Job ID = 6529605 SRX = SRX3380793 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:04:37 17121380 reads; of these: 17121380 (100.00%) were unpaired; of these: 686663 (4.01%) aligned 0 times 13143051 (76.76%) aligned exactly 1 time 3291666 (19.23%) aligned >1 times 95.99% overall alignment rate Time searching: 00:04:37 Overall time: 00:04:37 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] 2131635 / 16434717 = 0.1297 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 @ Tue, 30 Jun 2020 02:36:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.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 @ Tue, 30 Jun 2020 02:36:12: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:36:12: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:36:19: 1000000 INFO @ Tue, 30 Jun 2020 02:36:25: 2000000 INFO @ Tue, 30 Jun 2020 02:36:32: 3000000 INFO @ Tue, 30 Jun 2020 02:36:39: 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 @ Tue, 30 Jun 2020 02:36:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.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 @ Tue, 30 Jun 2020 02:36:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:36:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:36:45: 5000000 INFO @ Tue, 30 Jun 2020 02:36:48: 1000000 INFO @ Tue, 30 Jun 2020 02:36:51: 6000000 INFO @ Tue, 30 Jun 2020 02:36:54: 2000000 INFO @ Tue, 30 Jun 2020 02:36:57: 7000000 INFO @ Tue, 30 Jun 2020 02:37:00: 3000000 INFO @ Tue, 30 Jun 2020 02:37:03: 8000000 INFO @ Tue, 30 Jun 2020 02:37:06: 4000000 INFO @ Tue, 30 Jun 2020 02:37:09: 9000000 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 @ Tue, 30 Jun 2020 02:37:12: 5000000 INFO @ Tue, 30 Jun 2020 02:37:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.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 @ Tue, 30 Jun 2020 02:37:12: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:37:12: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:37:15: 10000000 INFO @ Tue, 30 Jun 2020 02:37:18: 6000000 INFO @ Tue, 30 Jun 2020 02:37:19: 1000000 INFO @ Tue, 30 Jun 2020 02:37:22: 11000000 INFO @ Tue, 30 Jun 2020 02:37:25: 7000000 INFO @ Tue, 30 Jun 2020 02:37:25: 2000000 INFO @ Tue, 30 Jun 2020 02:37:28: 12000000 INFO @ Tue, 30 Jun 2020 02:37:31: 8000000 INFO @ Tue, 30 Jun 2020 02:37:31: 3000000 INFO @ Tue, 30 Jun 2020 02:37:35: 13000000 INFO @ Tue, 30 Jun 2020 02:37:37: 9000000 INFO @ Tue, 30 Jun 2020 02:37:37: 4000000 INFO @ Tue, 30 Jun 2020 02:37:41: 14000000 INFO @ Tue, 30 Jun 2020 02:37:43: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:37:43: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:37:43: #1 total tags in treatment: 14303082 INFO @ Tue, 30 Jun 2020 02:37:43: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:37:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:37:43: 10000000 INFO @ Tue, 30 Jun 2020 02:37:43: 5000000 INFO @ Tue, 30 Jun 2020 02:37:43: #1 tags after filtering in treatment: 14303076 INFO @ Tue, 30 Jun 2020 02:37:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:37:43: #1 finished! INFO @ Tue, 30 Jun 2020 02:37:43: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:37:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:37:45: #2 number of paired peaks: 188 WARNING @ Tue, 30 Jun 2020 02:37:45: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Tue, 30 Jun 2020 02:37:45: start model_add_line... INFO @ Tue, 30 Jun 2020 02:37:45: start X-correlation... INFO @ Tue, 30 Jun 2020 02:37:45: end of X-cor INFO @ Tue, 30 Jun 2020 02:37:45: #2 finished! INFO @ Tue, 30 Jun 2020 02:37:45: #2 predicted fragment length is 116 bps INFO @ Tue, 30 Jun 2020 02:37:45: #2 alternative fragment length(s) may be 116 bps INFO @ Tue, 30 Jun 2020 02:37:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.05_model.r INFO @ Tue, 30 Jun 2020 02:37:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:37:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:37:49: 11000000 INFO @ Tue, 30 Jun 2020 02:37:49: 6000000 INFO @ Tue, 30 Jun 2020 02:37:55: 7000000 INFO @ Tue, 30 Jun 2020 02:37:56: 12000000 INFO @ Tue, 30 Jun 2020 02:38:01: 8000000 INFO @ Tue, 30 Jun 2020 02:38:01: 13000000 INFO @ Tue, 30 Jun 2020 02:38:07: 9000000 INFO @ Tue, 30 Jun 2020 02:38:07: 14000000 INFO @ Tue, 30 Jun 2020 02:38:09: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:38:09: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:38:09: #1 total tags in treatment: 14303082 INFO @ Tue, 30 Jun 2020 02:38:09: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:38:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:38:10: #1 tags after filtering in treatment: 14303076 INFO @ Tue, 30 Jun 2020 02:38:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:38:10: #1 finished! INFO @ Tue, 30 Jun 2020 02:38:10: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:38:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:38:11: #2 number of paired peaks: 188 WARNING @ Tue, 30 Jun 2020 02:38:11: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Tue, 30 Jun 2020 02:38:11: start model_add_line... INFO @ Tue, 30 Jun 2020 02:38:11: start X-correlation... INFO @ Tue, 30 Jun 2020 02:38:11: end of X-cor INFO @ Tue, 30 Jun 2020 02:38:11: #2 finished! INFO @ Tue, 30 Jun 2020 02:38:11: #2 predicted fragment length is 116 bps INFO @ Tue, 30 Jun 2020 02:38:11: #2 alternative fragment length(s) may be 116 bps INFO @ Tue, 30 Jun 2020 02:38:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.10_model.r INFO @ Tue, 30 Jun 2020 02:38:11: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:38:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:38:13: 10000000 INFO @ Tue, 30 Jun 2020 02:38:17: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:38:19: 11000000 INFO @ Tue, 30 Jun 2020 02:38:25: 12000000 INFO @ Tue, 30 Jun 2020 02:38:31: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:38:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:38:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:38:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.05_summits.bed INFO @ Tue, 30 Jun 2020 02:38:34: Done! pass1 - making usageList (468 chroms): 2 millis pass2 - checking and writing primary data (3856 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:38:37: 14000000 INFO @ Tue, 30 Jun 2020 02:38:39: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:38:39: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:38:39: #1 total tags in treatment: 14303082 INFO @ Tue, 30 Jun 2020 02:38:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:38:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:38:40: #1 tags after filtering in treatment: 14303076 INFO @ Tue, 30 Jun 2020 02:38:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:38:40: #1 finished! INFO @ Tue, 30 Jun 2020 02:38:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:38:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:38:41: #2 number of paired peaks: 188 WARNING @ Tue, 30 Jun 2020 02:38:41: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Tue, 30 Jun 2020 02:38:41: start model_add_line... INFO @ Tue, 30 Jun 2020 02:38:41: start X-correlation... INFO @ Tue, 30 Jun 2020 02:38:41: end of X-cor INFO @ Tue, 30 Jun 2020 02:38:41: #2 finished! INFO @ Tue, 30 Jun 2020 02:38:41: #2 predicted fragment length is 116 bps INFO @ Tue, 30 Jun 2020 02:38:41: #2 alternative fragment length(s) may be 116 bps INFO @ Tue, 30 Jun 2020 02:38:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.20_model.r INFO @ Tue, 30 Jun 2020 02:38:41: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:38:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:38:45: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:39:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:39:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:39:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.10_summits.bed INFO @ Tue, 30 Jun 2020 02:39:02: Done! pass1 - making usageList (292 chroms): 1 millis pass2 - checking and writing primary data (1348 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:39:15: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:39:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:39:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:39:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380793/SRX3380793.20_summits.bed INFO @ Tue, 30 Jun 2020 02:39:32: Done! pass1 - making usageList (112 chroms): 1 millis pass2 - checking and writing primary data (316 records, 4 fields): 7 millis CompletedMACS2peakCalling