Job ID = 5720656 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,672,022 reads read : 7,672,022 reads written : 7,672,022 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289753.sra.cache’: 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: 00:02:25 7672022 reads; of these: 7672022 (100.00%) were unpaired; of these: 2007808 (26.17%) aligned 0 times 3988354 (51.99%) aligned exactly 1 time 1675860 (21.84%) aligned >1 times 73.83% overall alignment rate Time searching: 00:02:25 Overall time: 00:02:25 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 1126187 / 5664214 = 0.1988 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, 16 Apr 2020 00:51:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Apr 2020 00:51:54: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:51:54: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:51:59: 1000000 INFO @ Thu, 16 Apr 2020 00:52:03: 2000000 INFO @ Thu, 16 Apr 2020 00:52:08: 3000000 INFO @ Thu, 16 Apr 2020 00:52:13: 4000000 INFO @ Thu, 16 Apr 2020 00:52:15: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:52:15: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:52:15: #1 total tags in treatment: 4538027 INFO @ Thu, 16 Apr 2020 00:52:15: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:52:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:52:16: #1 tags after filtering in treatment: 4538027 INFO @ Thu, 16 Apr 2020 00:52:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:52:16: #1 finished! INFO @ Thu, 16 Apr 2020 00:52:16: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:52:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:52:16: #2 number of paired peaks: 739 WARNING @ Thu, 16 Apr 2020 00:52:16: Fewer paired peaks (739) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 739 pairs to build model! INFO @ Thu, 16 Apr 2020 00:52:16: start model_add_line... INFO @ Thu, 16 Apr 2020 00:52:16: start X-correlation... INFO @ Thu, 16 Apr 2020 00:52:16: end of X-cor INFO @ Thu, 16 Apr 2020 00:52:16: #2 finished! INFO @ Thu, 16 Apr 2020 00:52:16: #2 predicted fragment length is 56 bps INFO @ Thu, 16 Apr 2020 00:52:16: #2 alternative fragment length(s) may be 56 bps INFO @ Thu, 16 Apr 2020 00:52:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.05_model.r WARNING @ Thu, 16 Apr 2020 00:52:16: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:52:16: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Thu, 16 Apr 2020 00:52:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:52:16: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:52:16: #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 @ Thu, 16 Apr 2020 00:52:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Apr 2020 00:52:24: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:52:24: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:52:26: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:52:29: 1000000 INFO @ Thu, 16 Apr 2020 00:52:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:52:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:52:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.05_summits.bed INFO @ Thu, 16 Apr 2020 00:52:31: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1346 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:52:35: 2000000 INFO @ Thu, 16 Apr 2020 00:52:40: 3000000 INFO @ Thu, 16 Apr 2020 00:52:46: 4000000 INFO @ Thu, 16 Apr 2020 00:52:49: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:52:49: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:52:49: #1 total tags in treatment: 4538027 INFO @ Thu, 16 Apr 2020 00:52:49: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:52:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:52:49: #1 tags after filtering in treatment: 4538027 INFO @ Thu, 16 Apr 2020 00:52:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:52:49: #1 finished! INFO @ Thu, 16 Apr 2020 00:52:49: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:52:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:52:50: #2 number of paired peaks: 739 WARNING @ Thu, 16 Apr 2020 00:52:50: Fewer paired peaks (739) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 739 pairs to build model! INFO @ Thu, 16 Apr 2020 00:52:50: start model_add_line... INFO @ Thu, 16 Apr 2020 00:52:50: start X-correlation... INFO @ Thu, 16 Apr 2020 00:52:50: end of X-cor INFO @ Thu, 16 Apr 2020 00:52:50: #2 finished! INFO @ Thu, 16 Apr 2020 00:52:50: #2 predicted fragment length is 56 bps INFO @ Thu, 16 Apr 2020 00:52:50: #2 alternative fragment length(s) may be 56 bps INFO @ Thu, 16 Apr 2020 00:52:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.10_model.r WARNING @ Thu, 16 Apr 2020 00:52:50: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:52:50: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Thu, 16 Apr 2020 00:52:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:52:50: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:52:50: #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 @ Thu, 16 Apr 2020 00:52:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Apr 2020 00:52:54: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:52:54: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:52:59: 1000000 INFO @ Thu, 16 Apr 2020 00:53:00: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:53:05: 2000000 INFO @ Thu, 16 Apr 2020 00:53:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:53:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:53:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.10_summits.bed INFO @ Thu, 16 Apr 2020 00:53:05: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (965 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:53:10: 3000000 INFO @ Thu, 16 Apr 2020 00:53:15: 4000000 INFO @ Thu, 16 Apr 2020 00:53:18: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:53:18: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:53:18: #1 total tags in treatment: 4538027 INFO @ Thu, 16 Apr 2020 00:53:18: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:53:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:53:18: #1 tags after filtering in treatment: 4538027 INFO @ Thu, 16 Apr 2020 00:53:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:53:18: #1 finished! INFO @ Thu, 16 Apr 2020 00:53:18: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:53:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:53:19: #2 number of paired peaks: 739 WARNING @ Thu, 16 Apr 2020 00:53:19: Fewer paired peaks (739) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 739 pairs to build model! INFO @ Thu, 16 Apr 2020 00:53:19: start model_add_line... INFO @ Thu, 16 Apr 2020 00:53:19: start X-correlation... INFO @ Thu, 16 Apr 2020 00:53:19: end of X-cor INFO @ Thu, 16 Apr 2020 00:53:19: #2 finished! INFO @ Thu, 16 Apr 2020 00:53:19: #2 predicted fragment length is 56 bps INFO @ Thu, 16 Apr 2020 00:53:19: #2 alternative fragment length(s) may be 56 bps INFO @ Thu, 16 Apr 2020 00:53:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.20_model.r WARNING @ Thu, 16 Apr 2020 00:53:19: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:53:19: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Thu, 16 Apr 2020 00:53:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:53:19: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:53:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:53:29: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:53:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:53:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:53:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592476/SRX2592476.20_summits.bed INFO @ Thu, 16 Apr 2020 00:53:33: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (715 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。