Job ID = 14159502 SRX = SRX3180817 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: 00:01:18 6362102 reads; of these: 6362102 (100.00%) were unpaired; of these: 711701 (11.19%) aligned 0 times 4713248 (74.08%) aligned exactly 1 time 937153 (14.73%) aligned >1 times 88.81% overall alignment rate Time searching: 00:01:18 Overall time: 00:01:18 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] 934144 / 5650401 = 0.1653 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 22:14:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.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 22:14:27: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:14:27: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:14:33: 1000000 INFO @ Wed, 08 Dec 2021 22:14:40: 2000000 INFO @ Wed, 08 Dec 2021 22:14:46: 3000000 INFO @ Wed, 08 Dec 2021 22:14:53: 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 @ Wed, 08 Dec 2021 22:14:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.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 22:14:57: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:14:57: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:14:57: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:14:57: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:14:57: #1 total tags in treatment: 4716257 INFO @ Wed, 08 Dec 2021 22:14:57: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:14:57: #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 22:14:57: #1 tags after filtering in treatment: 4716257 INFO @ Wed, 08 Dec 2021 22:14:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:14:57: #1 finished! INFO @ Wed, 08 Dec 2021 22:14:57: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:14:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:14:58: #2 number of paired peaks: 424 WARNING @ Wed, 08 Dec 2021 22:14:58: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Wed, 08 Dec 2021 22:14:58: start model_add_line... INFO @ Wed, 08 Dec 2021 22:14:58: start X-correlation... INFO @ Wed, 08 Dec 2021 22:14:58: end of X-cor INFO @ Wed, 08 Dec 2021 22:14:58: #2 finished! INFO @ Wed, 08 Dec 2021 22:14:58: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 22:14:58: #2 alternative fragment length(s) may be 50,514 bps INFO @ Wed, 08 Dec 2021 22:14:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.05_model.r WARNING @ Wed, 08 Dec 2021 22:14:58: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:14:58: #2 You may need to consider one of the other alternative d(s): 50,514 WARNING @ Wed, 08 Dec 2021 22:14:58: #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 22:14:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:14:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:15:04: 1000000 INFO @ Wed, 08 Dec 2021 22:15:07: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:15:10: 2000000 INFO @ Wed, 08 Dec 2021 22:15:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:15:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:15:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.05_summits.bed INFO @ Wed, 08 Dec 2021 22:15:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (508 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:15:16: 3000000 INFO @ Wed, 08 Dec 2021 22:15:22: 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 @ Wed, 08 Dec 2021 22:15:27: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:15:27: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:15:27: #1 total tags in treatment: 4716257 INFO @ Wed, 08 Dec 2021 22:15:27: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:15:27: #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 22:15:27: #1 tags after filtering in treatment: 4716257 INFO @ Wed, 08 Dec 2021 22:15:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:15:27: #1 finished! INFO @ Wed, 08 Dec 2021 22:15:27: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:15:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:15:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.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 22:15:27: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:15:27: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:15:27: #2 number of paired peaks: 424 WARNING @ Wed, 08 Dec 2021 22:15:27: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Wed, 08 Dec 2021 22:15:27: start model_add_line... INFO @ Wed, 08 Dec 2021 22:15:27: start X-correlation... INFO @ Wed, 08 Dec 2021 22:15:27: end of X-cor INFO @ Wed, 08 Dec 2021 22:15:27: #2 finished! INFO @ Wed, 08 Dec 2021 22:15:27: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 22:15:27: #2 alternative fragment length(s) may be 50,514 bps INFO @ Wed, 08 Dec 2021 22:15:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.10_model.r WARNING @ Wed, 08 Dec 2021 22:15:27: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:15:27: #2 You may need to consider one of the other alternative d(s): 50,514 WARNING @ Wed, 08 Dec 2021 22:15:27: #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 22:15:27: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:15:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:15:33: 1000000 INFO @ Wed, 08 Dec 2021 22:15:37: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:15:38: 2000000 INFO @ Wed, 08 Dec 2021 22:15:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:15:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:15:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.10_summits.bed INFO @ Wed, 08 Dec 2021 22:15:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (316 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:15:44: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:15:49: 4000000 INFO @ Wed, 08 Dec 2021 22:15:53: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:15:53: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:15:53: #1 total tags in treatment: 4716257 INFO @ Wed, 08 Dec 2021 22:15:53: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:15:53: #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 22:15:53: #1 tags after filtering in treatment: 4716257 INFO @ Wed, 08 Dec 2021 22:15:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:15:53: #1 finished! INFO @ Wed, 08 Dec 2021 22:15:53: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:15:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:15:53: #2 number of paired peaks: 424 WARNING @ Wed, 08 Dec 2021 22:15:53: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Wed, 08 Dec 2021 22:15:53: start model_add_line... INFO @ Wed, 08 Dec 2021 22:15:53: start X-correlation... INFO @ Wed, 08 Dec 2021 22:15:53: end of X-cor INFO @ Wed, 08 Dec 2021 22:15:53: #2 finished! INFO @ Wed, 08 Dec 2021 22:15:53: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 22:15:53: #2 alternative fragment length(s) may be 50,514 bps INFO @ Wed, 08 Dec 2021 22:15:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.20_model.r WARNING @ Wed, 08 Dec 2021 22:15:53: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:15:53: #2 You may need to consider one of the other alternative d(s): 50,514 WARNING @ Wed, 08 Dec 2021 22:15:53: #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 22:15:53: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:15:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:16:03: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:16:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:16:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:16:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180817/SRX3180817.20_summits.bed INFO @ Wed, 08 Dec 2021 22:16:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (130 records, 4 fields): 3 millis CompletedMACS2peakCalling