Job ID = 6453224 SRX = SRX1091595 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:08:34 prefetch.2.10.7: 1) Downloading 'SRR2096479'... 2020-06-21T08:08:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:10:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:10:39 prefetch.2.10.7: 'SRR2096479' is valid 2020-06-21T08:10:39 prefetch.2.10.7: 1) 'SRR2096479' was downloaded successfully 2020-06-21T08:10:39 prefetch.2.10.7: 'SRR2096479' has 0 unresolved dependencies Read 5237227 spots for SRR2096479/SRR2096479.sra Written 5237227 spots for SRR2096479/SRR2096479.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: 00:03:40 5237227 reads; of these: 5237227 (100.00%) were unpaired; of these: 108772 (2.08%) aligned 0 times 4248967 (81.13%) aligned exactly 1 time 879488 (16.79%) aligned >1 times 97.92% overall alignment rate Time searching: 00:03:40 Overall time: 00:03:40 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] 215589 / 5128455 = 0.0420 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 17:17:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.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 17:17:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:17:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:17:53: 1000000 INFO @ Sun, 21 Jun 2020 17:18:01: 2000000 INFO @ Sun, 21 Jun 2020 17:18:09: 3000000 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 17:18:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.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 17:18:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:18:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:18:18: 4000000 INFO @ Sun, 21 Jun 2020 17:18:24: 1000000 INFO @ Sun, 21 Jun 2020 17:18:26: #1 tag size is determined as 149 bps INFO @ Sun, 21 Jun 2020 17:18:26: #1 tag size = 149 INFO @ Sun, 21 Jun 2020 17:18:26: #1 total tags in treatment: 4912866 INFO @ Sun, 21 Jun 2020 17:18:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:18:26: #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 17:18:26: #1 tags after filtering in treatment: 4912606 INFO @ Sun, 21 Jun 2020 17:18:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:18:26: #1 finished! INFO @ Sun, 21 Jun 2020 17:18:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:18:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:18:27: #2 number of paired peaks: 531 WARNING @ Sun, 21 Jun 2020 17:18:27: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Sun, 21 Jun 2020 17:18:27: start model_add_line... INFO @ Sun, 21 Jun 2020 17:18:27: start X-correlation... INFO @ Sun, 21 Jun 2020 17:18:27: end of X-cor INFO @ Sun, 21 Jun 2020 17:18:27: #2 finished! INFO @ Sun, 21 Jun 2020 17:18:27: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 17:18:27: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 17:18:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.05_model.r WARNING @ Sun, 21 Jun 2020 17:18:27: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:18:27: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Sun, 21 Jun 2020 17:18:27: #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 17:18:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:18:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:18:32: 2000000 INFO @ Sun, 21 Jun 2020 17:18:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:18:41: 3000000 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 17:18:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:18:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:18:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.05_summits.bed INFO @ Sun, 21 Jun 2020 17:18:44: Done! pass1 - making usageList (342 chroms): 2 millis pass2 - checking and writing primary data (2371 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:18:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.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 17:18:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:18:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:18:50: 4000000 INFO @ Sun, 21 Jun 2020 17:18:56: 1000000 INFO @ Sun, 21 Jun 2020 17:18:59: #1 tag size is determined as 149 bps INFO @ Sun, 21 Jun 2020 17:18:59: #1 tag size = 149 INFO @ Sun, 21 Jun 2020 17:18:59: #1 total tags in treatment: 4912866 INFO @ Sun, 21 Jun 2020 17:18:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:18:59: #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 17:18:59: #1 tags after filtering in treatment: 4912606 INFO @ Sun, 21 Jun 2020 17:18:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:18:59: #1 finished! INFO @ Sun, 21 Jun 2020 17:18:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:18:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:19:00: #2 number of paired peaks: 531 WARNING @ Sun, 21 Jun 2020 17:19:00: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Sun, 21 Jun 2020 17:19:00: start model_add_line... INFO @ Sun, 21 Jun 2020 17:19:00: start X-correlation... INFO @ Sun, 21 Jun 2020 17:19:00: end of X-cor INFO @ Sun, 21 Jun 2020 17:19:00: #2 finished! INFO @ Sun, 21 Jun 2020 17:19:00: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 17:19:00: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 17:19:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.10_model.r WARNING @ Sun, 21 Jun 2020 17:19:00: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:19:00: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Sun, 21 Jun 2020 17:19:00: #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 17:19:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:19:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:19:06: 2000000 INFO @ Sun, 21 Jun 2020 17:19:11: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:19:16: 3000000 INFO @ Sun, 21 Jun 2020 17:19:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:19:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:19:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.10_summits.bed INFO @ Sun, 21 Jun 2020 17:19:16: Done! pass1 - making usageList (238 chroms): 1 millis pass2 - checking and writing primary data (641 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:19:26: 4000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:19:36: #1 tag size is determined as 149 bps INFO @ Sun, 21 Jun 2020 17:19:36: #1 tag size = 149 INFO @ Sun, 21 Jun 2020 17:19:36: #1 total tags in treatment: 4912866 INFO @ Sun, 21 Jun 2020 17:19:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:19:36: #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 17:19:36: #1 tags after filtering in treatment: 4912606 INFO @ Sun, 21 Jun 2020 17:19:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:19:36: #1 finished! INFO @ Sun, 21 Jun 2020 17:19:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:19:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:19:36: #2 number of paired peaks: 531 WARNING @ Sun, 21 Jun 2020 17:19:36: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Sun, 21 Jun 2020 17:19:36: start model_add_line... INFO @ Sun, 21 Jun 2020 17:19:36: start X-correlation... INFO @ Sun, 21 Jun 2020 17:19:36: end of X-cor INFO @ Sun, 21 Jun 2020 17:19:36: #2 finished! INFO @ Sun, 21 Jun 2020 17:19:36: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 17:19:36: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 17:19:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.20_model.r WARNING @ Sun, 21 Jun 2020 17:19:36: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:19:36: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Sun, 21 Jun 2020 17:19:36: #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 17:19:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:19:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:19:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:19:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:19:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:19:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1091595/SRX1091595.20_summits.bed INFO @ Sun, 21 Jun 2020 17:19:53: Done! pass1 - making usageList (132 chroms): 1 millis pass2 - checking and writing primary data (249 records, 4 fields): 5 millis CompletedMACS2peakCalling