Job ID = 5720659 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,119,660 reads read : 3,119,660 reads written : 3,119,660 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289755.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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:11 3119660 reads; of these: 3119660 (100.00%) were unpaired; of these: 1599886 (51.28%) aligned 0 times 1046437 (33.54%) aligned exactly 1 time 473337 (15.17%) aligned >1 times 48.72% overall alignment rate Time searching: 00:01:12 Overall time: 00:01:12 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] 133515 / 1519774 = 0.0879 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 00:49:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.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 00:49:44: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:49:44: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:49:51: 1000000 INFO @ Thu, 16 Apr 2020 00:49:55: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:49:55: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:49:55: #1 total tags in treatment: 1386259 INFO @ Thu, 16 Apr 2020 00:49:55: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:49:55: #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 00:49:55: #1 tags after filtering in treatment: 1386259 INFO @ Thu, 16 Apr 2020 00:49:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:49:55: #1 finished! INFO @ Thu, 16 Apr 2020 00:49:55: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:49:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:49:55: #2 number of paired peaks: 848 WARNING @ Thu, 16 Apr 2020 00:49:55: Fewer paired peaks (848) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 848 pairs to build model! INFO @ Thu, 16 Apr 2020 00:49:55: start model_add_line... INFO @ Thu, 16 Apr 2020 00:49:55: start X-correlation... INFO @ Thu, 16 Apr 2020 00:49:55: end of X-cor INFO @ Thu, 16 Apr 2020 00:49:55: #2 finished! INFO @ Thu, 16 Apr 2020 00:49:55: #2 predicted fragment length is 54 bps INFO @ Thu, 16 Apr 2020 00:49:55: #2 alternative fragment length(s) may be 54 bps INFO @ Thu, 16 Apr 2020 00:49:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.05_model.r WARNING @ Thu, 16 Apr 2020 00:49:55: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:49:55: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Thu, 16 Apr 2020 00:49:55: #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 00:49:55: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:49:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:49:59: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:50:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:50:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:50:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.05_summits.bed INFO @ Thu, 16 Apr 2020 00:50:01: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (936 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 00:50:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.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 00:50:14: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:50:14: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:50:20: 1000000 INFO @ Thu, 16 Apr 2020 00:50:22: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:50:22: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:50:22: #1 total tags in treatment: 1386259 INFO @ Thu, 16 Apr 2020 00:50:22: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:50:22: #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 00:50:22: #1 tags after filtering in treatment: 1386259 INFO @ Thu, 16 Apr 2020 00:50:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:50:22: #1 finished! INFO @ Thu, 16 Apr 2020 00:50:22: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:50:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:50:22: #2 number of paired peaks: 848 WARNING @ Thu, 16 Apr 2020 00:50:22: Fewer paired peaks (848) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 848 pairs to build model! INFO @ Thu, 16 Apr 2020 00:50:22: start model_add_line... INFO @ Thu, 16 Apr 2020 00:50:22: start X-correlation... INFO @ Thu, 16 Apr 2020 00:50:22: end of X-cor INFO @ Thu, 16 Apr 2020 00:50:22: #2 finished! INFO @ Thu, 16 Apr 2020 00:50:22: #2 predicted fragment length is 54 bps INFO @ Thu, 16 Apr 2020 00:50:22: #2 alternative fragment length(s) may be 54 bps INFO @ Thu, 16 Apr 2020 00:50:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.10_model.r WARNING @ Thu, 16 Apr 2020 00:50:22: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:50:22: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Thu, 16 Apr 2020 00:50:22: #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 00:50:22: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:50:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:50:26: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:50:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:50:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:50:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.10_summits.bed INFO @ Thu, 16 Apr 2020 00:50:28: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (748 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 00:50:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.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 00:50:44: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:50:44: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:50:50: 1000000 INFO @ Thu, 16 Apr 2020 00:50:52: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:50:52: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:50:52: #1 total tags in treatment: 1386259 INFO @ Thu, 16 Apr 2020 00:50:52: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:50:52: #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 00:50:52: #1 tags after filtering in treatment: 1386259 INFO @ Thu, 16 Apr 2020 00:50:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:50:52: #1 finished! INFO @ Thu, 16 Apr 2020 00:50:52: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:50:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:50:53: #2 number of paired peaks: 848 WARNING @ Thu, 16 Apr 2020 00:50:53: Fewer paired peaks (848) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 848 pairs to build model! INFO @ Thu, 16 Apr 2020 00:50:53: start model_add_line... INFO @ Thu, 16 Apr 2020 00:50:53: start X-correlation... INFO @ Thu, 16 Apr 2020 00:50:53: end of X-cor INFO @ Thu, 16 Apr 2020 00:50:53: #2 finished! INFO @ Thu, 16 Apr 2020 00:50:53: #2 predicted fragment length is 54 bps INFO @ Thu, 16 Apr 2020 00:50:53: #2 alternative fragment length(s) may be 54 bps INFO @ Thu, 16 Apr 2020 00:50:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.20_model.r WARNING @ Thu, 16 Apr 2020 00:50:53: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:50:53: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Thu, 16 Apr 2020 00:50:53: #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 00:50:53: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:50:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:50:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:51:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:51:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:51:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592478/SRX2592478.20_summits.bed INFO @ Thu, 16 Apr 2020 00:51:00: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (549 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。