Job ID = 5720706 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 863,470 reads read : 863,470 reads written : 863,470 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:19 863470 reads; of these: 863470 (100.00%) were unpaired; of these: 43919 (5.09%) aligned 0 times 530961 (61.49%) aligned exactly 1 time 288590 (33.42%) aligned >1 times 94.91% overall alignment rate Time searching: 00:00:19 Overall time: 00:00:19 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] 14649 / 819551 = 0.0179 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 00:59:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.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 00:59:06: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:59:06: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:59:11: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 00:59:11: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 00:59:11: #1 total tags in treatment: 804902 INFO @ Thu, 16 Apr 2020 00:59:11: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:59:11: #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 00:59:11: #1 tags after filtering in treatment: 804902 INFO @ Thu, 16 Apr 2020 00:59:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:59:11: #1 finished! INFO @ Thu, 16 Apr 2020 00:59:11: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:59:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:59:11: #2 number of paired peaks: 1120 INFO @ Thu, 16 Apr 2020 00:59:11: start model_add_line... INFO @ Thu, 16 Apr 2020 00:59:11: start X-correlation... INFO @ Thu, 16 Apr 2020 00:59:11: end of X-cor INFO @ Thu, 16 Apr 2020 00:59:11: #2 finished! INFO @ Thu, 16 Apr 2020 00:59:11: #2 predicted fragment length is 72 bps INFO @ Thu, 16 Apr 2020 00:59:11: #2 alternative fragment length(s) may be 72 bps INFO @ Thu, 16 Apr 2020 00:59:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.05_model.r WARNING @ Thu, 16 Apr 2020 00:59:11: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:59:11: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Thu, 16 Apr 2020 00:59:11: #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 00:59:11: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:59:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:59:13: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:59:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:59:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:59:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.05_summits.bed INFO @ Thu, 16 Apr 2020 00:59:14: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (435 records, 4 fields): 2 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 00:59:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.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 00:59:36: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:59:36: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:59:40: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 00:59:40: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 00:59:40: #1 total tags in treatment: 804902 INFO @ Thu, 16 Apr 2020 00:59:40: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:59:40: #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 00:59:40: #1 tags after filtering in treatment: 804902 INFO @ Thu, 16 Apr 2020 00:59:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:59:40: #1 finished! INFO @ Thu, 16 Apr 2020 00:59:40: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:59:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:59:40: #2 number of paired peaks: 1120 INFO @ Thu, 16 Apr 2020 00:59:40: start model_add_line... INFO @ Thu, 16 Apr 2020 00:59:40: start X-correlation... INFO @ Thu, 16 Apr 2020 00:59:40: end of X-cor INFO @ Thu, 16 Apr 2020 00:59:40: #2 finished! INFO @ Thu, 16 Apr 2020 00:59:40: #2 predicted fragment length is 72 bps INFO @ Thu, 16 Apr 2020 00:59:40: #2 alternative fragment length(s) may be 72 bps INFO @ Thu, 16 Apr 2020 00:59:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.10_model.r WARNING @ Thu, 16 Apr 2020 00:59:40: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:59:40: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Thu, 16 Apr 2020 00:59:40: #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 00:59:40: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:59:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:59:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:59:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:59:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:59:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.10_summits.bed INFO @ Thu, 16 Apr 2020 00:59:43: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (188 records, 4 fields): 1 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 01:00:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.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 01:00:06: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:00:06: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:00:11: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:00:11: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:00:11: #1 total tags in treatment: 804902 INFO @ Thu, 16 Apr 2020 01:00:11: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:00:11: #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 01:00:11: #1 tags after filtering in treatment: 804902 INFO @ Thu, 16 Apr 2020 01:00:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:00:11: #1 finished! INFO @ Thu, 16 Apr 2020 01:00:11: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:00:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:00:11: #2 number of paired peaks: 1120 INFO @ Thu, 16 Apr 2020 01:00:11: start model_add_line... INFO @ Thu, 16 Apr 2020 01:00:11: start X-correlation... INFO @ Thu, 16 Apr 2020 01:00:11: end of X-cor INFO @ Thu, 16 Apr 2020 01:00:11: #2 finished! INFO @ Thu, 16 Apr 2020 01:00:11: #2 predicted fragment length is 72 bps INFO @ Thu, 16 Apr 2020 01:00:11: #2 alternative fragment length(s) may be 72 bps INFO @ Thu, 16 Apr 2020 01:00:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.20_model.r WARNING @ Thu, 16 Apr 2020 01:00:11: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:00:11: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Thu, 16 Apr 2020 01:00:11: #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 01:00:11: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:00:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:00:13: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 01:00:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:00:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:00:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158170/SRX4158170.20_summits.bed INFO @ Thu, 16 Apr 2020 01:00:14: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (91 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。