Job ID = 6456579 SRX = SRX365697 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:15:24 prefetch.2.10.7: 1) Downloading 'SRR1013775'... 2020-06-21T11:15:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:16:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:16:31 prefetch.2.10.7: 'SRR1013775' is valid 2020-06-21T11:16:31 prefetch.2.10.7: 1) 'SRR1013775' was downloaded successfully Read 12038239 spots for SRR1013775/SRR1013775.sra Written 12038239 spots for SRR1013775/SRR1013775.sra 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: 00:02:33 12038239 reads; of these: 12038239 (100.00%) were unpaired; of these: 859765 (7.14%) aligned 0 times 8147944 (67.68%) aligned exactly 1 time 3030530 (25.17%) aligned >1 times 92.86% overall alignment rate Time searching: 00:02:33 Overall time: 00:02:33 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 2597938 / 11178474 = 0.2324 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 @ Sun, 21 Jun 2020 20:22:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.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 @ Sun, 21 Jun 2020 20:22:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:22:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:22:17: 1000000 INFO @ Sun, 21 Jun 2020 20:22:22: 2000000 INFO @ Sun, 21 Jun 2020 20:22:27: 3000000 INFO @ Sun, 21 Jun 2020 20:22:32: 4000000 INFO @ Sun, 21 Jun 2020 20:22:36: 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 @ Sun, 21 Jun 2020 20:22:41: 6000000 INFO @ Sun, 21 Jun 2020 20:22:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.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 @ Sun, 21 Jun 2020 20:22:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:22:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:22:46: 7000000 INFO @ Sun, 21 Jun 2020 20:22:48: 1000000 INFO @ Sun, 21 Jun 2020 20:22:52: 8000000 INFO @ Sun, 21 Jun 2020 20:22:53: 2000000 INFO @ Sun, 21 Jun 2020 20:22:55: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:22:55: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:22:55: #1 total tags in treatment: 8580536 INFO @ Sun, 21 Jun 2020 20:22:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:22:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:22:55: #1 tags after filtering in treatment: 8580460 INFO @ Sun, 21 Jun 2020 20:22:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:22:55: #1 finished! INFO @ Sun, 21 Jun 2020 20:22:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:22:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:22:56: #2 number of paired peaks: 889 WARNING @ Sun, 21 Jun 2020 20:22:56: Fewer paired peaks (889) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 889 pairs to build model! INFO @ Sun, 21 Jun 2020 20:22:56: start model_add_line... INFO @ Sun, 21 Jun 2020 20:22:56: start X-correlation... INFO @ Sun, 21 Jun 2020 20:22:56: end of X-cor INFO @ Sun, 21 Jun 2020 20:22:56: #2 finished! INFO @ Sun, 21 Jun 2020 20:22:56: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 20:22:56: #2 alternative fragment length(s) may be 3,37,590 bps INFO @ Sun, 21 Jun 2020 20:22:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.05_model.r WARNING @ Sun, 21 Jun 2020 20:22:56: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:22:56: #2 You may need to consider one of the other alternative d(s): 3,37,590 WARNING @ Sun, 21 Jun 2020 20:22:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:22:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:22:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:22:59: 3000000 INFO @ Sun, 21 Jun 2020 20:23:04: 4000000 INFO @ Sun, 21 Jun 2020 20:23:09: 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 @ Sun, 21 Jun 2020 20:23:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.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 @ Sun, 21 Jun 2020 20:23:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:23:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:23:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:23:15: 6000000 INFO @ Sun, 21 Jun 2020 20:23:18: 1000000 INFO @ Sun, 21 Jun 2020 20:23:21: 7000000 INFO @ Sun, 21 Jun 2020 20:23:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:23:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:23:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.05_summits.bed INFO @ Sun, 21 Jun 2020 20:23:23: Done! pass1 - making usageList (575 chroms): 2 millis pass2 - checking and writing primary data (2834 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:23:23: 2000000 INFO @ Sun, 21 Jun 2020 20:23:26: 8000000 INFO @ Sun, 21 Jun 2020 20:23:29: 3000000 INFO @ Sun, 21 Jun 2020 20:23:29: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:23:29: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:23:29: #1 total tags in treatment: 8580536 INFO @ Sun, 21 Jun 2020 20:23:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:23:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:23:30: #1 tags after filtering in treatment: 8580460 INFO @ Sun, 21 Jun 2020 20:23:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:23:30: #1 finished! INFO @ Sun, 21 Jun 2020 20:23:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:23:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:23:30: #2 number of paired peaks: 889 WARNING @ Sun, 21 Jun 2020 20:23:30: Fewer paired peaks (889) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 889 pairs to build model! INFO @ Sun, 21 Jun 2020 20:23:30: start model_add_line... INFO @ Sun, 21 Jun 2020 20:23:31: start X-correlation... INFO @ Sun, 21 Jun 2020 20:23:31: end of X-cor INFO @ Sun, 21 Jun 2020 20:23:31: #2 finished! INFO @ Sun, 21 Jun 2020 20:23:31: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 20:23:31: #2 alternative fragment length(s) may be 3,37,590 bps INFO @ Sun, 21 Jun 2020 20:23:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.10_model.r WARNING @ Sun, 21 Jun 2020 20:23:31: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:23:31: #2 You may need to consider one of the other alternative d(s): 3,37,590 WARNING @ Sun, 21 Jun 2020 20:23:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:23:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:23:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:23:34: 4000000 INFO @ Sun, 21 Jun 2020 20:23:39: 5000000 INFO @ Sun, 21 Jun 2020 20:23:45: 6000000 INFO @ Sun, 21 Jun 2020 20:23:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:23:50: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:23:56: 8000000 INFO @ Sun, 21 Jun 2020 20:23:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:23:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:23:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.10_summits.bed INFO @ Sun, 21 Jun 2020 20:23:57: Done! pass1 - making usageList (355 chroms): 1 millis pass2 - checking and writing primary data (977 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:23:59: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:23:59: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:23:59: #1 total tags in treatment: 8580536 INFO @ Sun, 21 Jun 2020 20:23:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:23:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:23:59: #1 tags after filtering in treatment: 8580460 INFO @ Sun, 21 Jun 2020 20:23:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:23:59: #1 finished! INFO @ Sun, 21 Jun 2020 20:23:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:23:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:24:00: #2 number of paired peaks: 889 WARNING @ Sun, 21 Jun 2020 20:24:00: Fewer paired peaks (889) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 889 pairs to build model! INFO @ Sun, 21 Jun 2020 20:24:00: start model_add_line... INFO @ Sun, 21 Jun 2020 20:24:00: start X-correlation... INFO @ Sun, 21 Jun 2020 20:24:00: end of X-cor INFO @ Sun, 21 Jun 2020 20:24:00: #2 finished! INFO @ Sun, 21 Jun 2020 20:24:00: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 20:24:00: #2 alternative fragment length(s) may be 3,37,590 bps INFO @ Sun, 21 Jun 2020 20:24:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.20_model.r WARNING @ Sun, 21 Jun 2020 20:24:00: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:24:00: #2 You may need to consider one of the other alternative d(s): 3,37,590 WARNING @ Sun, 21 Jun 2020 20:24:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:24:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:24:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:24:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:24:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:24:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:24:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX365697/SRX365697.20_summits.bed INFO @ Sun, 21 Jun 2020 20:24:27: Done! pass1 - making usageList (116 chroms): 0 millis pass2 - checking and writing primary data (240 records, 4 fields): 6 millis CompletedMACS2peakCalling