Job ID = 10166038 SRX = SRX8331159 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: 00:13:19 38052982 reads; of these: 38052982 (100.00%) were unpaired; of these: 163031 (0.43%) aligned 0 times 32328613 (84.96%) aligned exactly 1 time 5561338 (14.61%) aligned >1 times 99.57% overall alignment rate Time searching: 00:13:19 Overall time: 00:13:19 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 16 files... [bam_rmdupse_core] 24440869 / 37889951 = 0.6450 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:47:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.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 @ Thu, 08 Oct 2020 20:47:14: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:47:14: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:47:20: 1000000 INFO @ Thu, 08 Oct 2020 20:47:26: 2000000 INFO @ Thu, 08 Oct 2020 20:47:31: 3000000 INFO @ Thu, 08 Oct 2020 20:47:36: 4000000 INFO @ Thu, 08 Oct 2020 20:47:42: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:47:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.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 @ Thu, 08 Oct 2020 20:47:44: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:47:44: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:47:48: 6000000 INFO @ Thu, 08 Oct 2020 20:47:50: 1000000 INFO @ Thu, 08 Oct 2020 20:47:53: 7000000 INFO @ Thu, 08 Oct 2020 20:47:56: 2000000 INFO @ Thu, 08 Oct 2020 20:47:59: 8000000 INFO @ Thu, 08 Oct 2020 20:48:02: 3000000 INFO @ Thu, 08 Oct 2020 20:48:04: 9000000 INFO @ Thu, 08 Oct 2020 20:48:07: 4000000 INFO @ Thu, 08 Oct 2020 20:48:10: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:48:13: 5000000 INFO @ Thu, 08 Oct 2020 20:48:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.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 @ Thu, 08 Oct 2020 20:48:14: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:48:14: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:48:16: 11000000 INFO @ Thu, 08 Oct 2020 20:48:19: 6000000 INFO @ Thu, 08 Oct 2020 20:48:20: 1000000 INFO @ Thu, 08 Oct 2020 20:48:21: 12000000 INFO @ Thu, 08 Oct 2020 20:48:25: 7000000 INFO @ Thu, 08 Oct 2020 20:48:26: 2000000 INFO @ Thu, 08 Oct 2020 20:48:27: 13000000 INFO @ Thu, 08 Oct 2020 20:48:30: #1 tag size is determined as 51 bps INFO @ Thu, 08 Oct 2020 20:48:30: #1 tag size = 51 INFO @ Thu, 08 Oct 2020 20:48:30: #1 total tags in treatment: 13449082 INFO @ Thu, 08 Oct 2020 20:48:30: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:48:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:48:30: #1 tags after filtering in treatment: 13449082 INFO @ Thu, 08 Oct 2020 20:48:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:48:30: #1 finished! INFO @ Thu, 08 Oct 2020 20:48:30: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:48:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:48:30: 8000000 INFO @ Thu, 08 Oct 2020 20:48:31: #2 number of paired peaks: 421 WARNING @ Thu, 08 Oct 2020 20:48:31: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Thu, 08 Oct 2020 20:48:31: start model_add_line... INFO @ Thu, 08 Oct 2020 20:48:31: start X-correlation... INFO @ Thu, 08 Oct 2020 20:48:31: end of X-cor INFO @ Thu, 08 Oct 2020 20:48:31: #2 finished! INFO @ Thu, 08 Oct 2020 20:48:31: #2 predicted fragment length is 68 bps INFO @ Thu, 08 Oct 2020 20:48:31: #2 alternative fragment length(s) may be 3,68 bps INFO @ Thu, 08 Oct 2020 20:48:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.05_model.r WARNING @ Thu, 08 Oct 2020 20:48:31: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:48:31: #2 You may need to consider one of the other alternative d(s): 3,68 WARNING @ Thu, 08 Oct 2020 20:48:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:48:31: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:48:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:48:32: 3000000 INFO @ Thu, 08 Oct 2020 20:48:36: 9000000 INFO @ Thu, 08 Oct 2020 20:48:38: 4000000 INFO @ Thu, 08 Oct 2020 20:48:42: 10000000 INFO @ Thu, 08 Oct 2020 20:48:44: 5000000 INFO @ Thu, 08 Oct 2020 20:48:48: 11000000 INFO @ Thu, 08 Oct 2020 20:48:50: 6000000 INFO @ Thu, 08 Oct 2020 20:48:53: 12000000 INFO @ Thu, 08 Oct 2020 20:48:56: 7000000 INFO @ Thu, 08 Oct 2020 20:48:58: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:48:59: 13000000 INFO @ Thu, 08 Oct 2020 20:49:02: 8000000 INFO @ Thu, 08 Oct 2020 20:49:02: #1 tag size is determined as 51 bps INFO @ Thu, 08 Oct 2020 20:49:02: #1 tag size = 51 INFO @ Thu, 08 Oct 2020 20:49:02: #1 total tags in treatment: 13449082 INFO @ Thu, 08 Oct 2020 20:49:02: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:49:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:49:02: #1 tags after filtering in treatment: 13449082 INFO @ Thu, 08 Oct 2020 20:49:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:49:02: #1 finished! INFO @ Thu, 08 Oct 2020 20:49:02: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:49:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:49:03: #2 number of paired peaks: 421 WARNING @ Thu, 08 Oct 2020 20:49:03: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Thu, 08 Oct 2020 20:49:03: start model_add_line... INFO @ Thu, 08 Oct 2020 20:49:03: start X-correlation... INFO @ Thu, 08 Oct 2020 20:49:03: end of X-cor INFO @ Thu, 08 Oct 2020 20:49:03: #2 finished! INFO @ Thu, 08 Oct 2020 20:49:03: #2 predicted fragment length is 68 bps INFO @ Thu, 08 Oct 2020 20:49:03: #2 alternative fragment length(s) may be 3,68 bps INFO @ Thu, 08 Oct 2020 20:49:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.10_model.r WARNING @ Thu, 08 Oct 2020 20:49:03: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:49:03: #2 You may need to consider one of the other alternative d(s): 3,68 WARNING @ Thu, 08 Oct 2020 20:49:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:49:03: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:49:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:49:07: 9000000 INFO @ Thu, 08 Oct 2020 20:49:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:49:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:49:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.05_summits.bed INFO @ Thu, 08 Oct 2020 20:49:13: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (13881 records, 4 fields): 13 millis INFO @ Thu, 08 Oct 2020 20:49:13: 10000000 CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:49:18: 11000000 INFO @ Thu, 08 Oct 2020 20:49:24: 12000000 INFO @ Thu, 08 Oct 2020 20:49:29: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:49:29: 13000000 INFO @ Thu, 08 Oct 2020 20:49:32: #1 tag size is determined as 51 bps INFO @ Thu, 08 Oct 2020 20:49:32: #1 tag size = 51 INFO @ Thu, 08 Oct 2020 20:49:32: #1 total tags in treatment: 13449082 INFO @ Thu, 08 Oct 2020 20:49:32: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:49:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:49:32: #1 tags after filtering in treatment: 13449082 INFO @ Thu, 08 Oct 2020 20:49:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:49:32: #1 finished! INFO @ Thu, 08 Oct 2020 20:49:32: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:49:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:49:33: #2 number of paired peaks: 421 WARNING @ Thu, 08 Oct 2020 20:49:33: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Thu, 08 Oct 2020 20:49:33: start model_add_line... INFO @ Thu, 08 Oct 2020 20:49:33: start X-correlation... INFO @ Thu, 08 Oct 2020 20:49:33: end of X-cor INFO @ Thu, 08 Oct 2020 20:49:33: #2 finished! INFO @ Thu, 08 Oct 2020 20:49:33: #2 predicted fragment length is 68 bps INFO @ Thu, 08 Oct 2020 20:49:33: #2 alternative fragment length(s) may be 3,68 bps INFO @ Thu, 08 Oct 2020 20:49:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.20_model.r WARNING @ Thu, 08 Oct 2020 20:49:33: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:49:33: #2 You may need to consider one of the other alternative d(s): 3,68 WARNING @ Thu, 08 Oct 2020 20:49:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:49:33: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:49:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:49:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:49:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:49:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.10_summits.bed INFO @ Thu, 08 Oct 2020 20:49:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2290 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:49:57: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:50:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:50:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:50:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331159/SRX8331159.20_summits.bed INFO @ Thu, 08 Oct 2020 20:50:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (434 records, 4 fields): 1 millis CompletedMACS2peakCalling