Job ID = 14158339 SRX = SRX7739513 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: 00:03:08 14804578 reads; of these: 14804578 (100.00%) were unpaired; of these: 1482034 (10.01%) aligned 0 times 11106068 (75.02%) aligned exactly 1 time 2216476 (14.97%) aligned >1 times 89.99% overall alignment rate Time searching: 00:03:08 Overall time: 00:03:08 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 8 files... [bam_rmdupse_core] 3844078 / 13322544 = 0.2885 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 16:22:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.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 16:22:31: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:22:31: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:22:36: 1000000 INFO @ Wed, 08 Dec 2021 16:22:41: 2000000 INFO @ Wed, 08 Dec 2021 16:22:45: 3000000 INFO @ Wed, 08 Dec 2021 16:22:50: 4000000 INFO @ Wed, 08 Dec 2021 16:22:54: 5000000 INFO @ Wed, 08 Dec 2021 16:22:59: 6000000 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 16:23:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.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 16:23:01: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:23:01: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:23:03: 7000000 INFO @ Wed, 08 Dec 2021 16:23:07: 1000000 INFO @ Wed, 08 Dec 2021 16:23:08: 8000000 INFO @ Wed, 08 Dec 2021 16:23:12: 2000000 INFO @ Wed, 08 Dec 2021 16:23:12: 9000000 INFO @ Wed, 08 Dec 2021 16:23:15: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 16:23:15: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 16:23:15: #1 total tags in treatment: 9478466 INFO @ Wed, 08 Dec 2021 16:23:15: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:23:15: #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 16:23:15: #1 tags after filtering in treatment: 9478466 INFO @ Wed, 08 Dec 2021 16:23:15: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 16:23:15: #1 finished! INFO @ Wed, 08 Dec 2021 16:23:15: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:23:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:23:15: #2 number of paired peaks: 404 WARNING @ Wed, 08 Dec 2021 16:23:15: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Wed, 08 Dec 2021 16:23:15: start model_add_line... INFO @ Wed, 08 Dec 2021 16:23:15: start X-correlation... INFO @ Wed, 08 Dec 2021 16:23:15: end of X-cor INFO @ Wed, 08 Dec 2021 16:23:15: #2 finished! INFO @ Wed, 08 Dec 2021 16:23:15: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 16:23:15: #2 alternative fragment length(s) may be 3,47 bps INFO @ Wed, 08 Dec 2021 16:23:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.05_model.r WARNING @ Wed, 08 Dec 2021 16:23:16: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 16:23:16: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Wed, 08 Dec 2021 16:23:16: #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 16:23:16: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:23:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:23:17: 3000000 INFO @ Wed, 08 Dec 2021 16:23:22: 4000000 INFO @ Wed, 08 Dec 2021 16:23:27: 5000000 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 16:23:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.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 16:23:31: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:23:31: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:23:32: 6000000 INFO @ Wed, 08 Dec 2021 16:23:33: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:23:36: 1000000 INFO @ Wed, 08 Dec 2021 16:23:37: 7000000 INFO @ Wed, 08 Dec 2021 16:23:41: 2000000 INFO @ Wed, 08 Dec 2021 16:23:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.05_peaks.xls INFO @ Wed, 08 Dec 2021 16:23:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:23:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.05_summits.bed INFO @ Wed, 08 Dec 2021 16:23:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (696 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:23:43: 8000000 INFO @ Wed, 08 Dec 2021 16:23:45: 3000000 INFO @ Wed, 08 Dec 2021 16:23:48: 9000000 INFO @ Wed, 08 Dec 2021 16:23:50: 4000000 INFO @ Wed, 08 Dec 2021 16:23:50: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 16:23:50: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 16:23:50: #1 total tags in treatment: 9478466 INFO @ Wed, 08 Dec 2021 16:23:50: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:23:50: #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 16:23:50: #1 tags after filtering in treatment: 9478466 INFO @ Wed, 08 Dec 2021 16:23:50: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 16:23:50: #1 finished! INFO @ Wed, 08 Dec 2021 16:23:50: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:23:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:23:51: #2 number of paired peaks: 404 WARNING @ Wed, 08 Dec 2021 16:23:51: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Wed, 08 Dec 2021 16:23:51: start model_add_line... INFO @ Wed, 08 Dec 2021 16:23:51: start X-correlation... INFO @ Wed, 08 Dec 2021 16:23:51: end of X-cor INFO @ Wed, 08 Dec 2021 16:23:51: #2 finished! INFO @ Wed, 08 Dec 2021 16:23:51: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 16:23:51: #2 alternative fragment length(s) may be 3,47 bps INFO @ Wed, 08 Dec 2021 16:23:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.10_model.r WARNING @ Wed, 08 Dec 2021 16:23:51: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 16:23:51: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Wed, 08 Dec 2021 16:23:51: #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 16:23:51: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:23:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:23:55: 5000000 INFO @ Wed, 08 Dec 2021 16:23:59: 6000000 INFO @ Wed, 08 Dec 2021 16:24:04: 7000000 INFO @ Wed, 08 Dec 2021 16:24:08: 8000000 INFO @ Wed, 08 Dec 2021 16:24:10: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 16:24:13: 9000000 INFO @ Wed, 08 Dec 2021 16:24:15: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 16:24:15: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 16:24:15: #1 total tags in treatment: 9478466 INFO @ Wed, 08 Dec 2021 16:24:15: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:24:15: #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 16:24:15: #1 tags after filtering in treatment: 9478466 INFO @ Wed, 08 Dec 2021 16:24:15: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 16:24:15: #1 finished! INFO @ Wed, 08 Dec 2021 16:24:15: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:24:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:24:16: #2 number of paired peaks: 404 WARNING @ Wed, 08 Dec 2021 16:24:16: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Wed, 08 Dec 2021 16:24:16: start model_add_line... INFO @ Wed, 08 Dec 2021 16:24:16: start X-correlation... INFO @ Wed, 08 Dec 2021 16:24:16: end of X-cor INFO @ Wed, 08 Dec 2021 16:24:16: #2 finished! INFO @ Wed, 08 Dec 2021 16:24:16: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 16:24:16: #2 alternative fragment length(s) may be 3,47 bps INFO @ Wed, 08 Dec 2021 16:24:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.20_model.r WARNING @ Wed, 08 Dec 2021 16:24:16: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 16:24:16: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Wed, 08 Dec 2021 16:24:16: #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 16:24:16: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:24:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:24:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.10_peaks.xls INFO @ Wed, 08 Dec 2021 16:24:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:24:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.10_summits.bed INFO @ Wed, 08 Dec 2021 16:24:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (484 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:24:34: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 16:24:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.20_peaks.xls INFO @ Wed, 08 Dec 2021 16:24:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:24:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7739513/SRX7739513.20_summits.bed INFO @ Wed, 08 Dec 2021 16:24:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (206 records, 4 fields): 1 millis CompletedMACS2peakCalling