Job ID = 5720393 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,383,071 reads read : 2,383,071 reads written : 2,383,071 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289665.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: 00:00:49 2383071 reads; of these: 2383071 (100.00%) were unpaired; of these: 161601 (6.78%) aligned 0 times 1792032 (75.20%) aligned exactly 1 time 429438 (18.02%) aligned >1 times 93.22% overall alignment rate Time searching: 00:00:49 Overall time: 00:00:49 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] 230924 / 2221470 = 0.1040 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 00:19:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.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 00:19:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:19:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:19:19: 1000000 INFO @ Thu, 16 Apr 2020 00:19:24: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:19:24: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:19:24: #1 total tags in treatment: 1990546 INFO @ Thu, 16 Apr 2020 00:19:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:19:24: #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 00:19:24: #1 tags after filtering in treatment: 1990546 INFO @ Thu, 16 Apr 2020 00:19:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:19:24: #1 finished! INFO @ Thu, 16 Apr 2020 00:19:24: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:19:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:19:25: #2 number of paired peaks: 1019 INFO @ Thu, 16 Apr 2020 00:19:25: start model_add_line... INFO @ Thu, 16 Apr 2020 00:19:25: start X-correlation... INFO @ Thu, 16 Apr 2020 00:19:25: end of X-cor INFO @ Thu, 16 Apr 2020 00:19:25: #2 finished! INFO @ Thu, 16 Apr 2020 00:19:25: #2 predicted fragment length is 94 bps INFO @ Thu, 16 Apr 2020 00:19:25: #2 alternative fragment length(s) may be 94 bps INFO @ Thu, 16 Apr 2020 00:19:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.05_model.r WARNING @ Thu, 16 Apr 2020 00:19:25: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:19:25: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Thu, 16 Apr 2020 00:19:25: #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 00:19:25: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:19:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:19:29: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:19:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:19:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:19:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.05_summits.bed INFO @ Thu, 16 Apr 2020 00:19:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2446 records, 4 fields): 3 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 00:19:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.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 00:19:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:19:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:19:48: 1000000 INFO @ Thu, 16 Apr 2020 00:19:54: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:19:54: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:19:54: #1 total tags in treatment: 1990546 INFO @ Thu, 16 Apr 2020 00:19:54: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:19:54: #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 00:19:54: #1 tags after filtering in treatment: 1990546 INFO @ Thu, 16 Apr 2020 00:19:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:19:54: #1 finished! INFO @ Thu, 16 Apr 2020 00:19:54: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:19:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:19:54: #2 number of paired peaks: 1019 INFO @ Thu, 16 Apr 2020 00:19:54: start model_add_line... INFO @ Thu, 16 Apr 2020 00:19:54: start X-correlation... INFO @ Thu, 16 Apr 2020 00:19:54: end of X-cor INFO @ Thu, 16 Apr 2020 00:19:54: #2 finished! INFO @ Thu, 16 Apr 2020 00:19:54: #2 predicted fragment length is 94 bps INFO @ Thu, 16 Apr 2020 00:19:54: #2 alternative fragment length(s) may be 94 bps INFO @ Thu, 16 Apr 2020 00:19:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.10_model.r WARNING @ Thu, 16 Apr 2020 00:19:54: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:19:54: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Thu, 16 Apr 2020 00:19:54: #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 00:19:54: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:19:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:19:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:20:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:20:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:20:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.10_summits.bed INFO @ Thu, 16 Apr 2020 00:20:01: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1124 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 00:20:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.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 00:20:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:20:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:20:18: 1000000 INFO @ Thu, 16 Apr 2020 00:20:24: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:20:24: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:20:24: #1 total tags in treatment: 1990546 INFO @ Thu, 16 Apr 2020 00:20:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:20:24: #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 00:20:24: #1 tags after filtering in treatment: 1990546 INFO @ Thu, 16 Apr 2020 00:20:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:20:24: #1 finished! INFO @ Thu, 16 Apr 2020 00:20:24: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:20:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:20:24: #2 number of paired peaks: 1019 INFO @ Thu, 16 Apr 2020 00:20:24: start model_add_line... INFO @ Thu, 16 Apr 2020 00:20:24: start X-correlation... INFO @ Thu, 16 Apr 2020 00:20:24: end of X-cor INFO @ Thu, 16 Apr 2020 00:20:24: #2 finished! INFO @ Thu, 16 Apr 2020 00:20:24: #2 predicted fragment length is 94 bps INFO @ Thu, 16 Apr 2020 00:20:24: #2 alternative fragment length(s) may be 94 bps INFO @ Thu, 16 Apr 2020 00:20:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.20_model.r WARNING @ Thu, 16 Apr 2020 00:20:24: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:20:24: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Thu, 16 Apr 2020 00:20:24: #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 00:20:24: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:20:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:20:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:20:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:20:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:20:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592388/SRX2592388.20_summits.bed INFO @ Thu, 16 Apr 2020 00:20:30: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (370 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。