Job ID = 5720664 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,590,153 reads read : 6,590,153 reads written : 6,590,153 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289760.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: 00:01:46 6590153 reads; of these: 6590153 (100.00%) were unpaired; of these: 2637684 (40.02%) aligned 0 times 2888236 (43.83%) aligned exactly 1 time 1064233 (16.15%) aligned >1 times 59.98% overall alignment rate Time searching: 00:01:47 Overall time: 00:01:47 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] 295174 / 3952469 = 0.0747 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 00:53:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.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 00:53:00: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:53:00: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:53:06: 1000000 INFO @ Thu, 16 Apr 2020 00:53:13: 2000000 INFO @ Thu, 16 Apr 2020 00:53:18: 3000000 INFO @ Thu, 16 Apr 2020 00:53:22: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:53:22: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:53:22: #1 total tags in treatment: 3657295 INFO @ Thu, 16 Apr 2020 00:53:22: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:53:22: #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 00:53:22: #1 tags after filtering in treatment: 3657295 INFO @ Thu, 16 Apr 2020 00:53:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:53:22: #1 finished! INFO @ Thu, 16 Apr 2020 00:53:22: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:53:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:53:22: #2 number of paired peaks: 356 WARNING @ Thu, 16 Apr 2020 00:53:22: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Thu, 16 Apr 2020 00:53:22: start model_add_line... INFO @ Thu, 16 Apr 2020 00:53:22: start X-correlation... INFO @ Thu, 16 Apr 2020 00:53:23: end of X-cor INFO @ Thu, 16 Apr 2020 00:53:23: #2 finished! INFO @ Thu, 16 Apr 2020 00:53:23: #2 predicted fragment length is 52 bps INFO @ Thu, 16 Apr 2020 00:53:23: #2 alternative fragment length(s) may be 52 bps INFO @ Thu, 16 Apr 2020 00:53:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.05_model.r WARNING @ Thu, 16 Apr 2020 00:53:23: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:53:23: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Thu, 16 Apr 2020 00:53:23: #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 00:53:23: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:53:23: #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 00:53:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.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 00:53:28: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:53:28: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:53:30: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:53:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:53:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:53:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.05_summits.bed INFO @ Thu, 16 Apr 2020 00:53:34: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (947 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:53:35: 1000000 INFO @ Thu, 16 Apr 2020 00:53:41: 2000000 INFO @ Thu, 16 Apr 2020 00:53:47: 3000000 INFO @ Thu, 16 Apr 2020 00:53:51: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:53:51: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:53:51: #1 total tags in treatment: 3657295 INFO @ Thu, 16 Apr 2020 00:53:51: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:53:51: #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 00:53:51: #1 tags after filtering in treatment: 3657295 INFO @ Thu, 16 Apr 2020 00:53:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:53:51: #1 finished! INFO @ Thu, 16 Apr 2020 00:53:51: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:53:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:53:51: #2 number of paired peaks: 356 WARNING @ Thu, 16 Apr 2020 00:53:51: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Thu, 16 Apr 2020 00:53:51: start model_add_line... INFO @ Thu, 16 Apr 2020 00:53:51: start X-correlation... INFO @ Thu, 16 Apr 2020 00:53:51: end of X-cor INFO @ Thu, 16 Apr 2020 00:53:51: #2 finished! INFO @ Thu, 16 Apr 2020 00:53:51: #2 predicted fragment length is 52 bps INFO @ Thu, 16 Apr 2020 00:53:51: #2 alternative fragment length(s) may be 52 bps INFO @ Thu, 16 Apr 2020 00:53:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.10_model.r WARNING @ Thu, 16 Apr 2020 00:53:51: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:53:51: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Thu, 16 Apr 2020 00:53:51: #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 00:53:51: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:53:51: #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 00:53:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.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 00:53:58: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:53:58: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:53:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:54:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:54:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:54:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.10_summits.bed INFO @ Thu, 16 Apr 2020 00:54:03: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (645 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:54:05: 1000000 INFO @ Thu, 16 Apr 2020 00:54:12: 2000000 INFO @ Thu, 16 Apr 2020 00:54:19: 3000000 INFO @ Thu, 16 Apr 2020 00:54:24: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:54:24: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:54:24: #1 total tags in treatment: 3657295 INFO @ Thu, 16 Apr 2020 00:54:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:54:24: #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 00:54:24: #1 tags after filtering in treatment: 3657295 INFO @ Thu, 16 Apr 2020 00:54:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:54:24: #1 finished! INFO @ Thu, 16 Apr 2020 00:54:24: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:54:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:54:24: #2 number of paired peaks: 356 WARNING @ Thu, 16 Apr 2020 00:54:24: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Thu, 16 Apr 2020 00:54:24: start model_add_line... INFO @ Thu, 16 Apr 2020 00:54:24: start X-correlation... INFO @ Thu, 16 Apr 2020 00:54:24: end of X-cor INFO @ Thu, 16 Apr 2020 00:54:24: #2 finished! INFO @ Thu, 16 Apr 2020 00:54:24: #2 predicted fragment length is 52 bps INFO @ Thu, 16 Apr 2020 00:54:24: #2 alternative fragment length(s) may be 52 bps INFO @ Thu, 16 Apr 2020 00:54:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.20_model.r WARNING @ Thu, 16 Apr 2020 00:54:24: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:54:24: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Thu, 16 Apr 2020 00:54:24: #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 00:54:24: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:54:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:54:31: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:54:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:54:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:54:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592483/SRX2592483.20_summits.bed INFO @ Thu, 16 Apr 2020 00:54:36: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (324 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。