Job ID = 14158075 SRX = SRX10040010 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: 00:04:27 17754014 reads; of these: 17754014 (100.00%) were unpaired; of these: 404886 (2.28%) aligned 0 times 14872529 (83.77%) aligned exactly 1 time 2476599 (13.95%) aligned >1 times 97.72% overall alignment rate Time searching: 00:04:27 Overall time: 00:04:27 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] 2365141 / 17349128 = 0.1363 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 14:19:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.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 14:19:39: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:19:39: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:19:44: 1000000 INFO @ Wed, 08 Dec 2021 14:19:48: 2000000 INFO @ Wed, 08 Dec 2021 14:19:53: 3000000 INFO @ Wed, 08 Dec 2021 14:19:58: 4000000 INFO @ Wed, 08 Dec 2021 14:20:03: 5000000 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 14:20:08: 6000000 INFO @ Wed, 08 Dec 2021 14:20:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.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 14:20:09: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:20:09: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:20:13: 7000000 INFO @ Wed, 08 Dec 2021 14:20:14: 1000000 INFO @ Wed, 08 Dec 2021 14:20:17: 8000000 INFO @ Wed, 08 Dec 2021 14:20:19: 2000000 INFO @ Wed, 08 Dec 2021 14:20:22: 9000000 INFO @ Wed, 08 Dec 2021 14:20:24: 3000000 INFO @ Wed, 08 Dec 2021 14:20:27: 10000000 INFO @ Wed, 08 Dec 2021 14:20:28: 4000000 INFO @ Wed, 08 Dec 2021 14:20:32: 11000000 INFO @ Wed, 08 Dec 2021 14:20:33: 5000000 INFO @ Wed, 08 Dec 2021 14:20:37: 12000000 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 14:20:38: 6000000 INFO @ Wed, 08 Dec 2021 14:20:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.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 14:20:39: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:20:39: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:20:42: 13000000 INFO @ Wed, 08 Dec 2021 14:20:43: 7000000 INFO @ Wed, 08 Dec 2021 14:20:44: 1000000 INFO @ Wed, 08 Dec 2021 14:20:47: 14000000 INFO @ Wed, 08 Dec 2021 14:20:48: 8000000 INFO @ Wed, 08 Dec 2021 14:20:49: 2000000 INFO @ Wed, 08 Dec 2021 14:20:52: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 14:20:52: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 14:20:52: #1 total tags in treatment: 14983987 INFO @ Wed, 08 Dec 2021 14:20:52: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:20:52: #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 14:20:52: #1 tags after filtering in treatment: 14983987 INFO @ Wed, 08 Dec 2021 14:20:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:20:52: #1 finished! INFO @ Wed, 08 Dec 2021 14:20:52: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:20:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:20:53: #2 number of paired peaks: 111 WARNING @ Wed, 08 Dec 2021 14:20:53: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Wed, 08 Dec 2021 14:20:53: start model_add_line... INFO @ Wed, 08 Dec 2021 14:20:53: start X-correlation... INFO @ Wed, 08 Dec 2021 14:20:53: end of X-cor INFO @ Wed, 08 Dec 2021 14:20:53: #2 finished! INFO @ Wed, 08 Dec 2021 14:20:53: #2 predicted fragment length is 52 bps INFO @ Wed, 08 Dec 2021 14:20:53: #2 alternative fragment length(s) may be 1,52,189,434,474,491,540 bps INFO @ Wed, 08 Dec 2021 14:20:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.05_model.r WARNING @ Wed, 08 Dec 2021 14:20:53: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:20:53: #2 You may need to consider one of the other alternative d(s): 1,52,189,434,474,491,540 WARNING @ Wed, 08 Dec 2021 14:20:53: #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 14:20:53: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:20:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:20:53: 9000000 INFO @ Wed, 08 Dec 2021 14:20:53: 3000000 INFO @ Wed, 08 Dec 2021 14:20:58: 10000000 INFO @ Wed, 08 Dec 2021 14:20:58: 4000000 INFO @ Wed, 08 Dec 2021 14:21:03: 11000000 INFO @ Wed, 08 Dec 2021 14:21:03: 5000000 INFO @ Wed, 08 Dec 2021 14:21:08: 12000000 INFO @ Wed, 08 Dec 2021 14:21:08: 6000000 INFO @ Wed, 08 Dec 2021 14:21:13: 13000000 INFO @ Wed, 08 Dec 2021 14:21:13: 7000000 INFO @ Wed, 08 Dec 2021 14:21:17: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:21:18: 14000000 INFO @ Wed, 08 Dec 2021 14:21:18: 8000000 INFO @ Wed, 08 Dec 2021 14:21:23: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 14:21:23: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 14:21:23: #1 total tags in treatment: 14983987 INFO @ Wed, 08 Dec 2021 14:21:23: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:21:23: #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 14:21:23: 9000000 INFO @ Wed, 08 Dec 2021 14:21:23: #1 tags after filtering in treatment: 14983987 INFO @ Wed, 08 Dec 2021 14:21:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:21:23: #1 finished! INFO @ Wed, 08 Dec 2021 14:21:23: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:21:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:21:24: #2 number of paired peaks: 111 WARNING @ Wed, 08 Dec 2021 14:21:24: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Wed, 08 Dec 2021 14:21:24: start model_add_line... INFO @ Wed, 08 Dec 2021 14:21:24: start X-correlation... INFO @ Wed, 08 Dec 2021 14:21:24: end of X-cor INFO @ Wed, 08 Dec 2021 14:21:24: #2 finished! INFO @ Wed, 08 Dec 2021 14:21:24: #2 predicted fragment length is 52 bps INFO @ Wed, 08 Dec 2021 14:21:24: #2 alternative fragment length(s) may be 1,52,189,434,474,491,540 bps INFO @ Wed, 08 Dec 2021 14:21:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.10_model.r WARNING @ Wed, 08 Dec 2021 14:21:24: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:21:24: #2 You may need to consider one of the other alternative d(s): 1,52,189,434,474,491,540 WARNING @ Wed, 08 Dec 2021 14:21:24: #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 14:21:24: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:21:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:21:27: 10000000 INFO @ Wed, 08 Dec 2021 14:21:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:21:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:21:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.05_summits.bed INFO @ Wed, 08 Dec 2021 14:21:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (571 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:21:32: 11000000 INFO @ Wed, 08 Dec 2021 14:21:37: 12000000 INFO @ Wed, 08 Dec 2021 14:21:42: 13000000 INFO @ Wed, 08 Dec 2021 14:21:47: 14000000 INFO @ Wed, 08 Dec 2021 14:21:49: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:21:52: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 14:21:52: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 14:21:52: #1 total tags in treatment: 14983987 INFO @ Wed, 08 Dec 2021 14:21:52: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:21:52: #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 14:21:52: #1 tags after filtering in treatment: 14983987 INFO @ Wed, 08 Dec 2021 14:21:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:21:52: #1 finished! INFO @ Wed, 08 Dec 2021 14:21:52: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:21:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:21:53: #2 number of paired peaks: 111 WARNING @ Wed, 08 Dec 2021 14:21:53: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Wed, 08 Dec 2021 14:21:53: start model_add_line... INFO @ Wed, 08 Dec 2021 14:21:53: start X-correlation... INFO @ Wed, 08 Dec 2021 14:21:53: end of X-cor INFO @ Wed, 08 Dec 2021 14:21:53: #2 finished! INFO @ Wed, 08 Dec 2021 14:21:53: #2 predicted fragment length is 52 bps INFO @ Wed, 08 Dec 2021 14:21:53: #2 alternative fragment length(s) may be 1,52,189,434,474,491,540 bps INFO @ Wed, 08 Dec 2021 14:21:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.20_model.r WARNING @ Wed, 08 Dec 2021 14:21:53: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:21:53: #2 You may need to consider one of the other alternative d(s): 1,52,189,434,474,491,540 WARNING @ Wed, 08 Dec 2021 14:21:53: #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 14:21:53: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:21:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:22:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:22:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:22:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.10_summits.bed INFO @ Wed, 08 Dec 2021 14:22:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (300 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:22:18: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:22:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:22:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:22:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10040010/SRX10040010.20_summits.bed INFO @ Wed, 08 Dec 2021 14:22:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (95 records, 4 fields): 1 millis CompletedMACS2peakCalling