Job ID = 5720877 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,845,497 reads read : 19,845,497 reads written : 19,845,497 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR8997108.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: 00:06:55 19845497 reads; of these: 19845497 (100.00%) were unpaired; of these: 5684775 (28.65%) aligned 0 times 10202871 (51.41%) aligned exactly 1 time 3957851 (19.94%) aligned >1 times 71.35% overall alignment rate Time searching: 00:06:55 Overall time: 00:06:55 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_sort_core] merging from 8 files... [bam_rmdupse_core] 9502856 / 14160722 = 0.6711 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 02:52:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.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 02:52:06: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:52:06: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:52:11: 1000000 INFO @ Thu, 16 Apr 2020 02:52:16: 2000000 INFO @ Thu, 16 Apr 2020 02:52:21: 3000000 INFO @ Thu, 16 Apr 2020 02:52:26: 4000000 INFO @ Thu, 16 Apr 2020 02:52:29: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 02:52:29: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 02:52:29: #1 total tags in treatment: 4657866 INFO @ Thu, 16 Apr 2020 02:52:29: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:52:29: #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 02:52:29: #1 tags after filtering in treatment: 4657866 INFO @ Thu, 16 Apr 2020 02:52:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:52:29: #1 finished! INFO @ Thu, 16 Apr 2020 02:52:29: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:52:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:52:30: #2 number of paired peaks: 746 WARNING @ Thu, 16 Apr 2020 02:52:30: Fewer paired peaks (746) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 746 pairs to build model! INFO @ Thu, 16 Apr 2020 02:52:30: start model_add_line... INFO @ Thu, 16 Apr 2020 02:52:30: start X-correlation... INFO @ Thu, 16 Apr 2020 02:52:30: end of X-cor INFO @ Thu, 16 Apr 2020 02:52:30: #2 finished! INFO @ Thu, 16 Apr 2020 02:52:30: #2 predicted fragment length is 78 bps INFO @ Thu, 16 Apr 2020 02:52:30: #2 alternative fragment length(s) may be 78 bps INFO @ Thu, 16 Apr 2020 02:52:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.05_model.r WARNING @ Thu, 16 Apr 2020 02:52:30: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:52:30: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Thu, 16 Apr 2020 02:52:30: #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 02:52:30: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:52:30: #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 02:52:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.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 02:52:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:52:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:52:39: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:52:40: 1000000 INFO @ Thu, 16 Apr 2020 02:52:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:52:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:52:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.05_summits.bed INFO @ Thu, 16 Apr 2020 02:52:44: Done! INFO @ Thu, 16 Apr 2020 02:52:45: 2000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2587 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:52:51: 3000000 INFO @ Thu, 16 Apr 2020 02:52:56: 4000000 INFO @ Thu, 16 Apr 2020 02:52:59: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 02:52:59: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 02:52:59: #1 total tags in treatment: 4657866 INFO @ Thu, 16 Apr 2020 02:52:59: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:52:59: #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 02:52:59: #1 tags after filtering in treatment: 4657866 INFO @ Thu, 16 Apr 2020 02:52:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:52:59: #1 finished! INFO @ Thu, 16 Apr 2020 02:52:59: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:52:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:53:00: #2 number of paired peaks: 746 WARNING @ Thu, 16 Apr 2020 02:53:00: Fewer paired peaks (746) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 746 pairs to build model! INFO @ Thu, 16 Apr 2020 02:53:00: start model_add_line... INFO @ Thu, 16 Apr 2020 02:53:00: start X-correlation... INFO @ Thu, 16 Apr 2020 02:53:00: end of X-cor INFO @ Thu, 16 Apr 2020 02:53:00: #2 finished! INFO @ Thu, 16 Apr 2020 02:53:00: #2 predicted fragment length is 78 bps INFO @ Thu, 16 Apr 2020 02:53:00: #2 alternative fragment length(s) may be 78 bps INFO @ Thu, 16 Apr 2020 02:53:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.10_model.r WARNING @ Thu, 16 Apr 2020 02:53:00: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:53:00: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Thu, 16 Apr 2020 02:53:00: #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 02:53:00: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:53:00: #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 02:53:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.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 02:53:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:53:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:53:10: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:53:11: 1000000 INFO @ Thu, 16 Apr 2020 02:53:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:53:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:53:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.10_summits.bed INFO @ Thu, 16 Apr 2020 02:53:15: Done! INFO @ Thu, 16 Apr 2020 02:53:17: 2000000 pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (966 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:53:23: 3000000 INFO @ Thu, 16 Apr 2020 02:53:29: 4000000 INFO @ Thu, 16 Apr 2020 02:53:33: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 02:53:33: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 02:53:33: #1 total tags in treatment: 4657866 INFO @ Thu, 16 Apr 2020 02:53:33: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:53:33: #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 02:53:33: #1 tags after filtering in treatment: 4657866 INFO @ Thu, 16 Apr 2020 02:53:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:53:33: #1 finished! INFO @ Thu, 16 Apr 2020 02:53:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:53:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:53:33: #2 number of paired peaks: 746 WARNING @ Thu, 16 Apr 2020 02:53:33: Fewer paired peaks (746) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 746 pairs to build model! INFO @ Thu, 16 Apr 2020 02:53:33: start model_add_line... INFO @ Thu, 16 Apr 2020 02:53:33: start X-correlation... INFO @ Thu, 16 Apr 2020 02:53:33: end of X-cor INFO @ Thu, 16 Apr 2020 02:53:33: #2 finished! INFO @ Thu, 16 Apr 2020 02:53:33: #2 predicted fragment length is 78 bps INFO @ Thu, 16 Apr 2020 02:53:33: #2 alternative fragment length(s) may be 78 bps INFO @ Thu, 16 Apr 2020 02:53:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.20_model.r WARNING @ Thu, 16 Apr 2020 02:53:33: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:53:33: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Thu, 16 Apr 2020 02:53:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 02:53:33: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:53:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:53:43: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:53:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:53:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:53:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775905/SRX5775905.20_summits.bed INFO @ Thu, 16 Apr 2020 02:53:48: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (485 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。