Job ID = 5720560 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,417,050 reads read : 8,417,050 reads written : 8,417,050 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289704.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: 00:02:26 8417050 reads; of these: 8417050 (100.00%) were unpaired; of these: 655424 (7.79%) aligned 0 times 6237111 (74.10%) aligned exactly 1 time 1524515 (18.11%) aligned >1 times 92.21% overall alignment rate Time searching: 00:02:26 Overall time: 00:02:26 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] 2033889 / 7761626 = 0.2620 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 00:36:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.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 00:36:06: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:36:06: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:36:13: 1000000 INFO @ Thu, 16 Apr 2020 00:36:20: 2000000 INFO @ Thu, 16 Apr 2020 00:36:26: 3000000 INFO @ Thu, 16 Apr 2020 00:36:33: 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 @ Thu, 16 Apr 2020 00:36:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.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 00:36:36: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:36:36: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:36:40: 5000000 INFO @ Thu, 16 Apr 2020 00:36:43: 1000000 INFO @ Thu, 16 Apr 2020 00:36:45: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:36:45: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:36:45: #1 total tags in treatment: 5727737 INFO @ Thu, 16 Apr 2020 00:36:45: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:36:45: #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 00:36:45: #1 tags after filtering in treatment: 5727737 INFO @ Thu, 16 Apr 2020 00:36:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:36:45: #1 finished! INFO @ Thu, 16 Apr 2020 00:36:45: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:36:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:36:46: #2 number of paired peaks: 175 WARNING @ Thu, 16 Apr 2020 00:36:46: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Thu, 16 Apr 2020 00:36:46: start model_add_line... INFO @ Thu, 16 Apr 2020 00:36:46: start X-correlation... INFO @ Thu, 16 Apr 2020 00:36:46: end of X-cor INFO @ Thu, 16 Apr 2020 00:36:46: #2 finished! INFO @ Thu, 16 Apr 2020 00:36:46: #2 predicted fragment length is 84 bps INFO @ Thu, 16 Apr 2020 00:36:46: #2 alternative fragment length(s) may be 84 bps INFO @ Thu, 16 Apr 2020 00:36:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.05_model.r WARNING @ Thu, 16 Apr 2020 00:36:46: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:36:46: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Thu, 16 Apr 2020 00:36:46: #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 00:36:46: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:36:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:36:50: 2000000 INFO @ Thu, 16 Apr 2020 00:36:55: 3000000 INFO @ Thu, 16 Apr 2020 00:36:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:37:01: 4000000 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 00:37:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:37:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:37:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.05_summits.bed INFO @ Thu, 16 Apr 2020 00:37:05: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (13778 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:37:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.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 00:37:06: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:37:06: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:37:07: 5000000 INFO @ Thu, 16 Apr 2020 00:37:12: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:37:12: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:37:12: #1 total tags in treatment: 5727737 INFO @ Thu, 16 Apr 2020 00:37:12: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:37:12: #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 00:37:12: #1 tags after filtering in treatment: 5727737 INFO @ Thu, 16 Apr 2020 00:37:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:37:12: #1 finished! INFO @ Thu, 16 Apr 2020 00:37:12: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:37:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:37:13: #2 number of paired peaks: 175 WARNING @ Thu, 16 Apr 2020 00:37:13: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Thu, 16 Apr 2020 00:37:13: start model_add_line... INFO @ Thu, 16 Apr 2020 00:37:13: start X-correlation... INFO @ Thu, 16 Apr 2020 00:37:13: end of X-cor INFO @ Thu, 16 Apr 2020 00:37:13: #2 finished! INFO @ Thu, 16 Apr 2020 00:37:13: #2 predicted fragment length is 84 bps INFO @ Thu, 16 Apr 2020 00:37:13: #2 alternative fragment length(s) may be 84 bps INFO @ Thu, 16 Apr 2020 00:37:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.10_model.r WARNING @ Thu, 16 Apr 2020 00:37:13: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:37:13: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Thu, 16 Apr 2020 00:37:13: #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 00:37:13: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:37:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:37:13: 1000000 INFO @ Thu, 16 Apr 2020 00:37:20: 2000000 INFO @ Thu, 16 Apr 2020 00:37:26: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:37:27: 3000000 INFO @ Thu, 16 Apr 2020 00:37:33: 4000000 INFO @ Thu, 16 Apr 2020 00:37:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:37:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:37:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.10_summits.bed INFO @ Thu, 16 Apr 2020 00:37:33: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (10068 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:37:40: 5000000 INFO @ Thu, 16 Apr 2020 00:37:44: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:37:44: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:37:44: #1 total tags in treatment: 5727737 INFO @ Thu, 16 Apr 2020 00:37:44: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:37:44: #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 00:37:45: #1 tags after filtering in treatment: 5727737 INFO @ Thu, 16 Apr 2020 00:37:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:37:45: #1 finished! INFO @ Thu, 16 Apr 2020 00:37:45: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:37:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:37:45: #2 number of paired peaks: 175 WARNING @ Thu, 16 Apr 2020 00:37:45: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Thu, 16 Apr 2020 00:37:45: start model_add_line... INFO @ Thu, 16 Apr 2020 00:37:45: start X-correlation... INFO @ Thu, 16 Apr 2020 00:37:45: end of X-cor INFO @ Thu, 16 Apr 2020 00:37:45: #2 finished! INFO @ Thu, 16 Apr 2020 00:37:45: #2 predicted fragment length is 84 bps INFO @ Thu, 16 Apr 2020 00:37:45: #2 alternative fragment length(s) may be 84 bps INFO @ Thu, 16 Apr 2020 00:37:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.20_model.r WARNING @ Thu, 16 Apr 2020 00:37:45: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:37:45: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Thu, 16 Apr 2020 00:37:45: #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 00:37:45: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:37:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:37:57: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:38:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:38:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:38:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592427/SRX2592427.20_summits.bed INFO @ Thu, 16 Apr 2020 00:38:04: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5903 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。