Job ID = 16435539 SRX = SRX13110340 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: 00:06:38 17216894 reads; of these: 17216894 (100.00%) were unpaired; of these: 2927490 (17.00%) aligned 0 times 12176676 (70.73%) aligned exactly 1 time 2112728 (12.27%) aligned >1 times 83.00% overall alignment rate Time searching: 00:06:38 Overall time: 00:06:38 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] 7715600 / 14289404 = 0.5400 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:58:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.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 @ Tue, 02 Aug 2022 10:58:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:58:41: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:58:48: 1000000 INFO @ Tue, 02 Aug 2022 10:58:56: 2000000 INFO @ Tue, 02 Aug 2022 10:59:04: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:59:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.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 @ Tue, 02 Aug 2022 10:59:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:59:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:59:11: 4000000 INFO @ Tue, 02 Aug 2022 10:59:16: 1000000 INFO @ Tue, 02 Aug 2022 10:59:19: 5000000 INFO @ Tue, 02 Aug 2022 10:59:23: 2000000 INFO @ Tue, 02 Aug 2022 10:59:27: 6000000 INFO @ Tue, 02 Aug 2022 10:59:31: 3000000 INFO @ Tue, 02 Aug 2022 10:59:31: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:59:31: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:59:31: #1 total tags in treatment: 6573804 INFO @ Tue, 02 Aug 2022 10:59:31: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:59:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:59:31: #1 tags after filtering in treatment: 6573804 INFO @ Tue, 02 Aug 2022 10:59:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:59:31: #1 finished! INFO @ Tue, 02 Aug 2022 10:59:31: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:59:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:59:32: #2 number of paired peaks: 439 WARNING @ Tue, 02 Aug 2022 10:59:32: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Tue, 02 Aug 2022 10:59:32: start model_add_line... INFO @ Tue, 02 Aug 2022 10:59:32: start X-correlation... INFO @ Tue, 02 Aug 2022 10:59:32: end of X-cor INFO @ Tue, 02 Aug 2022 10:59:32: #2 finished! INFO @ Tue, 02 Aug 2022 10:59:32: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:59:32: #2 alternative fragment length(s) may be 4,71 bps INFO @ Tue, 02 Aug 2022 10:59:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.05_model.r WARNING @ Tue, 02 Aug 2022 10:59:32: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:59:32: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Tue, 02 Aug 2022 10:59:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:59:32: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:59:32: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:59:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.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 @ Tue, 02 Aug 2022 10:59:38: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:59:38: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:59:40: 4000000 INFO @ Tue, 02 Aug 2022 10:59:46: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:59:47: 1000000 INFO @ Tue, 02 Aug 2022 10:59:48: 5000000 INFO @ Tue, 02 Aug 2022 10:59:54: 2000000 INFO @ Tue, 02 Aug 2022 10:59:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:59:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:59:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.05_summits.bed INFO @ Tue, 02 Aug 2022 10:59:55: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (606 records, 4 fields): 45 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:59:57: 6000000 INFO @ Tue, 02 Aug 2022 11:00:00: 3000000 INFO @ Tue, 02 Aug 2022 11:00:01: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:00:01: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:00:01: #1 total tags in treatment: 6573804 INFO @ Tue, 02 Aug 2022 11:00:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:00:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:00:01: #1 tags after filtering in treatment: 6573804 INFO @ Tue, 02 Aug 2022 11:00:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:00:01: #1 finished! INFO @ Tue, 02 Aug 2022 11:00:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:00:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:00:02: #2 number of paired peaks: 439 WARNING @ Tue, 02 Aug 2022 11:00:02: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Tue, 02 Aug 2022 11:00:02: start model_add_line... INFO @ Tue, 02 Aug 2022 11:00:02: start X-correlation... INFO @ Tue, 02 Aug 2022 11:00:02: end of X-cor INFO @ Tue, 02 Aug 2022 11:00:02: #2 finished! INFO @ Tue, 02 Aug 2022 11:00:02: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 11:00:02: #2 alternative fragment length(s) may be 4,71 bps INFO @ Tue, 02 Aug 2022 11:00:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.10_model.r WARNING @ Tue, 02 Aug 2022 11:00:02: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:00:02: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Tue, 02 Aug 2022 11:00:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:00:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:00:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:00:08: 4000000 INFO @ Tue, 02 Aug 2022 11:00:16: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:00:16: 5000000 INFO @ Tue, 02 Aug 2022 11:00:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:00:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:00:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.10_summits.bed INFO @ Tue, 02 Aug 2022 11:00:23: 6000000 INFO @ Tue, 02 Aug 2022 11:00:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (422 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:00:27: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:00:27: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:00:27: #1 total tags in treatment: 6573804 INFO @ Tue, 02 Aug 2022 11:00:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:00:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:00:27: #1 tags after filtering in treatment: 6573804 INFO @ Tue, 02 Aug 2022 11:00:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:00:27: #1 finished! INFO @ Tue, 02 Aug 2022 11:00:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:00:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:00:27: #2 number of paired peaks: 439 WARNING @ Tue, 02 Aug 2022 11:00:27: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Tue, 02 Aug 2022 11:00:27: start model_add_line... INFO @ Tue, 02 Aug 2022 11:00:27: start X-correlation... INFO @ Tue, 02 Aug 2022 11:00:27: end of X-cor INFO @ Tue, 02 Aug 2022 11:00:27: #2 finished! INFO @ Tue, 02 Aug 2022 11:00:27: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 11:00:27: #2 alternative fragment length(s) may be 4,71 bps INFO @ Tue, 02 Aug 2022 11:00:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.20_model.r WARNING @ Tue, 02 Aug 2022 11:00:27: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:00:27: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Tue, 02 Aug 2022 11:00:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:00:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:00:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:00:41: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:00:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:00:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:00:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110340/SRX13110340.20_summits.bed INFO @ Tue, 02 Aug 2022 11:00:48: Done! pass1 - making usageList (6 chroms): 14 millis pass2 - checking and writing primary data (234 records, 4 fields): 41 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。