Job ID = 14160687 SRX = SRX8331163 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: 00:16:10 36853792 reads; of these: 36853792 (100.00%) were unpaired; of these: 181481 (0.49%) aligned 0 times 31276072 (84.87%) aligned exactly 1 time 5396239 (14.64%) aligned >1 times 99.51% overall alignment rate Time searching: 00:16:10 Overall time: 00:16:10 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_sort_core] merging from 16 files... [bam_rmdupse_core] 31916105 / 36672311 = 0.8703 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 04:08:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.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 04:08:45: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:08:45: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:08:55: 1000000 INFO @ Thu, 09 Dec 2021 04:09:04: 2000000 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 04:09:14: 3000000 INFO @ Thu, 09 Dec 2021 04:09:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.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 04:09:15: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:09:15: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:09:23: 1000000 INFO @ Thu, 09 Dec 2021 04:09:23: 4000000 INFO @ Thu, 09 Dec 2021 04:09:30: 2000000 INFO @ Thu, 09 Dec 2021 04:09:31: #1 tag size is determined as 59 bps INFO @ Thu, 09 Dec 2021 04:09:31: #1 tag size = 59 INFO @ Thu, 09 Dec 2021 04:09:31: #1 total tags in treatment: 4756206 INFO @ Thu, 09 Dec 2021 04:09:31: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:09:31: #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 04:09:31: #1 tags after filtering in treatment: 4756206 INFO @ Thu, 09 Dec 2021 04:09:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:09:31: #1 finished! INFO @ Thu, 09 Dec 2021 04:09:31: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:09:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:09:31: #2 number of paired peaks: 861 WARNING @ Thu, 09 Dec 2021 04:09:31: Fewer paired peaks (861) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 861 pairs to build model! INFO @ Thu, 09 Dec 2021 04:09:31: start model_add_line... INFO @ Thu, 09 Dec 2021 04:09:31: start X-correlation... INFO @ Thu, 09 Dec 2021 04:09:31: end of X-cor INFO @ Thu, 09 Dec 2021 04:09:31: #2 finished! INFO @ Thu, 09 Dec 2021 04:09:31: #2 predicted fragment length is 74 bps INFO @ Thu, 09 Dec 2021 04:09:31: #2 alternative fragment length(s) may be 4,74 bps INFO @ Thu, 09 Dec 2021 04:09:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.05_model.r WARNING @ Thu, 09 Dec 2021 04:09:31: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:09:31: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Thu, 09 Dec 2021 04:09:31: #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 04:09:31: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:09:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:09:38: 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 @ Thu, 09 Dec 2021 04:09:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.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 04:09:45: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:09:45: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:09:45: 4000000 INFO @ Thu, 09 Dec 2021 04:09:46: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:09:51: #1 tag size is determined as 59 bps INFO @ Thu, 09 Dec 2021 04:09:51: #1 tag size = 59 INFO @ Thu, 09 Dec 2021 04:09:51: #1 total tags in treatment: 4756206 INFO @ Thu, 09 Dec 2021 04:09:51: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:09:51: #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 04:09:51: #1 tags after filtering in treatment: 4756206 INFO @ Thu, 09 Dec 2021 04:09:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:09:51: #1 finished! INFO @ Thu, 09 Dec 2021 04:09:51: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:09:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:09:51: #2 number of paired peaks: 861 WARNING @ Thu, 09 Dec 2021 04:09:51: Fewer paired peaks (861) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 861 pairs to build model! INFO @ Thu, 09 Dec 2021 04:09:51: start model_add_line... INFO @ Thu, 09 Dec 2021 04:09:51: start X-correlation... INFO @ Thu, 09 Dec 2021 04:09:51: end of X-cor INFO @ Thu, 09 Dec 2021 04:09:51: #2 finished! INFO @ Thu, 09 Dec 2021 04:09:51: #2 predicted fragment length is 74 bps INFO @ Thu, 09 Dec 2021 04:09:51: #2 alternative fragment length(s) may be 4,74 bps INFO @ Thu, 09 Dec 2021 04:09:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.10_model.r WARNING @ Thu, 09 Dec 2021 04:09:51: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:09:51: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Thu, 09 Dec 2021 04:09:51: #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 04:09:51: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:09:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:09:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:09:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:09:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.05_summits.bed INFO @ Thu, 09 Dec 2021 04:09:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1564 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:09:55: 1000000 INFO @ Thu, 09 Dec 2021 04:10:04: 2000000 INFO @ Thu, 09 Dec 2021 04:10:06: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:10:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:10:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:10:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.10_summits.bed INFO @ Thu, 09 Dec 2021 04:10:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (802 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:10:14: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:10:23: 4000000 INFO @ Thu, 09 Dec 2021 04:10:30: #1 tag size is determined as 59 bps INFO @ Thu, 09 Dec 2021 04:10:30: #1 tag size = 59 INFO @ Thu, 09 Dec 2021 04:10:30: #1 total tags in treatment: 4756206 INFO @ Thu, 09 Dec 2021 04:10:30: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:10:30: #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 04:10:30: #1 tags after filtering in treatment: 4756206 INFO @ Thu, 09 Dec 2021 04:10:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:10:30: #1 finished! INFO @ Thu, 09 Dec 2021 04:10:30: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:10:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:10:31: #2 number of paired peaks: 861 WARNING @ Thu, 09 Dec 2021 04:10:31: Fewer paired peaks (861) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 861 pairs to build model! INFO @ Thu, 09 Dec 2021 04:10:31: start model_add_line... INFO @ Thu, 09 Dec 2021 04:10:31: start X-correlation... INFO @ Thu, 09 Dec 2021 04:10:31: end of X-cor INFO @ Thu, 09 Dec 2021 04:10:31: #2 finished! INFO @ Thu, 09 Dec 2021 04:10:31: #2 predicted fragment length is 74 bps INFO @ Thu, 09 Dec 2021 04:10:31: #2 alternative fragment length(s) may be 4,74 bps INFO @ Thu, 09 Dec 2021 04:10:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.20_model.r WARNING @ Thu, 09 Dec 2021 04:10:31: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:10:31: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Thu, 09 Dec 2021 04:10:31: #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 04:10:31: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:10:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:10:46: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:10:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:10:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:10:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331163/SRX8331163.20_summits.bed INFO @ Thu, 09 Dec 2021 04:10:53: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (387 records, 4 fields): 2 millis CompletedMACS2peakCalling