01: 3000000 INFO @ Thu, 09 Dec 2021 04:41:06: 4000000 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 04:41:12: 5000000 INFO @ Thu, 09 Dec 2021 04:41:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.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 04:41:14: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:41:14: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:41:14: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:41:14: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:41:14: #1 total tags in treatment: 5381637 INFO @ Thu, 09 Dec 2021 04:41:14: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:41:14: #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 04:41:14: #1 tags after filtering in treatment: 5381637 INFO @ Thu, 09 Dec 2021 04:41:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:41:14: #1 finished! INFO @ Thu, 09 Dec 2021 04:41:14: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:41:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:41:15: #2 number of paired peaks: 600 WARNING @ Thu, 09 Dec 2021 04:41:15: Fewer paired peaks (600) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 600 pairs to build model! INFO @ Thu, 09 Dec 2021 04:41:15: start model_add_line... INFO @ Thu, 09 Dec 2021 04:41:15: start X-correlation... INFO @ Thu, 09 Dec 2021 04:41:15: end of X-cor INFO @ Thu, 09 Dec 2021 04:41:15: #2 finished! INFO @ Thu, 09 Dec 2021 04:41:15: #2 predicted fragment length is 62 bps INFO @ Thu, 09 Dec 2021 04:41:15: #2 alternative fragment length(s) may be 4,62 bps INFO @ Thu, 09 Dec 2021 04:41:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.05_model.r WARNING @ Thu, 09 Dec 2021 04:41:15: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:41:15: #2 You may need to consider one of the other alternative d(s): 4,62 WARNING @ Thu, 09 Dec 2021 04:41:15: #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 04:41:15: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:41:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:41:20: 1000000 INFO @ Thu, 09 Dec 2021 04:41:25: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:41:26: 2000000 INFO @ Thu, 09 Dec 2021 04:41:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:41:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:41:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.05_summits.bed INFO @ Thu, 09 Dec 2021 04:41:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (599 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:41:31: 3000000 INFO @ Thu, 09 Dec 2021 04:41:37: 4000000 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 04:41:43: 5000000 INFO @ Thu, 09 Dec 2021 04:41:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.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 04:41:44: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:41:44: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:41:46: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:41:46: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:41:46: #1 total tags in treatment: 5381637 INFO @ Thu, 09 Dec 2021 04:41:46: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:41:46: #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 04:41:46: #1 tags after filtering in treatment: 5381637 INFO @ Thu, 09 Dec 2021 04:41:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:41:46: #1 finished! INFO @ Thu, 09 Dec 2021 04:41:46: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:41:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:41:46: #2 number of paired peaks: 600 WARNING @ Thu, 09 Dec 2021 04:41:46: Fewer paired peaks (600) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 600 pairs to build model! INFO @ Thu, 09 Dec 2021 04:41:46: start model_add_line... INFO @ Thu, 09 Dec 2021 04:41:46: start X-correlation... INFO @ Thu, 09 Dec 2021 04:41:46: end of X-cor INFO @ Thu, 09 Dec 2021 04:41:46: #2 finished! INFO @ Thu, 09 Dec 2021 04:41:46: #2 predicted fragment length is 62 bps INFO @ Thu, 09 Dec 2021 04:41:46: #2 alternative fragment length(s) may be 4,62 bps INFO @ Thu, 09 Dec 2021 04:41:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.10_model.r WARNING @ Thu, 09 Dec 2021 04:41:46: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:41:46: #2 You may need to consider one of the other alternative d(s): 4,62 WARNING @ Thu, 09 Dec 2021 04:41:46: #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 04:41:46: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:41:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:41:50: 1000000 INFO @ Thu, 09 Dec 2021 04:41:56: 2000000 INFO @ Thu, 09 Dec 2021 04:41:57: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:42:01: 3000000 INFO @ Thu, 09 Dec 2021 04:42:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:42:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:42:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.10_summits.bed INFO @ Thu, 09 Dec 2021 04:42:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (454 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:42:07: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:42:13: 5000000 INFO @ Thu, 09 Dec 2021 04:42:15: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:42:15: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:42:15: #1 total tags in treatment: 5381637 INFO @ Thu, 09 Dec 2021 04:42:15: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:42:15: #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 04:42:15: #1 tags after filtering in treatment: 5381637 INFO @ Thu, 09 Dec 2021 04:42:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:42:15: #1 finished! INFO @ Thu, 09 Dec 2021 04:42:15: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:42:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:42:16: #2 number of paired peaks: 600 WARNING @ Thu, 09 Dec 2021 04:42:16: Fewer paired peaks (600) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 600 pairs to build model! INFO @ Thu, 09 Dec 2021 04:42:16: start model_add_line... INFO @ Thu, 09 Dec 2021 04:42:16: start X-correlation... INFO @ Thu, 09 Dec 2021 04:42:16: end of X-cor INFO @ Thu, 09 Dec 2021 04:42:16: #2 finished! INFO @ Thu, 09 Dec 2021 04:42:16: #2 predicted fragment length is 62 bps INFO @ Thu, 09 Dec 2021 04:42:16: #2 alternative fragment length(s) may be 4,62 bps INFO @ Thu, 09 Dec 2021 04:42:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.20_model.r WARNING @ Thu, 09 Dec 2021 04:42:16: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:42:16: #2 You may need to consider one of the other alternative d(s): 4,62 WARNING @ Thu, 09 Dec 2021 04:42:16: #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 04:42:16: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:42:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:42:26: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:42:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:42:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:42:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10569207/SRX10569207.20_summits.bed INFO @ Thu, 09 Dec 2021 04:42:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (223 records, 4 fields): 1 millis CompletedMACS2peakCalling