Job ID = 5720808 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 14,947,345 reads read : 29,894,690 reads written : 29,894,690 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: 00:14:08 14947345 reads; of these: 14947345 (100.00%) were paired; of these: 9514635 (63.65%) aligned concordantly 0 times 4318184 (28.89%) aligned concordantly exactly 1 time 1114526 (7.46%) aligned concordantly >1 times ---- 9514635 pairs aligned concordantly 0 times; of these: 20703 (0.22%) aligned discordantly 1 time ---- 9493932 pairs aligned 0 times concordantly or discordantly; of these: 18987864 mates make up the pairs; of these: 18427691 (97.05%) aligned 0 times 172762 (0.91%) aligned exactly 1 time 387411 (2.04%) aligned >1 times 38.36% overall alignment rate Time searching: 00:14:08 Overall time: 00:14:08 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_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2372339 / 5435013 = 0.4365 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 02:02:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.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 02:02:04: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:02:04: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:02:11: 1000000 INFO @ Thu, 16 Apr 2020 02:02:18: 2000000 INFO @ Thu, 16 Apr 2020 02:02:24: 3000000 INFO @ Thu, 16 Apr 2020 02:02:31: 4000000 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 02:02:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.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 02:02:34: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:02:34: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:02:38: 5000000 INFO @ Thu, 16 Apr 2020 02:02:41: 1000000 INFO @ Thu, 16 Apr 2020 02:02:45: 6000000 INFO @ Thu, 16 Apr 2020 02:02:48: 2000000 INFO @ Thu, 16 Apr 2020 02:02:50: #1 tag size is determined as 77 bps INFO @ Thu, 16 Apr 2020 02:02:50: #1 tag size = 77 INFO @ Thu, 16 Apr 2020 02:02:50: #1 total tags in treatment: 3063310 INFO @ Thu, 16 Apr 2020 02:02:50: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:02:50: #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 02:02:50: #1 tags after filtering in treatment: 3009097 INFO @ Thu, 16 Apr 2020 02:02:50: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 16 Apr 2020 02:02:50: #1 finished! INFO @ Thu, 16 Apr 2020 02:02:50: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:02:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:02:51: #2 number of paired peaks: 357 WARNING @ Thu, 16 Apr 2020 02:02:51: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Thu, 16 Apr 2020 02:02:51: start model_add_line... INFO @ Thu, 16 Apr 2020 02:02:51: start X-correlation... INFO @ Thu, 16 Apr 2020 02:02:51: end of X-cor INFO @ Thu, 16 Apr 2020 02:02:51: #2 finished! INFO @ Thu, 16 Apr 2020 02:02:51: #2 predicted fragment length is 132 bps INFO @ Thu, 16 Apr 2020 02:02:51: #2 alternative fragment length(s) may be 132 bps INFO @ Thu, 16 Apr 2020 02:02:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.05_model.r WARNING @ Thu, 16 Apr 2020 02:02:51: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:02:51: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Thu, 16 Apr 2020 02:02:51: #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 02:02:51: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:02:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:02:54: 3000000 INFO @ Thu, 16 Apr 2020 02:02:57: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:03:00: 4000000 INFO @ Thu, 16 Apr 2020 02:03:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:03:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:03:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.05_summits.bed INFO @ Thu, 16 Apr 2020 02:03:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (322 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 02:03:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.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 02:03:04: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:03:04: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:03:05: 5000000 INFO @ Thu, 16 Apr 2020 02:03:10: 1000000 INFO @ Thu, 16 Apr 2020 02:03:11: 6000000 INFO @ Thu, 16 Apr 2020 02:03:15: #1 tag size is determined as 77 bps INFO @ Thu, 16 Apr 2020 02:03:15: #1 tag size = 77 INFO @ Thu, 16 Apr 2020 02:03:15: #1 total tags in treatment: 3063310 INFO @ Thu, 16 Apr 2020 02:03:15: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:03:15: #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 02:03:15: #1 tags after filtering in treatment: 3009097 INFO @ Thu, 16 Apr 2020 02:03:15: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 16 Apr 2020 02:03:15: #1 finished! INFO @ Thu, 16 Apr 2020 02:03:15: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:03:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:03:15: #2 number of paired peaks: 357 WARNING @ Thu, 16 Apr 2020 02:03:15: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Thu, 16 Apr 2020 02:03:15: start model_add_line... INFO @ Thu, 16 Apr 2020 02:03:16: start X-correlation... INFO @ Thu, 16 Apr 2020 02:03:16: end of X-cor INFO @ Thu, 16 Apr 2020 02:03:16: #2 finished! INFO @ Thu, 16 Apr 2020 02:03:16: #2 predicted fragment length is 132 bps INFO @ Thu, 16 Apr 2020 02:03:16: #2 alternative fragment length(s) may be 132 bps INFO @ Thu, 16 Apr 2020 02:03:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.10_model.r WARNING @ Thu, 16 Apr 2020 02:03:16: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:03:16: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Thu, 16 Apr 2020 02:03:16: #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 02:03:16: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:03:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:03:16: 2000000 INFO @ Thu, 16 Apr 2020 02:03:22: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:03:22: 3000000 INFO @ Thu, 16 Apr 2020 02:03:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:03:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:03:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.10_summits.bed INFO @ Thu, 16 Apr 2020 02:03:25: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (135 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:03:27: 4000000 INFO @ Thu, 16 Apr 2020 02:03:32: 5000000 INFO @ Thu, 16 Apr 2020 02:03:38: 6000000 INFO @ Thu, 16 Apr 2020 02:03:42: #1 tag size is determined as 77 bps INFO @ Thu, 16 Apr 2020 02:03:42: #1 tag size = 77 INFO @ Thu, 16 Apr 2020 02:03:42: #1 total tags in treatment: 3063310 INFO @ Thu, 16 Apr 2020 02:03:42: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:03:42: #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 02:03:42: #1 tags after filtering in treatment: 3009097 INFO @ Thu, 16 Apr 2020 02:03:42: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 16 Apr 2020 02:03:42: #1 finished! INFO @ Thu, 16 Apr 2020 02:03:42: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:03:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:03:42: #2 number of paired peaks: 357 WARNING @ Thu, 16 Apr 2020 02:03:42: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Thu, 16 Apr 2020 02:03:42: start model_add_line... INFO @ Thu, 16 Apr 2020 02:03:42: start X-correlation... INFO @ Thu, 16 Apr 2020 02:03:42: end of X-cor INFO @ Thu, 16 Apr 2020 02:03:42: #2 finished! INFO @ Thu, 16 Apr 2020 02:03:42: #2 predicted fragment length is 132 bps INFO @ Thu, 16 Apr 2020 02:03:42: #2 alternative fragment length(s) may be 132 bps INFO @ Thu, 16 Apr 2020 02:03:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.20_model.r WARNING @ Thu, 16 Apr 2020 02:03:42: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:03:42: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Thu, 16 Apr 2020 02:03:42: #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 02:03:42: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:03:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:03:48: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:03:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:03:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:03:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5309720/SRX5309720.20_summits.bed INFO @ Thu, 16 Apr 2020 02:03:51: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (59 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。