Job ID = 6454698 SRX = SRX2520646 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:37:56 prefetch.2.10.7: 1) Downloading 'SRR5206765'... 2020-06-21T09:37:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:40:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:40:08 prefetch.2.10.7: 'SRR5206765' is valid 2020-06-21T09:40:08 prefetch.2.10.7: 1) 'SRR5206765' was downloaded successfully Read 14188970 spots for SRR5206765/SRR5206765.sra Written 14188970 spots for SRR5206765/SRR5206765.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: 00:03:55 14188970 reads; of these: 14188970 (100.00%) were unpaired; of these: 323477 (2.28%) aligned 0 times 9614573 (67.76%) aligned exactly 1 time 4250920 (29.96%) aligned >1 times 97.72% overall alignment rate Time searching: 00:03:55 Overall time: 00:03:55 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3202161 / 13865493 = 0.2309 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 18:48:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.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 18:48:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:15: 1000000 INFO @ Sun, 21 Jun 2020 18:48:20: 2000000 INFO @ Sun, 21 Jun 2020 18:48:26: 3000000 INFO @ Sun, 21 Jun 2020 18:48:31: 4000000 INFO @ Sun, 21 Jun 2020 18:48:37: 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 18:48:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.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 18:48:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:42: 6000000 INFO @ Sun, 21 Jun 2020 18:48:45: 1000000 INFO @ Sun, 21 Jun 2020 18:48:48: 7000000 INFO @ Sun, 21 Jun 2020 18:48:51: 2000000 INFO @ Sun, 21 Jun 2020 18:48:54: 8000000 INFO @ Sun, 21 Jun 2020 18:48:57: 3000000 INFO @ Sun, 21 Jun 2020 18:49:01: 9000000 INFO @ Sun, 21 Jun 2020 18:49:03: 4000000 INFO @ Sun, 21 Jun 2020 18:49:07: 10000000 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 18:49:09: 5000000 INFO @ Sun, 21 Jun 2020 18:49:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.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 18:49:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:49:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:49:11: #1 total tags in treatment: 10663332 INFO @ Sun, 21 Jun 2020 18:49:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:11: #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 18:49:11: #1 tags after filtering in treatment: 10663241 INFO @ Sun, 21 Jun 2020 18:49:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:11: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:12: #2 number of paired peaks: 481 WARNING @ Sun, 21 Jun 2020 18:49:12: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Sun, 21 Jun 2020 18:49:12: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:12: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:12: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:12: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:12: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 18:49:12: #2 alternative fragment length(s) may be 2,58,89,109 bps INFO @ Sun, 21 Jun 2020 18:49:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.05_model.r WARNING @ Sun, 21 Jun 2020 18:49:12: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:49:12: #2 You may need to consider one of the other alternative d(s): 2,58,89,109 WARNING @ Sun, 21 Jun 2020 18:49:12: #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 18:49:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:49:15: 6000000 INFO @ Sun, 21 Jun 2020 18:49:15: 1000000 INFO @ Sun, 21 Jun 2020 18:49:21: 2000000 INFO @ Sun, 21 Jun 2020 18:49:21: 7000000 INFO @ Sun, 21 Jun 2020 18:49:27: 3000000 INFO @ Sun, 21 Jun 2020 18:49:27: 8000000 INFO @ Sun, 21 Jun 2020 18:49:33: 4000000 INFO @ Sun, 21 Jun 2020 18:49:34: 9000000 INFO @ Sun, 21 Jun 2020 18:49:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:49:39: 5000000 INFO @ Sun, 21 Jun 2020 18:49:40: 10000000 INFO @ Sun, 21 Jun 2020 18:49:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:49:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:49:44: #1 total tags in treatment: 10663332 INFO @ Sun, 21 Jun 2020 18:49:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:44: #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 18:49:45: #1 tags after filtering in treatment: 10663241 INFO @ Sun, 21 Jun 2020 18:49:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:45: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:45: 6000000 INFO @ Sun, 21 Jun 2020 18:49:45: #2 number of paired peaks: 481 WARNING @ Sun, 21 Jun 2020 18:49:45: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Sun, 21 Jun 2020 18:49:45: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:46: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:46: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:46: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:46: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 18:49:46: #2 alternative fragment length(s) may be 2,58,89,109 bps INFO @ Sun, 21 Jun 2020 18:49:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.10_model.r WARNING @ Sun, 21 Jun 2020 18:49:46: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:49:46: #2 You may need to consider one of the other alternative d(s): 2,58,89,109 WARNING @ Sun, 21 Jun 2020 18:49:46: #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 18:49:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:49:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:49:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:49:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.05_summits.bed INFO @ Sun, 21 Jun 2020 18:49:48: Done! pass1 - making usageList (402 chroms): 1 millis pass2 - checking and writing primary data (1349 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:49:51: 7000000 INFO @ Sun, 21 Jun 2020 18:49:56: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:50:02: 9000000 INFO @ Sun, 21 Jun 2020 18:50:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:50:07: 10000000 INFO @ Sun, 21 Jun 2020 18:50:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:50:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:50:11: #1 total tags in treatment: 10663332 INFO @ Sun, 21 Jun 2020 18:50:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:11: #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 18:50:12: #1 tags after filtering in treatment: 10663241 INFO @ Sun, 21 Jun 2020 18:50:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:12: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:50:12: #2 number of paired peaks: 481 WARNING @ Sun, 21 Jun 2020 18:50:12: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Sun, 21 Jun 2020 18:50:12: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:12: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:12: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:12: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:12: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 18:50:12: #2 alternative fragment length(s) may be 2,58,89,109 bps INFO @ Sun, 21 Jun 2020 18:50:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.20_model.r WARNING @ Sun, 21 Jun 2020 18:50:13: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:50:13: #2 You may need to consider one of the other alternative d(s): 2,58,89,109 WARNING @ Sun, 21 Jun 2020 18:50:13: #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 18:50:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:50:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:50:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:50:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.10_summits.bed INFO @ Sun, 21 Jun 2020 18:50:18: Done! pass1 - making usageList (152 chroms): 1 millis pass2 - checking and writing primary data (399 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:50:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:50:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:50:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:50:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520646/SRX2520646.20_summits.bed INFO @ Sun, 21 Jun 2020 18:50:45: Done! pass1 - making usageList (80 chroms): 1 millis pass2 - checking and writing primary data (157 records, 4 fields): 6 millis CompletedMACS2peakCalling