Job ID = 5720591 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,858,510 reads read : 8,858,510 reads written : 8,858,510 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289720.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: 00:02:16 8858510 reads; of these: 8858510 (100.00%) were unpaired; of these: 2408070 (27.18%) aligned 0 times 4948587 (55.86%) aligned exactly 1 time 1501853 (16.95%) aligned >1 times 72.82% overall alignment rate Time searching: 00:02:16 Overall time: 00:02:16 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] 556447 / 6450440 = 0.0863 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 00:45:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.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 00:45:15: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:45:15: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:45:22: 1000000 INFO @ Thu, 16 Apr 2020 00:45:28: 2000000 INFO @ Thu, 16 Apr 2020 00:45:36: 3000000 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 00:45:43: 4000000 INFO @ Thu, 16 Apr 2020 00:45:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.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 00:45:45: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:45:45: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:45:50: 5000000 INFO @ Thu, 16 Apr 2020 00:45:52: 1000000 INFO @ Thu, 16 Apr 2020 00:45:57: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:45:57: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:45:57: #1 total tags in treatment: 5893993 INFO @ Thu, 16 Apr 2020 00:45:57: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:45:57: #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 00:45:57: #1 tags after filtering in treatment: 5893993 INFO @ Thu, 16 Apr 2020 00:45:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:45:57: #1 finished! INFO @ Thu, 16 Apr 2020 00:45:57: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:45:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:45:57: #2 number of paired peaks: 408 WARNING @ Thu, 16 Apr 2020 00:45:57: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Thu, 16 Apr 2020 00:45:57: start model_add_line... INFO @ Thu, 16 Apr 2020 00:45:58: start X-correlation... INFO @ Thu, 16 Apr 2020 00:45:58: end of X-cor INFO @ Thu, 16 Apr 2020 00:45:58: #2 finished! INFO @ Thu, 16 Apr 2020 00:45:58: #2 predicted fragment length is 52 bps INFO @ Thu, 16 Apr 2020 00:45:58: #2 alternative fragment length(s) may be 52 bps INFO @ Thu, 16 Apr 2020 00:45:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.05_model.r WARNING @ Thu, 16 Apr 2020 00:45:58: #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 00:45:58: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Thu, 16 Apr 2020 00:45:58: #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 00:45:58: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:45:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:45:59: 2000000 INFO @ Thu, 16 Apr 2020 00:46:06: 3000000 INFO @ Thu, 16 Apr 2020 00:46:10: #3 Call peaks for each chromosome... 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 00:46:12: 4000000 INFO @ Thu, 16 Apr 2020 00:46:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.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 00:46:15: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:46:15: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:46:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:46:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:46:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.05_summits.bed INFO @ Thu, 16 Apr 2020 00:46:16: Done! INFO @ Thu, 16 Apr 2020 00:46:19: 5000000 pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1380 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:46:23: 1000000 INFO @ Thu, 16 Apr 2020 00:46:26: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:46:26: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:46:26: #1 total tags in treatment: 5893993 INFO @ Thu, 16 Apr 2020 00:46:26: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:46:26: #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 00:46:26: #1 tags after filtering in treatment: 5893993 INFO @ Thu, 16 Apr 2020 00:46:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:46:26: #1 finished! INFO @ Thu, 16 Apr 2020 00:46:26: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:46:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:46:26: #2 number of paired peaks: 408 WARNING @ Thu, 16 Apr 2020 00:46:26: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Thu, 16 Apr 2020 00:46:26: start model_add_line... INFO @ Thu, 16 Apr 2020 00:46:26: start X-correlation... INFO @ Thu, 16 Apr 2020 00:46:26: end of X-cor INFO @ Thu, 16 Apr 2020 00:46:26: #2 finished! INFO @ Thu, 16 Apr 2020 00:46:26: #2 predicted fragment length is 52 bps INFO @ Thu, 16 Apr 2020 00:46:26: #2 alternative fragment length(s) may be 52 bps INFO @ Thu, 16 Apr 2020 00:46:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.10_model.r WARNING @ Thu, 16 Apr 2020 00:46:26: #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 00:46:26: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Thu, 16 Apr 2020 00:46:26: #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 00:46:26: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:46:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:46:30: 2000000 INFO @ Thu, 16 Apr 2020 00:46:38: 3000000 INFO @ Thu, 16 Apr 2020 00:46:38: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:46:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:46:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:46:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.10_summits.bed INFO @ Thu, 16 Apr 2020 00:46:45: Done! INFO @ Thu, 16 Apr 2020 00:46:45: 4000000 pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (881 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:46:52: 5000000 INFO @ Thu, 16 Apr 2020 00:46:58: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:46:58: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:46:58: #1 total tags in treatment: 5893993 INFO @ Thu, 16 Apr 2020 00:46:58: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:46:58: #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 00:46:59: #1 tags after filtering in treatment: 5893993 INFO @ Thu, 16 Apr 2020 00:46:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:46:59: #1 finished! INFO @ Thu, 16 Apr 2020 00:46:59: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:46:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:46:59: #2 number of paired peaks: 408 WARNING @ Thu, 16 Apr 2020 00:46:59: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Thu, 16 Apr 2020 00:46:59: start model_add_line... INFO @ Thu, 16 Apr 2020 00:46:59: start X-correlation... INFO @ Thu, 16 Apr 2020 00:46:59: end of X-cor INFO @ Thu, 16 Apr 2020 00:46:59: #2 finished! INFO @ Thu, 16 Apr 2020 00:46:59: #2 predicted fragment length is 52 bps INFO @ Thu, 16 Apr 2020 00:46:59: #2 alternative fragment length(s) may be 52 bps INFO @ Thu, 16 Apr 2020 00:46:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.20_model.r WARNING @ Thu, 16 Apr 2020 00:46:59: #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 00:46:59: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Thu, 16 Apr 2020 00:46:59: #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 00:46:59: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:46:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:47:11: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:47:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:47:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:47:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592443/SRX2592443.20_summits.bed INFO @ Thu, 16 Apr 2020 00:47:17: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (578 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。