Job ID = 14159485 SRX = SRX3180814 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: 00:05:26 20542845 reads; of these: 20542845 (100.00%) were unpaired; of these: 783252 (3.81%) aligned 0 times 16187506 (78.80%) aligned exactly 1 time 3572087 (17.39%) aligned >1 times 96.19% overall alignment rate Time searching: 00:05:26 Overall time: 00:05:26 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 12 files... [bam_rmdupse_core] 4663524 / 19759593 = 0.2360 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 22:20:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.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 22:20:49: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:20:49: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:20:59: 1000000 INFO @ Wed, 08 Dec 2021 22:21:09: 2000000 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 22:21:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.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 22:21:18: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:21:18: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:21:19: 3000000 INFO @ Wed, 08 Dec 2021 22:21:28: 1000000 INFO @ Wed, 08 Dec 2021 22:21:30: 4000000 INFO @ Wed, 08 Dec 2021 22:21:36: 2000000 INFO @ Wed, 08 Dec 2021 22:21:41: 5000000 INFO @ Wed, 08 Dec 2021 22:21:44: 3000000 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 22:21:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.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 22:21:49: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:21:49: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:21:52: 6000000 INFO @ Wed, 08 Dec 2021 22:21:52: 4000000 INFO @ Wed, 08 Dec 2021 22:21:56: 1000000 INFO @ Wed, 08 Dec 2021 22:22:00: 5000000 INFO @ Wed, 08 Dec 2021 22:22:02: 7000000 INFO @ Wed, 08 Dec 2021 22:22:04: 2000000 INFO @ Wed, 08 Dec 2021 22:22:09: 6000000 INFO @ Wed, 08 Dec 2021 22:22:11: 3000000 INFO @ Wed, 08 Dec 2021 22:22:12: 8000000 INFO @ Wed, 08 Dec 2021 22:22:18: 7000000 INFO @ Wed, 08 Dec 2021 22:22:19: 4000000 INFO @ Wed, 08 Dec 2021 22:22:22: 9000000 INFO @ Wed, 08 Dec 2021 22:22:26: 5000000 INFO @ Wed, 08 Dec 2021 22:22:27: 8000000 INFO @ Wed, 08 Dec 2021 22:22:32: 10000000 INFO @ Wed, 08 Dec 2021 22:22:34: 6000000 INFO @ Wed, 08 Dec 2021 22:22:35: 9000000 INFO @ Wed, 08 Dec 2021 22:22:41: 7000000 INFO @ Wed, 08 Dec 2021 22:22:42: 11000000 INFO @ Wed, 08 Dec 2021 22:22:43: 10000000 INFO @ Wed, 08 Dec 2021 22:22:49: 8000000 INFO @ Wed, 08 Dec 2021 22:22:51: 11000000 INFO @ Wed, 08 Dec 2021 22:22:53: 12000000 INFO @ Wed, 08 Dec 2021 22:22:56: 9000000 INFO @ Wed, 08 Dec 2021 22:22:59: 12000000 INFO @ Wed, 08 Dec 2021 22:23:03: 13000000 INFO @ Wed, 08 Dec 2021 22:23:04: 10000000 INFO @ Wed, 08 Dec 2021 22:23:07: 13000000 INFO @ Wed, 08 Dec 2021 22:23:11: 11000000 INFO @ Wed, 08 Dec 2021 22:23:13: 14000000 INFO @ Wed, 08 Dec 2021 22:23:15: 14000000 INFO @ Wed, 08 Dec 2021 22:23:20: 12000000 INFO @ Wed, 08 Dec 2021 22:23:23: 15000000 INFO @ Wed, 08 Dec 2021 22:23:23: 15000000 INFO @ Wed, 08 Dec 2021 22:23:24: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:23:24: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:23:24: #1 total tags in treatment: 15096069 INFO @ Wed, 08 Dec 2021 22:23:24: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:23:24: #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 22:23:24: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:23:24: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:23:24: #1 total tags in treatment: 15096069 INFO @ Wed, 08 Dec 2021 22:23:24: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:23:24: #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 22:23:24: #1 tags after filtering in treatment: 15096069 INFO @ Wed, 08 Dec 2021 22:23:24: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:23:24: #1 finished! INFO @ Wed, 08 Dec 2021 22:23:24: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:23:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:23:24: #1 tags after filtering in treatment: 15096069 INFO @ Wed, 08 Dec 2021 22:23:24: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:23:24: #1 finished! INFO @ Wed, 08 Dec 2021 22:23:24: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:23:24: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:23:26: #2 number of paired peaks: 373 WARNING @ Wed, 08 Dec 2021 22:23:26: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Wed, 08 Dec 2021 22:23:26: start model_add_line... INFO @ Wed, 08 Dec 2021 22:23:26: #2 number of paired peaks: 373 WARNING @ Wed, 08 Dec 2021 22:23:26: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Wed, 08 Dec 2021 22:23:26: start model_add_line... INFO @ Wed, 08 Dec 2021 22:23:26: start X-correlation... INFO @ Wed, 08 Dec 2021 22:23:26: end of X-cor INFO @ Wed, 08 Dec 2021 22:23:26: #2 finished! INFO @ Wed, 08 Dec 2021 22:23:26: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 22:23:26: #2 alternative fragment length(s) may be 1,35,533,553 bps INFO @ Wed, 08 Dec 2021 22:23:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.05_model.r WARNING @ Wed, 08 Dec 2021 22:23:26: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:23:26: #2 You may need to consider one of the other alternative d(s): 1,35,533,553 WARNING @ Wed, 08 Dec 2021 22:23:26: #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 22:23:26: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:23:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:23:26: start X-correlation... INFO @ Wed, 08 Dec 2021 22:23:26: end of X-cor INFO @ Wed, 08 Dec 2021 22:23:26: #2 finished! INFO @ Wed, 08 Dec 2021 22:23:26: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 22:23:26: #2 alternative fragment length(s) may be 1,35,533,553 bps INFO @ Wed, 08 Dec 2021 22:23:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.10_model.r WARNING @ Wed, 08 Dec 2021 22:23:26: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:23:26: #2 You may need to consider one of the other alternative d(s): 1,35,533,553 WARNING @ Wed, 08 Dec 2021 22:23:26: #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 22:23:26: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:23:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:23:27: 13000000 INFO @ Wed, 08 Dec 2021 22:23:34: 14000000 INFO @ Wed, 08 Dec 2021 22:23:41: 15000000 INFO @ Wed, 08 Dec 2021 22:23:42: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:23:42: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:23:42: #1 total tags in treatment: 15096069 INFO @ Wed, 08 Dec 2021 22:23:42: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:23:42: #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 22:23:42: #1 tags after filtering in treatment: 15096069 INFO @ Wed, 08 Dec 2021 22:23:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:23:42: #1 finished! INFO @ Wed, 08 Dec 2021 22:23:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:23:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:23:44: #2 number of paired peaks: 373 WARNING @ Wed, 08 Dec 2021 22:23:44: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Wed, 08 Dec 2021 22:23:44: start model_add_line... INFO @ Wed, 08 Dec 2021 22:23:44: start X-correlation... INFO @ Wed, 08 Dec 2021 22:23:44: end of X-cor INFO @ Wed, 08 Dec 2021 22:23:44: #2 finished! INFO @ Wed, 08 Dec 2021 22:23:44: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 22:23:44: #2 alternative fragment length(s) may be 1,35,533,553 bps INFO @ Wed, 08 Dec 2021 22:23:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.20_model.r WARNING @ Wed, 08 Dec 2021 22:23:44: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:23:44: #2 You may need to consider one of the other alternative d(s): 1,35,533,553 WARNING @ Wed, 08 Dec 2021 22:23:44: #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 22:23:44: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:23:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:24:01: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:24:01: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:24:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:24:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:24:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.05_summits.bed INFO @ Wed, 08 Dec 2021 22:24:18: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:24:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:24:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:24:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.10_summits.bed INFO @ Wed, 08 Dec 2021 22:24:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:24:19: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:24:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:24:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:24:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180814/SRX3180814.20_summits.bed INFO @ Wed, 08 Dec 2021 22:24:36: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling