Job ID = 5720811 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,262,279 reads read : 26,524,558 reads written : 26,524,558 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: 00:17:03 13262279 reads; of these: 13262279 (100.00%) were paired; of these: 6297922 (47.49%) aligned concordantly 0 times 5594159 (42.18%) aligned concordantly exactly 1 time 1370198 (10.33%) aligned concordantly >1 times ---- 6297922 pairs aligned concordantly 0 times; of these: 14185 (0.23%) aligned discordantly 1 time ---- 6283737 pairs aligned 0 times concordantly or discordantly; of these: 12567474 mates make up the pairs; of these: 12072349 (96.06%) aligned 0 times 203409 (1.62%) aligned exactly 1 time 291716 (2.32%) aligned >1 times 54.49% overall alignment rate Time searching: 00:17:03 Overall time: 00:17:03 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] 2654531 / 6968867 = 0.3809 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 02:05:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.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 02:05:14: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:05:14: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:05:20: 1000000 INFO @ Thu, 16 Apr 2020 02:05:26: 2000000 INFO @ Thu, 16 Apr 2020 02:05:33: 3000000 INFO @ Thu, 16 Apr 2020 02:05:40: 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 02:05:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.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 02:05:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:05:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:05:46: 5000000 INFO @ Thu, 16 Apr 2020 02:05:50: 1000000 INFO @ Thu, 16 Apr 2020 02:05:53: 6000000 INFO @ Thu, 16 Apr 2020 02:05:58: 2000000 INFO @ Thu, 16 Apr 2020 02:05:59: 7000000 INFO @ Thu, 16 Apr 2020 02:06:05: 3000000 INFO @ Thu, 16 Apr 2020 02:06:06: 8000000 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 02:06:12: 4000000 INFO @ Thu, 16 Apr 2020 02:06:12: 9000000 INFO @ Thu, 16 Apr 2020 02:06:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.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 02:06:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:06:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:06:13: #1 tag size is determined as 77 bps INFO @ Thu, 16 Apr 2020 02:06:13: #1 tag size = 77 INFO @ Thu, 16 Apr 2020 02:06:13: #1 total tags in treatment: 4312210 INFO @ Thu, 16 Apr 2020 02:06:13: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:06:13: #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 02:06:13: #1 tags after filtering in treatment: 4223009 INFO @ Thu, 16 Apr 2020 02:06:13: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 16 Apr 2020 02:06:13: #1 finished! INFO @ Thu, 16 Apr 2020 02:06:13: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:06:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:06:13: #2 number of paired peaks: 289 WARNING @ Thu, 16 Apr 2020 02:06:13: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Thu, 16 Apr 2020 02:06:13: start model_add_line... INFO @ Thu, 16 Apr 2020 02:06:13: start X-correlation... INFO @ Thu, 16 Apr 2020 02:06:13: end of X-cor INFO @ Thu, 16 Apr 2020 02:06:13: #2 finished! INFO @ Thu, 16 Apr 2020 02:06:13: #2 predicted fragment length is 150 bps INFO @ Thu, 16 Apr 2020 02:06:13: #2 alternative fragment length(s) may be 150 bps INFO @ Thu, 16 Apr 2020 02:06:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.05_model.r WARNING @ Thu, 16 Apr 2020 02:06:13: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:06:13: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Thu, 16 Apr 2020 02:06:13: #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 02:06:13: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:06:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:06:18: 5000000 INFO @ Thu, 16 Apr 2020 02:06:20: 1000000 INFO @ Thu, 16 Apr 2020 02:06:23: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:06:25: 6000000 INFO @ Thu, 16 Apr 2020 02:06:26: 2000000 INFO @ Thu, 16 Apr 2020 02:06:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:06:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:06:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.05_summits.bed INFO @ Thu, 16 Apr 2020 02:06:27: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (503 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:06:31: 7000000 INFO @ Thu, 16 Apr 2020 02:06:32: 3000000 INFO @ Thu, 16 Apr 2020 02:06:38: 8000000 INFO @ Thu, 16 Apr 2020 02:06:40: 4000000 INFO @ Thu, 16 Apr 2020 02:06:45: 9000000 INFO @ Thu, 16 Apr 2020 02:06:46: #1 tag size is determined as 77 bps INFO @ Thu, 16 Apr 2020 02:06:46: #1 tag size = 77 INFO @ Thu, 16 Apr 2020 02:06:46: #1 total tags in treatment: 4312210 INFO @ Thu, 16 Apr 2020 02:06:46: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:06:46: #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 02:06:46: #1 tags after filtering in treatment: 4223009 INFO @ Thu, 16 Apr 2020 02:06:46: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 16 Apr 2020 02:06:46: #1 finished! INFO @ Thu, 16 Apr 2020 02:06:46: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:06:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:06:46: #2 number of paired peaks: 289 WARNING @ Thu, 16 Apr 2020 02:06:46: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Thu, 16 Apr 2020 02:06:46: start model_add_line... INFO @ Thu, 16 Apr 2020 02:06:46: start X-correlation... INFO @ Thu, 16 Apr 2020 02:06:46: end of X-cor INFO @ Thu, 16 Apr 2020 02:06:46: #2 finished! INFO @ Thu, 16 Apr 2020 02:06:46: #2 predicted fragment length is 150 bps INFO @ Thu, 16 Apr 2020 02:06:46: #2 alternative fragment length(s) may be 150 bps INFO @ Thu, 16 Apr 2020 02:06:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.10_model.r WARNING @ Thu, 16 Apr 2020 02:06:46: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:06:46: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Thu, 16 Apr 2020 02:06:46: #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 02:06:46: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:06:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:06:47: 5000000 INFO @ Thu, 16 Apr 2020 02:06:54: 6000000 INFO @ Thu, 16 Apr 2020 02:06:55: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:07:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:07:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:07:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.10_summits.bed INFO @ Thu, 16 Apr 2020 02:07:00: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (223 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:07:00: 7000000 INFO @ Thu, 16 Apr 2020 02:07:07: 8000000 INFO @ Thu, 16 Apr 2020 02:07:13: 9000000 INFO @ Thu, 16 Apr 2020 02:07:14: #1 tag size is determined as 77 bps INFO @ Thu, 16 Apr 2020 02:07:14: #1 tag size = 77 INFO @ Thu, 16 Apr 2020 02:07:14: #1 total tags in treatment: 4312210 INFO @ Thu, 16 Apr 2020 02:07:14: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:07:14: #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 02:07:14: #1 tags after filtering in treatment: 4223009 INFO @ Thu, 16 Apr 2020 02:07:14: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 16 Apr 2020 02:07:14: #1 finished! INFO @ Thu, 16 Apr 2020 02:07:14: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:07:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:07:15: #2 number of paired peaks: 289 WARNING @ Thu, 16 Apr 2020 02:07:15: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Thu, 16 Apr 2020 02:07:15: start model_add_line... INFO @ Thu, 16 Apr 2020 02:07:15: start X-correlation... INFO @ Thu, 16 Apr 2020 02:07:15: end of X-cor INFO @ Thu, 16 Apr 2020 02:07:15: #2 finished! INFO @ Thu, 16 Apr 2020 02:07:15: #2 predicted fragment length is 150 bps INFO @ Thu, 16 Apr 2020 02:07:15: #2 alternative fragment length(s) may be 150 bps INFO @ Thu, 16 Apr 2020 02:07:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.20_model.r WARNING @ Thu, 16 Apr 2020 02:07:15: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:07:15: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Thu, 16 Apr 2020 02:07:15: #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 02:07:15: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:07:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:07:24: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:07:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:07:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:07:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5309726/SRX5309726.20_summits.bed INFO @ Thu, 16 Apr 2020 02:07:28: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (88 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。