Job ID = 6452993 SRX = SRX085411 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:08:33 prefetch.2.10.7: 1) Downloading 'SRR317189'... 2020-06-21T08:08:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:12:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:12:59 prefetch.2.10.7: 1) 'SRR317189' was downloaded successfully Read 21464648 spots for SRR317189/SRR317189.sra Written 21464648 spots for SRR317189/SRR317189.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: 00:00:01 Multiseed full-index search: 00:02:24 21464648 reads; of these: 21464648 (100.00%) were unpaired; of these: 13623291 (63.47%) aligned 0 times 5718171 (26.64%) aligned exactly 1 time 2123186 (9.89%) aligned >1 times 36.53% overall alignment rate Time searching: 00:02:25 Overall time: 00:02:25 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] 1060031 / 7841357 = 0.1352 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 17:19:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.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 17:19:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:19:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:19:18: 1000000 INFO @ Sun, 21 Jun 2020 17:19:23: 2000000 INFO @ Sun, 21 Jun 2020 17:19:29: 3000000 INFO @ Sun, 21 Jun 2020 17:19:34: 4000000 INFO @ Sun, 21 Jun 2020 17:19:40: 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 17:19:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.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 17:19:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:19:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:19:46: 6000000 INFO @ Sun, 21 Jun 2020 17:19:48: 1000000 INFO @ Sun, 21 Jun 2020 17:19:50: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:19:50: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:19:50: #1 total tags in treatment: 6781326 INFO @ Sun, 21 Jun 2020 17:19:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:19:50: #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 17:19:51: #1 tags after filtering in treatment: 6781213 INFO @ Sun, 21 Jun 2020 17:19:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:19:51: #1 finished! INFO @ Sun, 21 Jun 2020 17:19:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:19:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:19:51: #2 number of paired peaks: 967 WARNING @ Sun, 21 Jun 2020 17:19:51: Fewer paired peaks (967) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 967 pairs to build model! INFO @ Sun, 21 Jun 2020 17:19:51: start model_add_line... INFO @ Sun, 21 Jun 2020 17:19:51: start X-correlation... INFO @ Sun, 21 Jun 2020 17:19:51: end of X-cor INFO @ Sun, 21 Jun 2020 17:19:51: #2 finished! INFO @ Sun, 21 Jun 2020 17:19:51: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 17:19:51: #2 alternative fragment length(s) may be 57 bps INFO @ Sun, 21 Jun 2020 17:19:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.05_model.r WARNING @ Sun, 21 Jun 2020 17:19:51: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:19:51: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sun, 21 Jun 2020 17:19:51: #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 17:19:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:19:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:19:53: 2000000 INFO @ Sun, 21 Jun 2020 17:19:58: 3000000 INFO @ Sun, 21 Jun 2020 17:20:03: 4000000 INFO @ Sun, 21 Jun 2020 17:20:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:20:08: 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 17:20:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.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 17:20:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:20:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:20:13: 6000000 INFO @ Sun, 21 Jun 2020 17:20:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:20:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:20:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.05_summits.bed INFO @ Sun, 21 Jun 2020 17:20:15: Done! pass1 - making usageList (409 chroms): 1 millis pass2 - checking and writing primary data (2353 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:20:18: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:20:18: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:20:18: #1 total tags in treatment: 6781326 INFO @ Sun, 21 Jun 2020 17:20:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:20:18: #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 17:20:18: 1000000 INFO @ Sun, 21 Jun 2020 17:20:18: #1 tags after filtering in treatment: 6781213 INFO @ Sun, 21 Jun 2020 17:20:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:20:18: #1 finished! INFO @ Sun, 21 Jun 2020 17:20:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:20:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:20:19: #2 number of paired peaks: 967 WARNING @ Sun, 21 Jun 2020 17:20:19: Fewer paired peaks (967) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 967 pairs to build model! INFO @ Sun, 21 Jun 2020 17:20:19: start model_add_line... INFO @ Sun, 21 Jun 2020 17:20:19: start X-correlation... INFO @ Sun, 21 Jun 2020 17:20:19: end of X-cor INFO @ Sun, 21 Jun 2020 17:20:19: #2 finished! INFO @ Sun, 21 Jun 2020 17:20:19: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 17:20:19: #2 alternative fragment length(s) may be 57 bps INFO @ Sun, 21 Jun 2020 17:20:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.10_model.r WARNING @ Sun, 21 Jun 2020 17:20:19: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:20:19: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sun, 21 Jun 2020 17:20:19: #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 17:20:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:20:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:20:24: 2000000 INFO @ Sun, 21 Jun 2020 17:20:30: 3000000 INFO @ Sun, 21 Jun 2020 17:20:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:20:35: 4000000 INFO @ Sun, 21 Jun 2020 17:20:41: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:20:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:20:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:20:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.10_summits.bed INFO @ Sun, 21 Jun 2020 17:20:44: Done! pass1 - making usageList (285 chroms): 1 millis pass2 - checking and writing primary data (962 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:20:47: 6000000 INFO @ Sun, 21 Jun 2020 17:20:51: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:20:51: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:20:51: #1 total tags in treatment: 6781326 INFO @ Sun, 21 Jun 2020 17:20:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:20:51: #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 17:20:52: #1 tags after filtering in treatment: 6781213 INFO @ Sun, 21 Jun 2020 17:20:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:20:52: #1 finished! INFO @ Sun, 21 Jun 2020 17:20:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:20:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:20:52: #2 number of paired peaks: 967 WARNING @ Sun, 21 Jun 2020 17:20:52: Fewer paired peaks (967) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 967 pairs to build model! INFO @ Sun, 21 Jun 2020 17:20:52: start model_add_line... INFO @ Sun, 21 Jun 2020 17:20:52: start X-correlation... INFO @ Sun, 21 Jun 2020 17:20:52: end of X-cor INFO @ Sun, 21 Jun 2020 17:20:52: #2 finished! INFO @ Sun, 21 Jun 2020 17:20:52: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 17:20:52: #2 alternative fragment length(s) may be 57 bps INFO @ Sun, 21 Jun 2020 17:20:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.20_model.r WARNING @ Sun, 21 Jun 2020 17:20:53: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:20:53: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sun, 21 Jun 2020 17:20:53: #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 17:20:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:20:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:21:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:21:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:21:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:21:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX085411/SRX085411.20_summits.bed INFO @ Sun, 21 Jun 2020 17:21:16: Done! pass1 - making usageList (143 chroms): 1 millis pass2 - checking and writing primary data (350 records, 4 fields): 10 millis CompletedMACS2peakCalling