Job ID = 5720587 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,409,128 reads read : 10,409,128 reads written : 10,409,128 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289716.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: 00:02:49 10409128 reads; of these: 10409128 (100.00%) were unpaired; of these: 2337416 (22.46%) aligned 0 times 6347525 (60.98%) aligned exactly 1 time 1724187 (16.56%) aligned >1 times 77.54% overall alignment rate Time searching: 00:02:49 Overall time: 00:02:49 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] 711989 / 8071712 = 0.0882 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 00:42:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.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 00:42:46: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:42:46: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:42:51: 1000000 INFO @ Thu, 16 Apr 2020 00:42:56: 2000000 INFO @ Thu, 16 Apr 2020 00:43:01: 3000000 INFO @ Thu, 16 Apr 2020 00:43:06: 4000000 INFO @ Thu, 16 Apr 2020 00:43:11: 5000000 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 00:43:16: 6000000 INFO @ Thu, 16 Apr 2020 00:43:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.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 00:43:17: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:43:17: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:43:22: 7000000 INFO @ Thu, 16 Apr 2020 00:43:22: 1000000 INFO @ Thu, 16 Apr 2020 00:43:23: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:43:23: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:43:23: #1 total tags in treatment: 7359723 INFO @ Thu, 16 Apr 2020 00:43:23: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:43:23: #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 00:43:24: #1 tags after filtering in treatment: 7359723 INFO @ Thu, 16 Apr 2020 00:43:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:43:24: #1 finished! INFO @ Thu, 16 Apr 2020 00:43:24: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:43:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:43:24: #2 number of paired peaks: 291 WARNING @ Thu, 16 Apr 2020 00:43:24: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Thu, 16 Apr 2020 00:43:24: start model_add_line... INFO @ Thu, 16 Apr 2020 00:43:24: start X-correlation... INFO @ Thu, 16 Apr 2020 00:43:24: end of X-cor INFO @ Thu, 16 Apr 2020 00:43:24: #2 finished! INFO @ Thu, 16 Apr 2020 00:43:24: #2 predicted fragment length is 53 bps INFO @ Thu, 16 Apr 2020 00:43:24: #2 alternative fragment length(s) may be 53 bps INFO @ Thu, 16 Apr 2020 00:43:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.05_model.r WARNING @ Thu, 16 Apr 2020 00:43:24: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:43:24: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Thu, 16 Apr 2020 00:43:24: #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 00:43:24: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:43:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:43:27: 2000000 INFO @ Thu, 16 Apr 2020 00:43:32: 3000000 INFO @ Thu, 16 Apr 2020 00:43:37: 4000000 INFO @ Thu, 16 Apr 2020 00:43:40: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:43:42: 5000000 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 00:43:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.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 00:43:46: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:43:46: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:43:47: 6000000 INFO @ Thu, 16 Apr 2020 00:43:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:43:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:43:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.05_summits.bed INFO @ Thu, 16 Apr 2020 00:43:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1554 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:43:51: 1000000 INFO @ Thu, 16 Apr 2020 00:43:52: 7000000 INFO @ Thu, 16 Apr 2020 00:43:54: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:43:54: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:43:54: #1 total tags in treatment: 7359723 INFO @ Thu, 16 Apr 2020 00:43:54: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:43:54: #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 00:43:54: #1 tags after filtering in treatment: 7359723 INFO @ Thu, 16 Apr 2020 00:43:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:43:54: #1 finished! INFO @ Thu, 16 Apr 2020 00:43:54: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:43:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:43:54: #2 number of paired peaks: 291 WARNING @ Thu, 16 Apr 2020 00:43:54: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Thu, 16 Apr 2020 00:43:54: start model_add_line... INFO @ Thu, 16 Apr 2020 00:43:54: start X-correlation... INFO @ Thu, 16 Apr 2020 00:43:54: end of X-cor INFO @ Thu, 16 Apr 2020 00:43:54: #2 finished! INFO @ Thu, 16 Apr 2020 00:43:54: #2 predicted fragment length is 53 bps INFO @ Thu, 16 Apr 2020 00:43:54: #2 alternative fragment length(s) may be 53 bps INFO @ Thu, 16 Apr 2020 00:43:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.10_model.r WARNING @ Thu, 16 Apr 2020 00:43:54: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:43:54: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Thu, 16 Apr 2020 00:43:54: #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 00:43:54: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:43:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:43:56: 2000000 INFO @ Thu, 16 Apr 2020 00:44:01: 3000000 INFO @ Thu, 16 Apr 2020 00:44:06: 4000000 INFO @ Thu, 16 Apr 2020 00:44:10: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:44:12: 5000000 INFO @ Thu, 16 Apr 2020 00:44:17: 6000000 INFO @ Thu, 16 Apr 2020 00:44:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:44:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:44:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.10_summits.bed INFO @ Thu, 16 Apr 2020 00:44:18: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (863 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:44:22: 7000000 INFO @ Thu, 16 Apr 2020 00:44:24: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:44:24: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:44:24: #1 total tags in treatment: 7359723 INFO @ Thu, 16 Apr 2020 00:44:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:44:24: #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 00:44:24: #1 tags after filtering in treatment: 7359723 INFO @ Thu, 16 Apr 2020 00:44:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:44:24: #1 finished! INFO @ Thu, 16 Apr 2020 00:44:24: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:44:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:44:24: #2 number of paired peaks: 291 WARNING @ Thu, 16 Apr 2020 00:44:24: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Thu, 16 Apr 2020 00:44:24: start model_add_line... INFO @ Thu, 16 Apr 2020 00:44:25: start X-correlation... INFO @ Thu, 16 Apr 2020 00:44:25: end of X-cor INFO @ Thu, 16 Apr 2020 00:44:25: #2 finished! INFO @ Thu, 16 Apr 2020 00:44:25: #2 predicted fragment length is 53 bps INFO @ Thu, 16 Apr 2020 00:44:25: #2 alternative fragment length(s) may be 53 bps INFO @ Thu, 16 Apr 2020 00:44:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.20_model.r WARNING @ Thu, 16 Apr 2020 00:44:25: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:44:25: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Thu, 16 Apr 2020 00:44:25: #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 00:44:25: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:44:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:44:40: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:44:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:44:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:44:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592439/SRX2592439.20_summits.bed INFO @ Thu, 16 Apr 2020 00:44:48: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (578 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。