Job ID = 5721134 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,647,674 reads read : 5,295,348 reads written : 5,295,348 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: 00:05:26 2647674 reads; of these: 2647674 (100.00%) were paired; of these: 742944 (28.06%) aligned concordantly 0 times 1452637 (54.86%) aligned concordantly exactly 1 time 452093 (17.08%) aligned concordantly >1 times ---- 742944 pairs aligned concordantly 0 times; of these: 379436 (51.07%) aligned discordantly 1 time ---- 363508 pairs aligned 0 times concordantly or discordantly; of these: 727016 mates make up the pairs; of these: 304436 (41.87%) aligned 0 times 200674 (27.60%) aligned exactly 1 time 221906 (30.52%) aligned >1 times 94.25% overall alignment rate Time searching: 00:05:26 Overall time: 00:05:26 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_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] 139654 / 2272806 = 0.0614 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 05:19:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.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 05:19:20: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:19:20: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:19:25: 1000000 INFO @ Thu, 16 Apr 2020 05:19:29: 2000000 INFO @ Thu, 16 Apr 2020 05:19:34: 3000000 INFO @ Thu, 16 Apr 2020 05:19:39: 4000000 INFO @ Thu, 16 Apr 2020 05:19:42: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:19:42: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:19:42: #1 total tags in treatment: 1773825 INFO @ Thu, 16 Apr 2020 05:19:42: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:19:42: #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 05:19:42: #1 tags after filtering in treatment: 1714828 INFO @ Thu, 16 Apr 2020 05:19:42: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:19:42: #1 finished! INFO @ Thu, 16 Apr 2020 05:19:42: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:19:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:19:42: #2 number of paired peaks: 621 WARNING @ Thu, 16 Apr 2020 05:19:42: Fewer paired peaks (621) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 621 pairs to build model! INFO @ Thu, 16 Apr 2020 05:19:42: start model_add_line... INFO @ Thu, 16 Apr 2020 05:19:42: start X-correlation... INFO @ Thu, 16 Apr 2020 05:19:42: end of X-cor INFO @ Thu, 16 Apr 2020 05:19:42: #2 finished! INFO @ Thu, 16 Apr 2020 05:19:42: #2 predicted fragment length is 120 bps INFO @ Thu, 16 Apr 2020 05:19:42: #2 alternative fragment length(s) may be 120 bps INFO @ Thu, 16 Apr 2020 05:19:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.05_model.r WARNING @ Thu, 16 Apr 2020 05:19:42: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:19:42: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Thu, 16 Apr 2020 05:19:42: #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 05:19:42: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:19:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:19:46: #3 Call peaks for each chromosome... 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 05:19:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:19:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:19:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.05_summits.bed INFO @ Thu, 16 Apr 2020 05:19:48: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (468 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:19:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.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 05:19:50: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:19:50: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:19:54: 1000000 INFO @ Thu, 16 Apr 2020 05:19:59: 2000000 INFO @ Thu, 16 Apr 2020 05:20:04: 3000000 INFO @ Thu, 16 Apr 2020 05:20:09: 4000000 INFO @ Thu, 16 Apr 2020 05:20:12: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:20:12: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:20:12: #1 total tags in treatment: 1773825 INFO @ Thu, 16 Apr 2020 05:20:12: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:20:12: #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 05:20:12: #1 tags after filtering in treatment: 1714828 INFO @ Thu, 16 Apr 2020 05:20:12: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:20:12: #1 finished! INFO @ Thu, 16 Apr 2020 05:20:12: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:20:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:20:12: #2 number of paired peaks: 621 WARNING @ Thu, 16 Apr 2020 05:20:12: Fewer paired peaks (621) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 621 pairs to build model! INFO @ Thu, 16 Apr 2020 05:20:12: start model_add_line... INFO @ Thu, 16 Apr 2020 05:20:12: start X-correlation... INFO @ Thu, 16 Apr 2020 05:20:12: end of X-cor INFO @ Thu, 16 Apr 2020 05:20:12: #2 finished! INFO @ Thu, 16 Apr 2020 05:20:12: #2 predicted fragment length is 120 bps INFO @ Thu, 16 Apr 2020 05:20:12: #2 alternative fragment length(s) may be 120 bps INFO @ Thu, 16 Apr 2020 05:20:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.10_model.r WARNING @ Thu, 16 Apr 2020 05:20:12: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:20:12: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Thu, 16 Apr 2020 05:20:12: #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 05:20:12: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:20:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:20:16: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:20:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:20:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:20:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.10_summits.bed INFO @ Thu, 16 Apr 2020 05:20:18: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (256 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 05:20:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.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 05:20:20: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:20:20: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:20:25: 1000000 INFO @ Thu, 16 Apr 2020 05:20:29: 2000000 INFO @ Thu, 16 Apr 2020 05:20:34: 3000000 INFO @ Thu, 16 Apr 2020 05:20:39: 4000000 INFO @ Thu, 16 Apr 2020 05:20:42: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:20:42: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:20:42: #1 total tags in treatment: 1773825 INFO @ Thu, 16 Apr 2020 05:20:42: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:20:42: #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 05:20:42: #1 tags after filtering in treatment: 1714828 INFO @ Thu, 16 Apr 2020 05:20:42: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:20:42: #1 finished! INFO @ Thu, 16 Apr 2020 05:20:42: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:20:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:20:42: #2 number of paired peaks: 621 WARNING @ Thu, 16 Apr 2020 05:20:42: Fewer paired peaks (621) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 621 pairs to build model! INFO @ Thu, 16 Apr 2020 05:20:42: start model_add_line... INFO @ Thu, 16 Apr 2020 05:20:42: start X-correlation... INFO @ Thu, 16 Apr 2020 05:20:42: end of X-cor INFO @ Thu, 16 Apr 2020 05:20:42: #2 finished! INFO @ Thu, 16 Apr 2020 05:20:42: #2 predicted fragment length is 120 bps INFO @ Thu, 16 Apr 2020 05:20:42: #2 alternative fragment length(s) may be 120 bps INFO @ Thu, 16 Apr 2020 05:20:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.20_model.r WARNING @ Thu, 16 Apr 2020 05:20:42: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:20:42: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Thu, 16 Apr 2020 05:20:42: #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 05:20:42: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:20:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:20:46: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:20:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:20:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:20:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708275/SRX6708275.20_summits.bed INFO @ Thu, 16 Apr 2020 05:20:48: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (129 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。