Job ID = 6455933 SRX = SRX3068970 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:22:10 prefetch.2.10.7: 1) Downloading 'SRR5907446'... 2020-06-21T10:22:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:25:00 prefetch.2.10.7: 'SRR5907446' is valid 2020-06-21T10:25:00 prefetch.2.10.7: 1) 'SRR5907446' was downloaded successfully Read 14902767 spots for SRR5907446/SRR5907446.sra Written 14902767 spots for SRR5907446/SRR5907446.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: 00:03:32 14902767 reads; of these: 14902767 (100.00%) were unpaired; of these: 1106427 (7.42%) aligned 0 times 11208773 (75.21%) aligned exactly 1 time 2587567 (17.36%) aligned >1 times 92.58% overall alignment rate Time searching: 00:03:32 Overall time: 00:03:32 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] 3337058 / 13796340 = 0.2419 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 19:32:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.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 19:32:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:32:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:32:58: 1000000 INFO @ Sun, 21 Jun 2020 19:33:03: 2000000 INFO @ Sun, 21 Jun 2020 19:33:09: 3000000 INFO @ Sun, 21 Jun 2020 19:33:15: 4000000 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 19:33:21: 5000000 INFO @ Sun, 21 Jun 2020 19:33:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.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 19:33:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:33:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:33:27: 6000000 INFO @ Sun, 21 Jun 2020 19:33:29: 1000000 INFO @ Sun, 21 Jun 2020 19:33:34: 7000000 INFO @ Sun, 21 Jun 2020 19:33:35: 2000000 INFO @ Sun, 21 Jun 2020 19:33:40: 8000000 INFO @ Sun, 21 Jun 2020 19:33:42: 3000000 INFO @ Sun, 21 Jun 2020 19:33:47: 9000000 INFO @ Sun, 21 Jun 2020 19:33:49: 4000000 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 19:33:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.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 19:33:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:33:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:33:54: 10000000 INFO @ Sun, 21 Jun 2020 19:33:55: 5000000 INFO @ Sun, 21 Jun 2020 19:33:57: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:33:57: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:33:57: #1 total tags in treatment: 10459282 INFO @ Sun, 21 Jun 2020 19:33:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:33:57: #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 19:33:58: #1 tags after filtering in treatment: 10459276 INFO @ Sun, 21 Jun 2020 19:33:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:33:58: #1 finished! INFO @ Sun, 21 Jun 2020 19:33:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:33:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:33:58: #2 number of paired peaks: 634 WARNING @ Sun, 21 Jun 2020 19:33:58: Fewer paired peaks (634) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 634 pairs to build model! INFO @ Sun, 21 Jun 2020 19:33:58: start model_add_line... INFO @ Sun, 21 Jun 2020 19:33:59: start X-correlation... INFO @ Sun, 21 Jun 2020 19:33:59: end of X-cor INFO @ Sun, 21 Jun 2020 19:33:59: #2 finished! INFO @ Sun, 21 Jun 2020 19:33:59: #2 predicted fragment length is 117 bps INFO @ Sun, 21 Jun 2020 19:33:59: #2 alternative fragment length(s) may be 4,117,149 bps INFO @ Sun, 21 Jun 2020 19:33:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.05_model.r INFO @ Sun, 21 Jun 2020 19:33:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:33:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:33:59: 1000000 INFO @ Sun, 21 Jun 2020 19:34:02: 6000000 INFO @ Sun, 21 Jun 2020 19:34:05: 2000000 INFO @ Sun, 21 Jun 2020 19:34:08: 7000000 INFO @ Sun, 21 Jun 2020 19:34:12: 3000000 INFO @ Sun, 21 Jun 2020 19:34:15: 8000000 INFO @ Sun, 21 Jun 2020 19:34:19: 4000000 INFO @ Sun, 21 Jun 2020 19:34:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:34:22: 9000000 INFO @ Sun, 21 Jun 2020 19:34:25: 5000000 INFO @ Sun, 21 Jun 2020 19:34:28: 10000000 INFO @ Sun, 21 Jun 2020 19:34:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:34:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:34:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.05_summits.bed INFO @ Sun, 21 Jun 2020 19:34:31: Done! pass1 - making usageList (471 chroms): 1 millis pass2 - checking and writing primary data (1163 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:34:32: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:34:32: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:34:32: #1 total tags in treatment: 10459282 INFO @ Sun, 21 Jun 2020 19:34:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:34:32: #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 19:34:32: 6000000 INFO @ Sun, 21 Jun 2020 19:34:32: #1 tags after filtering in treatment: 10459276 INFO @ Sun, 21 Jun 2020 19:34:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:34:32: #1 finished! INFO @ Sun, 21 Jun 2020 19:34:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:34:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:34:33: #2 number of paired peaks: 634 WARNING @ Sun, 21 Jun 2020 19:34:33: Fewer paired peaks (634) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 634 pairs to build model! INFO @ Sun, 21 Jun 2020 19:34:33: start model_add_line... INFO @ Sun, 21 Jun 2020 19:34:33: start X-correlation... INFO @ Sun, 21 Jun 2020 19:34:33: end of X-cor INFO @ Sun, 21 Jun 2020 19:34:33: #2 finished! INFO @ Sun, 21 Jun 2020 19:34:33: #2 predicted fragment length is 117 bps INFO @ Sun, 21 Jun 2020 19:34:33: #2 alternative fragment length(s) may be 4,117,149 bps INFO @ Sun, 21 Jun 2020 19:34:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.10_model.r INFO @ Sun, 21 Jun 2020 19:34:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:34:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:34:38: 7000000 INFO @ Sun, 21 Jun 2020 19:34:44: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:34:50: 9000000 INFO @ Sun, 21 Jun 2020 19:34:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:34:56: 10000000 INFO @ Sun, 21 Jun 2020 19:34:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:34:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:34:59: #1 total tags in treatment: 10459282 INFO @ Sun, 21 Jun 2020 19:34:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:34:59: #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 19:35:00: #1 tags after filtering in treatment: 10459276 INFO @ Sun, 21 Jun 2020 19:35:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:00: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:00: #2 number of paired peaks: 634 WARNING @ Sun, 21 Jun 2020 19:35:00: Fewer paired peaks (634) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 634 pairs to build model! INFO @ Sun, 21 Jun 2020 19:35:00: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:00: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:00: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:00: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:00: #2 predicted fragment length is 117 bps INFO @ Sun, 21 Jun 2020 19:35:00: #2 alternative fragment length(s) may be 4,117,149 bps INFO @ Sun, 21 Jun 2020 19:35:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.20_model.r INFO @ Sun, 21 Jun 2020 19:35:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:35:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.10_summits.bed INFO @ Sun, 21 Jun 2020 19:35:05: Done! pass1 - making usageList (409 chroms): 1 millis pass2 - checking and writing primary data (898 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:35:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:35:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068970/SRX3068970.20_summits.bed INFO @ Sun, 21 Jun 2020 19:35:33: Done! pass1 - making usageList (236 chroms): 0 millis pass2 - checking and writing primary data (371 records, 4 fields): 8 millis CompletedMACS2peakCalling