Job ID = 12265053 SRX = SRX7246255 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: 00:04:22 17805098 reads; of these: 17805098 (100.00%) were unpaired; of these: 787720 (4.42%) aligned 0 times 13365567 (75.07%) aligned exactly 1 time 3651811 (20.51%) aligned >1 times 95.58% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 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] 9078443 / 17017378 = 0.5335 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:14:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.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 @ Sat, 03 Apr 2021 06:14:28: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:14:28: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:14:39: 1000000 INFO @ Sat, 03 Apr 2021 06:14:49: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:14:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.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 @ Sat, 03 Apr 2021 06:14:58: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:14:58: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:14:58: 3000000 INFO @ Sat, 03 Apr 2021 06:15:07: 1000000 INFO @ Sat, 03 Apr 2021 06:15:07: 4000000 INFO @ Sat, 03 Apr 2021 06:15:15: 2000000 INFO @ Sat, 03 Apr 2021 06:15:17: 5000000 INFO @ Sat, 03 Apr 2021 06:15:24: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:15:27: 6000000 INFO @ Sat, 03 Apr 2021 06:15:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.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 @ Sat, 03 Apr 2021 06:15:28: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:15:28: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:15:33: 4000000 INFO @ Sat, 03 Apr 2021 06:15:38: 7000000 INFO @ Sat, 03 Apr 2021 06:15:38: 1000000 INFO @ Sat, 03 Apr 2021 06:15:41: 5000000 INFO @ Sat, 03 Apr 2021 06:15:48: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:15:48: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:15:48: #1 total tags in treatment: 7938935 INFO @ Sat, 03 Apr 2021 06:15:48: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:15:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:15:48: #1 tags after filtering in treatment: 7938935 INFO @ Sat, 03 Apr 2021 06:15:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:15:48: #1 finished! INFO @ Sat, 03 Apr 2021 06:15:48: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:15:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:15:48: 2000000 INFO @ Sat, 03 Apr 2021 06:15:49: #2 number of paired peaks: 418 WARNING @ Sat, 03 Apr 2021 06:15:49: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Sat, 03 Apr 2021 06:15:49: start model_add_line... INFO @ Sat, 03 Apr 2021 06:15:49: start X-correlation... INFO @ Sat, 03 Apr 2021 06:15:49: end of X-cor INFO @ Sat, 03 Apr 2021 06:15:49: #2 finished! INFO @ Sat, 03 Apr 2021 06:15:49: #2 predicted fragment length is 83 bps INFO @ Sat, 03 Apr 2021 06:15:49: #2 alternative fragment length(s) may be 83,564 bps INFO @ Sat, 03 Apr 2021 06:15:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.05_model.r WARNING @ Sat, 03 Apr 2021 06:15:49: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:15:49: #2 You may need to consider one of the other alternative d(s): 83,564 WARNING @ Sat, 03 Apr 2021 06:15:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:15:49: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:15:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:15:50: 6000000 INFO @ Sat, 03 Apr 2021 06:15:58: 3000000 INFO @ Sat, 03 Apr 2021 06:15:59: 7000000 INFO @ Sat, 03 Apr 2021 06:16:07: 4000000 INFO @ Sat, 03 Apr 2021 06:16:08: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:16:08: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:16:08: #1 total tags in treatment: 7938935 INFO @ Sat, 03 Apr 2021 06:16:08: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:16:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:16:08: #1 tags after filtering in treatment: 7938935 INFO @ Sat, 03 Apr 2021 06:16:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:16:08: #1 finished! INFO @ Sat, 03 Apr 2021 06:16:08: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:16:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:16:09: #2 number of paired peaks: 418 WARNING @ Sat, 03 Apr 2021 06:16:09: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Sat, 03 Apr 2021 06:16:09: start model_add_line... INFO @ Sat, 03 Apr 2021 06:16:09: start X-correlation... INFO @ Sat, 03 Apr 2021 06:16:09: end of X-cor INFO @ Sat, 03 Apr 2021 06:16:09: #2 finished! INFO @ Sat, 03 Apr 2021 06:16:09: #2 predicted fragment length is 83 bps INFO @ Sat, 03 Apr 2021 06:16:09: #2 alternative fragment length(s) may be 83,564 bps INFO @ Sat, 03 Apr 2021 06:16:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.10_model.r WARNING @ Sat, 03 Apr 2021 06:16:09: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:16:09: #2 You may need to consider one of the other alternative d(s): 83,564 WARNING @ Sat, 03 Apr 2021 06:16:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:16:09: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:16:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:16:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:16:16: 5000000 INFO @ Sat, 03 Apr 2021 06:16:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:16:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:16:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.05_summits.bed INFO @ Sat, 03 Apr 2021 06:16:23: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3512 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:16:26: 6000000 INFO @ Sat, 03 Apr 2021 06:16:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:16:37: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:16:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:16:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:16:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.10_summits.bed INFO @ Sat, 03 Apr 2021 06:16:43: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1846 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:16:46: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:16:46: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:16:46: #1 total tags in treatment: 7938935 INFO @ Sat, 03 Apr 2021 06:16:46: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:16:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:16:47: #1 tags after filtering in treatment: 7938935 INFO @ Sat, 03 Apr 2021 06:16:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:16:47: #1 finished! INFO @ Sat, 03 Apr 2021 06:16:47: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:16:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:16:47: #2 number of paired peaks: 418 WARNING @ Sat, 03 Apr 2021 06:16:47: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Sat, 03 Apr 2021 06:16:47: start model_add_line... INFO @ Sat, 03 Apr 2021 06:16:47: start X-correlation... INFO @ Sat, 03 Apr 2021 06:16:47: end of X-cor INFO @ Sat, 03 Apr 2021 06:16:47: #2 finished! INFO @ Sat, 03 Apr 2021 06:16:47: #2 predicted fragment length is 83 bps INFO @ Sat, 03 Apr 2021 06:16:47: #2 alternative fragment length(s) may be 83,564 bps INFO @ Sat, 03 Apr 2021 06:16:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.20_model.r WARNING @ Sat, 03 Apr 2021 06:16:47: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:16:47: #2 You may need to consider one of the other alternative d(s): 83,564 WARNING @ Sat, 03 Apr 2021 06:16:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:16:47: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:16:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:17:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:17:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:17:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:17:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246255/SRX7246255.20_summits.bed INFO @ Sat, 03 Apr 2021 06:17:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (601 records, 4 fields): 3 millis CompletedMACS2peakCalling