Job ID = 5720235 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,512,400 reads read : 21,024,800 reads written : 10,512,400 reads 0-length : 10,512,400 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:10 10512400 reads; of these: 10512400 (100.00%) were unpaired; of these: 2736378 (26.03%) aligned 0 times 6560727 (62.41%) aligned exactly 1 time 1215295 (11.56%) aligned >1 times 73.97% overall alignment rate Time searching: 00:02:11 Overall time: 00:02:11 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_rmdupse_core] 2688372 / 7776022 = 0.3457 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 22:34:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.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 22:34:59: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:34:59: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:35:04: 1000000 INFO @ Wed, 15 Apr 2020 22:35:09: 2000000 INFO @ Wed, 15 Apr 2020 22:35:14: 3000000 INFO @ Wed, 15 Apr 2020 22:35:19: 4000000 INFO @ Wed, 15 Apr 2020 22:35:24: 5000000 INFO @ Wed, 15 Apr 2020 22:35:25: #1 tag size is determined as 51 bps INFO @ Wed, 15 Apr 2020 22:35:25: #1 tag size = 51 INFO @ Wed, 15 Apr 2020 22:35:25: #1 total tags in treatment: 5087650 INFO @ Wed, 15 Apr 2020 22:35:25: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:35:25: #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 22:35:25: #1 tags after filtering in treatment: 5087650 INFO @ Wed, 15 Apr 2020 22:35:25: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:35:25: #1 finished! INFO @ Wed, 15 Apr 2020 22:35:25: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:35:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:35:25: #2 number of paired peaks: 436 WARNING @ Wed, 15 Apr 2020 22:35:25: Fewer paired peaks (436) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 436 pairs to build model! INFO @ Wed, 15 Apr 2020 22:35:25: start model_add_line... INFO @ Wed, 15 Apr 2020 22:35:25: start X-correlation... INFO @ Wed, 15 Apr 2020 22:35:25: end of X-cor INFO @ Wed, 15 Apr 2020 22:35:25: #2 finished! INFO @ Wed, 15 Apr 2020 22:35:25: #2 predicted fragment length is 51 bps INFO @ Wed, 15 Apr 2020 22:35:25: #2 alternative fragment length(s) may be 4,51 bps INFO @ Wed, 15 Apr 2020 22:35:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.05_model.r WARNING @ Wed, 15 Apr 2020 22:35:25: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:35:25: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Wed, 15 Apr 2020 22:35:25: #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 22:35:25: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:35:25: #3 Pre-compute pvalue-qvalue table... 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 22:35:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.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 22:35:28: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:35:28: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:35:33: 1000000 INFO @ Wed, 15 Apr 2020 22:35:35: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:35:38: 2000000 INFO @ Wed, 15 Apr 2020 22:35:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.05_peaks.xls INFO @ Wed, 15 Apr 2020 22:35:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:35:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.05_summits.bed INFO @ Wed, 15 Apr 2020 22:35:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (634 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:35:43: 3000000 INFO @ Wed, 15 Apr 2020 22:35:49: 4000000 INFO @ Wed, 15 Apr 2020 22:35:54: 5000000 INFO @ Wed, 15 Apr 2020 22:35:54: #1 tag size is determined as 51 bps INFO @ Wed, 15 Apr 2020 22:35:54: #1 tag size = 51 INFO @ Wed, 15 Apr 2020 22:35:54: #1 total tags in treatment: 5087650 INFO @ Wed, 15 Apr 2020 22:35:54: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:35:54: #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 22:35:54: #1 tags after filtering in treatment: 5087650 INFO @ Wed, 15 Apr 2020 22:35:54: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:35:54: #1 finished! INFO @ Wed, 15 Apr 2020 22:35:54: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:35:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:35:54: #2 number of paired peaks: 436 WARNING @ Wed, 15 Apr 2020 22:35:54: Fewer paired peaks (436) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 436 pairs to build model! INFO @ Wed, 15 Apr 2020 22:35:54: start model_add_line... INFO @ Wed, 15 Apr 2020 22:35:55: start X-correlation... INFO @ Wed, 15 Apr 2020 22:35:55: end of X-cor INFO @ Wed, 15 Apr 2020 22:35:55: #2 finished! INFO @ Wed, 15 Apr 2020 22:35:55: #2 predicted fragment length is 51 bps INFO @ Wed, 15 Apr 2020 22:35:55: #2 alternative fragment length(s) may be 4,51 bps INFO @ Wed, 15 Apr 2020 22:35:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.10_model.r WARNING @ Wed, 15 Apr 2020 22:35:55: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:35:55: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Wed, 15 Apr 2020 22:35:55: #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 22:35:55: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:35:55: #3 Pre-compute pvalue-qvalue table... 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 22:35:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.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 22:35:58: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:35:58: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:36:03: 1000000 INFO @ Wed, 15 Apr 2020 22:36:05: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:36:08: 2000000 INFO @ Wed, 15 Apr 2020 22:36:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.10_peaks.xls INFO @ Wed, 15 Apr 2020 22:36:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:36:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.10_summits.bed INFO @ Wed, 15 Apr 2020 22:36:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (405 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:36:14: 3000000 INFO @ Wed, 15 Apr 2020 22:36:19: 4000000 INFO @ Wed, 15 Apr 2020 22:36:24: 5000000 INFO @ Wed, 15 Apr 2020 22:36:24: #1 tag size is determined as 51 bps INFO @ Wed, 15 Apr 2020 22:36:24: #1 tag size = 51 INFO @ Wed, 15 Apr 2020 22:36:24: #1 total tags in treatment: 5087650 INFO @ Wed, 15 Apr 2020 22:36:24: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:36:24: #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 22:36:24: #1 tags after filtering in treatment: 5087650 INFO @ Wed, 15 Apr 2020 22:36:24: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:36:24: #1 finished! INFO @ Wed, 15 Apr 2020 22:36:24: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:36:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:36:25: #2 number of paired peaks: 436 WARNING @ Wed, 15 Apr 2020 22:36:25: Fewer paired peaks (436) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 436 pairs to build model! INFO @ Wed, 15 Apr 2020 22:36:25: start model_add_line... INFO @ Wed, 15 Apr 2020 22:36:25: start X-correlation... INFO @ Wed, 15 Apr 2020 22:36:25: end of X-cor INFO @ Wed, 15 Apr 2020 22:36:25: #2 finished! INFO @ Wed, 15 Apr 2020 22:36:25: #2 predicted fragment length is 51 bps INFO @ Wed, 15 Apr 2020 22:36:25: #2 alternative fragment length(s) may be 4,51 bps INFO @ Wed, 15 Apr 2020 22:36:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.20_model.r WARNING @ Wed, 15 Apr 2020 22:36:25: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:36:25: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Wed, 15 Apr 2020 22:36:25: #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 22:36:25: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:36:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:36:35: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:36:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.20_peaks.xls INFO @ Wed, 15 Apr 2020 22:36:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:36:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720167/SRX6720167.20_summits.bed INFO @ Wed, 15 Apr 2020 22:36:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (153 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。