Job ID = 5720601 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,994,586 reads read : 7,994,586 reads written : 7,994,586 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289724.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: 00:02:01 7994586 reads; of these: 7994586 (100.00%) were unpaired; of these: 3903095 (48.82%) aligned 0 times 2947244 (36.87%) aligned exactly 1 time 1144247 (14.31%) aligned >1 times 51.18% overall alignment rate Time searching: 00:02:01 Overall time: 00:02:01 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] 2515256 / 4091491 = 0.6148 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 00:44:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.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 00:44:11: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:44:11: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:44:18: 1000000 INFO @ Thu, 16 Apr 2020 00:44:21: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:44:21: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:44:21: #1 total tags in treatment: 1576235 INFO @ Thu, 16 Apr 2020 00:44:21: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:44:21: #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 00:44:21: #1 tags after filtering in treatment: 1576235 INFO @ Thu, 16 Apr 2020 00:44:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:44:21: #1 finished! INFO @ Thu, 16 Apr 2020 00:44:21: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:44:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:44:21: #2 number of paired peaks: 498 WARNING @ Thu, 16 Apr 2020 00:44:21: Fewer paired peaks (498) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 498 pairs to build model! INFO @ Thu, 16 Apr 2020 00:44:21: start model_add_line... INFO @ Thu, 16 Apr 2020 00:44:21: start X-correlation... INFO @ Thu, 16 Apr 2020 00:44:21: end of X-cor INFO @ Thu, 16 Apr 2020 00:44:21: #2 finished! INFO @ Thu, 16 Apr 2020 00:44:21: #2 predicted fragment length is 58 bps INFO @ Thu, 16 Apr 2020 00:44:21: #2 alternative fragment length(s) may be 58 bps INFO @ Thu, 16 Apr 2020 00:44:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.05_model.r WARNING @ Thu, 16 Apr 2020 00:44:21: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:44:21: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Thu, 16 Apr 2020 00:44:21: #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 00:44:21: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:44:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:44:25: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:44:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:44:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:44:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.05_summits.bed INFO @ Thu, 16 Apr 2020 00:44:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6719 records, 4 fields): 7 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 00:44:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.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 00:44:41: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:44:41: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:44:47: 1000000 INFO @ Thu, 16 Apr 2020 00:44:50: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:44:50: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:44:50: #1 total tags in treatment: 1576235 INFO @ Thu, 16 Apr 2020 00:44:50: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:44:50: #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 00:44:50: #1 tags after filtering in treatment: 1576235 INFO @ Thu, 16 Apr 2020 00:44:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:44:50: #1 finished! INFO @ Thu, 16 Apr 2020 00:44:50: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:44:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:44:50: #2 number of paired peaks: 498 WARNING @ Thu, 16 Apr 2020 00:44:50: Fewer paired peaks (498) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 498 pairs to build model! INFO @ Thu, 16 Apr 2020 00:44:50: start model_add_line... INFO @ Thu, 16 Apr 2020 00:44:50: start X-correlation... INFO @ Thu, 16 Apr 2020 00:44:50: end of X-cor INFO @ Thu, 16 Apr 2020 00:44:50: #2 finished! INFO @ Thu, 16 Apr 2020 00:44:50: #2 predicted fragment length is 58 bps INFO @ Thu, 16 Apr 2020 00:44:50: #2 alternative fragment length(s) may be 58 bps INFO @ Thu, 16 Apr 2020 00:44:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.10_model.r WARNING @ Thu, 16 Apr 2020 00:44:50: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:44:50: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Thu, 16 Apr 2020 00:44:50: #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 00:44:50: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:44:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:44:54: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:44:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:44:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:44:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.10_summits.bed INFO @ Thu, 16 Apr 2020 00:44:55: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2277 records, 4 fields): 4 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 00:45:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.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 00:45:11: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:45:11: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:45:17: 1000000 INFO @ Thu, 16 Apr 2020 00:45:20: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:45:20: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:45:20: #1 total tags in treatment: 1576235 INFO @ Thu, 16 Apr 2020 00:45:20: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:45:20: #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 00:45:20: #1 tags after filtering in treatment: 1576235 INFO @ Thu, 16 Apr 2020 00:45:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:45:20: #1 finished! INFO @ Thu, 16 Apr 2020 00:45:20: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:45:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:45:20: #2 number of paired peaks: 498 WARNING @ Thu, 16 Apr 2020 00:45:20: Fewer paired peaks (498) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 498 pairs to build model! INFO @ Thu, 16 Apr 2020 00:45:20: start model_add_line... INFO @ Thu, 16 Apr 2020 00:45:20: start X-correlation... INFO @ Thu, 16 Apr 2020 00:45:20: end of X-cor INFO @ Thu, 16 Apr 2020 00:45:20: #2 finished! INFO @ Thu, 16 Apr 2020 00:45:20: #2 predicted fragment length is 58 bps INFO @ Thu, 16 Apr 2020 00:45:20: #2 alternative fragment length(s) may be 58 bps INFO @ Thu, 16 Apr 2020 00:45:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.20_model.r WARNING @ Thu, 16 Apr 2020 00:45:20: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:45:20: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Thu, 16 Apr 2020 00:45:20: #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 00:45:20: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:45:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:45:24: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:45:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:45:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:45:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592447/SRX2592447.20_summits.bed INFO @ Thu, 16 Apr 2020 00:45:26: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (375 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。