Job ID = 5720318 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,073,825 reads read : 26,073,825 reads written : 26,073,825 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:10:52 26073825 reads; of these: 26073825 (100.00%) were unpaired; of these: 871458 (3.34%) aligned 0 times 19202241 (73.65%) aligned exactly 1 time 6000126 (23.01%) aligned >1 times 96.66% overall alignment rate Time searching: 00:10:52 Overall time: 00:10:52 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] 5030990 / 25202367 = 0.1996 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 @ Wed, 15 Apr 2020 23:41:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.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, 15 Apr 2020 23:41:55: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:41:55: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:42:01: 1000000 INFO @ Wed, 15 Apr 2020 23:42:07: 2000000 INFO @ Wed, 15 Apr 2020 23:42:13: 3000000 INFO @ Wed, 15 Apr 2020 23:42:19: 4000000 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 @ Wed, 15 Apr 2020 23:42:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.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, 15 Apr 2020 23:42:25: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:42:25: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:42:25: 5000000 INFO @ Wed, 15 Apr 2020 23:42:32: 1000000 INFO @ Wed, 15 Apr 2020 23:42:32: 6000000 INFO @ Wed, 15 Apr 2020 23:42:38: 2000000 INFO @ Wed, 15 Apr 2020 23:42:39: 7000000 INFO @ Wed, 15 Apr 2020 23:42:45: 3000000 INFO @ Wed, 15 Apr 2020 23:42:46: 8000000 INFO @ Wed, 15 Apr 2020 23:42:52: 4000000 INFO @ Wed, 15 Apr 2020 23:42:53: 9000000 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 @ Wed, 15 Apr 2020 23:42:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.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, 15 Apr 2020 23:42:55: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:42:55: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:42:59: 5000000 INFO @ Wed, 15 Apr 2020 23:42:59: 10000000 INFO @ Wed, 15 Apr 2020 23:43:02: 1000000 INFO @ Wed, 15 Apr 2020 23:43:06: 6000000 INFO @ Wed, 15 Apr 2020 23:43:06: 11000000 INFO @ Wed, 15 Apr 2020 23:43:09: 2000000 INFO @ Wed, 15 Apr 2020 23:43:13: 7000000 INFO @ Wed, 15 Apr 2020 23:43:13: 12000000 INFO @ Wed, 15 Apr 2020 23:43:15: 3000000 INFO @ Wed, 15 Apr 2020 23:43:20: 8000000 INFO @ Wed, 15 Apr 2020 23:43:20: 13000000 INFO @ Wed, 15 Apr 2020 23:43:22: 4000000 INFO @ Wed, 15 Apr 2020 23:43:26: 9000000 INFO @ Wed, 15 Apr 2020 23:43:27: 14000000 INFO @ Wed, 15 Apr 2020 23:43:29: 5000000 INFO @ Wed, 15 Apr 2020 23:43:33: 10000000 INFO @ Wed, 15 Apr 2020 23:43:33: 15000000 INFO @ Wed, 15 Apr 2020 23:43:36: 6000000 INFO @ Wed, 15 Apr 2020 23:43:40: 16000000 INFO @ Wed, 15 Apr 2020 23:43:40: 11000000 INFO @ Wed, 15 Apr 2020 23:43:42: 7000000 INFO @ Wed, 15 Apr 2020 23:43:47: 17000000 INFO @ Wed, 15 Apr 2020 23:43:47: 12000000 INFO @ Wed, 15 Apr 2020 23:43:49: 8000000 INFO @ Wed, 15 Apr 2020 23:43:54: 18000000 INFO @ Wed, 15 Apr 2020 23:43:54: 13000000 INFO @ Wed, 15 Apr 2020 23:43:56: 9000000 INFO @ Wed, 15 Apr 2020 23:44:00: 19000000 INFO @ Wed, 15 Apr 2020 23:44:00: 14000000 INFO @ Wed, 15 Apr 2020 23:44:03: 10000000 INFO @ Wed, 15 Apr 2020 23:44:07: 20000000 INFO @ Wed, 15 Apr 2020 23:44:07: 15000000 INFO @ Wed, 15 Apr 2020 23:44:08: #1 tag size is determined as 76 bps INFO @ Wed, 15 Apr 2020 23:44:08: #1 tag size = 76 INFO @ Wed, 15 Apr 2020 23:44:08: #1 total tags in treatment: 20171377 INFO @ Wed, 15 Apr 2020 23:44:08: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:44:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:44:09: #1 tags after filtering in treatment: 20171377 INFO @ Wed, 15 Apr 2020 23:44:09: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:44:09: #1 finished! INFO @ Wed, 15 Apr 2020 23:44:09: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:44:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:44:10: 11000000 INFO @ Wed, 15 Apr 2020 23:44:10: #2 number of paired peaks: 351 WARNING @ Wed, 15 Apr 2020 23:44:10: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Wed, 15 Apr 2020 23:44:10: start model_add_line... INFO @ Wed, 15 Apr 2020 23:44:10: start X-correlation... INFO @ Wed, 15 Apr 2020 23:44:10: end of X-cor INFO @ Wed, 15 Apr 2020 23:44:10: #2 finished! INFO @ Wed, 15 Apr 2020 23:44:10: #2 predicted fragment length is 57 bps INFO @ Wed, 15 Apr 2020 23:44:10: #2 alternative fragment length(s) may be 1,57 bps INFO @ Wed, 15 Apr 2020 23:44:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.05_model.r WARNING @ Wed, 15 Apr 2020 23:44:10: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:44:10: #2 You may need to consider one of the other alternative d(s): 1,57 WARNING @ Wed, 15 Apr 2020 23:44:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:44:10: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:44:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:44:14: 16000000 INFO @ Wed, 15 Apr 2020 23:44:16: 12000000 INFO @ Wed, 15 Apr 2020 23:44:21: 17000000 INFO @ Wed, 15 Apr 2020 23:44:23: 13000000 INFO @ Wed, 15 Apr 2020 23:44:28: 18000000 INFO @ Wed, 15 Apr 2020 23:44:30: 14000000 INFO @ Wed, 15 Apr 2020 23:44:34: 19000000 INFO @ Wed, 15 Apr 2020 23:44:36: 15000000 INFO @ Wed, 15 Apr 2020 23:44:41: 20000000 INFO @ Wed, 15 Apr 2020 23:44:42: #1 tag size is determined as 76 bps INFO @ Wed, 15 Apr 2020 23:44:42: #1 tag size = 76 INFO @ Wed, 15 Apr 2020 23:44:42: #1 total tags in treatment: 20171377 INFO @ Wed, 15 Apr 2020 23:44:42: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:44:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:44:42: #1 tags after filtering in treatment: 20171377 INFO @ Wed, 15 Apr 2020 23:44:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:44:42: #1 finished! INFO @ Wed, 15 Apr 2020 23:44:42: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:44:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:44:43: 16000000 INFO @ Wed, 15 Apr 2020 23:44:44: #2 number of paired peaks: 351 WARNING @ Wed, 15 Apr 2020 23:44:44: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Wed, 15 Apr 2020 23:44:44: start model_add_line... INFO @ Wed, 15 Apr 2020 23:44:44: start X-correlation... INFO @ Wed, 15 Apr 2020 23:44:44: end of X-cor INFO @ Wed, 15 Apr 2020 23:44:44: #2 finished! INFO @ Wed, 15 Apr 2020 23:44:44: #2 predicted fragment length is 57 bps INFO @ Wed, 15 Apr 2020 23:44:44: #2 alternative fragment length(s) may be 1,57 bps INFO @ Wed, 15 Apr 2020 23:44:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.10_model.r WARNING @ Wed, 15 Apr 2020 23:44:44: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:44:44: #2 You may need to consider one of the other alternative d(s): 1,57 WARNING @ Wed, 15 Apr 2020 23:44:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:44:44: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:44:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:44:45: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:44:49: 17000000 INFO @ Wed, 15 Apr 2020 23:44:56: 18000000 INFO @ Wed, 15 Apr 2020 23:45:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.05_peaks.xls INFO @ Wed, 15 Apr 2020 23:45:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:45:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.05_summits.bed INFO @ Wed, 15 Apr 2020 23:45:01: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (2023 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:45:02: 19000000 INFO @ Wed, 15 Apr 2020 23:45:08: 20000000 INFO @ Wed, 15 Apr 2020 23:45:09: #1 tag size is determined as 76 bps INFO @ Wed, 15 Apr 2020 23:45:09: #1 tag size = 76 INFO @ Wed, 15 Apr 2020 23:45:09: #1 total tags in treatment: 20171377 INFO @ Wed, 15 Apr 2020 23:45:09: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:45:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:45:10: #1 tags after filtering in treatment: 20171377 INFO @ Wed, 15 Apr 2020 23:45:10: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:45:10: #1 finished! INFO @ Wed, 15 Apr 2020 23:45:10: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:45:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:45:11: #2 number of paired peaks: 351 WARNING @ Wed, 15 Apr 2020 23:45:11: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Wed, 15 Apr 2020 23:45:11: start model_add_line... INFO @ Wed, 15 Apr 2020 23:45:11: start X-correlation... INFO @ Wed, 15 Apr 2020 23:45:11: end of X-cor INFO @ Wed, 15 Apr 2020 23:45:11: #2 finished! INFO @ Wed, 15 Apr 2020 23:45:11: #2 predicted fragment length is 57 bps INFO @ Wed, 15 Apr 2020 23:45:11: #2 alternative fragment length(s) may be 1,57 bps INFO @ Wed, 15 Apr 2020 23:45:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.20_model.r WARNING @ Wed, 15 Apr 2020 23:45:11: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:45:11: #2 You may need to consider one of the other alternative d(s): 1,57 WARNING @ Wed, 15 Apr 2020 23:45:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:45:11: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:45:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:45:21: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:45:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.10_peaks.xls INFO @ Wed, 15 Apr 2020 23:45:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:45:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.10_summits.bed INFO @ Wed, 15 Apr 2020 23:45:40: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (646 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:45:47: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:46:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.20_peaks.xls INFO @ Wed, 15 Apr 2020 23:46:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:46:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971790/SRX7971790.20_summits.bed INFO @ Wed, 15 Apr 2020 23:46:04: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (218 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。