Job ID = 6456436 SRX = SRX3404031 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:59:16 prefetch.2.10.7: 1) Downloading 'SRR6303508'... 2020-06-21T10:59:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:01:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:01:07 prefetch.2.10.7: 'SRR6303508' is valid 2020-06-21T11:01:07 prefetch.2.10.7: 1) 'SRR6303508' was downloaded successfully 2020-06-21T11:01:07 prefetch.2.10.7: 'SRR6303508' has 0 unresolved dependencies Read 16204495 spots for SRR6303508/SRR6303508.sra Written 16204495 spots for SRR6303508/SRR6303508.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: 00:03:42 16204495 reads; of these: 16204495 (100.00%) were unpaired; of these: 737089 (4.55%) aligned 0 times 12647127 (78.05%) aligned exactly 1 time 2820279 (17.40%) aligned >1 times 95.45% overall alignment rate Time searching: 00:03:42 Overall time: 00:03:42 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] 4578227 / 15467406 = 0.2960 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 20:09:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.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 20:09:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:09:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:09:16: 1000000 INFO @ Sun, 21 Jun 2020 20:09:21: 2000000 INFO @ Sun, 21 Jun 2020 20:09:26: 3000000 INFO @ Sun, 21 Jun 2020 20:09:31: 4000000 INFO @ Sun, 21 Jun 2020 20:09:36: 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 20:09:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.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 20:09:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:09:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:09:41: 6000000 INFO @ Sun, 21 Jun 2020 20:09:46: 1000000 INFO @ Sun, 21 Jun 2020 20:09:46: 7000000 INFO @ Sun, 21 Jun 2020 20:09:51: 2000000 INFO @ Sun, 21 Jun 2020 20:09:52: 8000000 INFO @ Sun, 21 Jun 2020 20:09:57: 3000000 INFO @ Sun, 21 Jun 2020 20:09:57: 9000000 INFO @ Sun, 21 Jun 2020 20:10:02: 4000000 INFO @ Sun, 21 Jun 2020 20:10:03: 10000000 INFO @ Sun, 21 Jun 2020 20:10:08: 5000000 INFO @ Sun, 21 Jun 2020 20:10:08: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:10:08: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:10:08: #1 total tags in treatment: 10889179 INFO @ Sun, 21 Jun 2020 20:10:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:10:08: #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 20:10:08: #1 tags after filtering in treatment: 10888965 INFO @ Sun, 21 Jun 2020 20:10:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:10:08: #1 finished! INFO @ Sun, 21 Jun 2020 20:10:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:10:08: #2 looking for paired plus/minus strand peaks... 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 20:10:09: #2 number of paired peaks: 2314 INFO @ Sun, 21 Jun 2020 20:10:09: start model_add_line... INFO @ Sun, 21 Jun 2020 20:10:10: start X-correlation... INFO @ Sun, 21 Jun 2020 20:10:10: end of X-cor INFO @ Sun, 21 Jun 2020 20:10:10: #2 finished! INFO @ Sun, 21 Jun 2020 20:10:10: #2 predicted fragment length is 251 bps INFO @ Sun, 21 Jun 2020 20:10:10: #2 alternative fragment length(s) may be 251 bps INFO @ Sun, 21 Jun 2020 20:10:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.05_model.r INFO @ Sun, 21 Jun 2020 20:10:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:10:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:10:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.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 20:10:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:10:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:10:13: 6000000 INFO @ Sun, 21 Jun 2020 20:10:16: 1000000 INFO @ Sun, 21 Jun 2020 20:10:19: 7000000 INFO @ Sun, 21 Jun 2020 20:10:22: 2000000 INFO @ Sun, 21 Jun 2020 20:10:24: 8000000 INFO @ Sun, 21 Jun 2020 20:10:28: 3000000 INFO @ Sun, 21 Jun 2020 20:10:30: 9000000 INFO @ Sun, 21 Jun 2020 20:10:33: 4000000 INFO @ Sun, 21 Jun 2020 20:10:36: 10000000 INFO @ Sun, 21 Jun 2020 20:10:39: 5000000 INFO @ Sun, 21 Jun 2020 20:10:41: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:10:41: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:10:41: #1 total tags in treatment: 10889179 INFO @ Sun, 21 Jun 2020 20:10:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:10:41: #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 20:10:41: #1 tags after filtering in treatment: 10888965 INFO @ Sun, 21 Jun 2020 20:10:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:10:41: #1 finished! INFO @ Sun, 21 Jun 2020 20:10:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:10:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:10:42: #2 number of paired peaks: 2314 INFO @ Sun, 21 Jun 2020 20:10:42: start model_add_line... INFO @ Sun, 21 Jun 2020 20:10:42: start X-correlation... INFO @ Sun, 21 Jun 2020 20:10:42: end of X-cor INFO @ Sun, 21 Jun 2020 20:10:42: #2 finished! INFO @ Sun, 21 Jun 2020 20:10:42: #2 predicted fragment length is 251 bps INFO @ Sun, 21 Jun 2020 20:10:42: #2 alternative fragment length(s) may be 251 bps INFO @ Sun, 21 Jun 2020 20:10:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.10_model.r INFO @ Sun, 21 Jun 2020 20:10:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:10:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:10:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:10:45: 6000000 INFO @ Sun, 21 Jun 2020 20:10:50: 7000000 INFO @ Sun, 21 Jun 2020 20:10:56: 8000000 INFO @ Sun, 21 Jun 2020 20:11:01: 9000000 INFO @ Sun, 21 Jun 2020 20:11:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:11:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:11:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.05_summits.bed INFO @ Sun, 21 Jun 2020 20:11:02: Done! pass1 - making usageList (295 chroms): 4 millis pass2 - checking and writing primary data (20236 records, 4 fields): 29 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:11:07: 10000000 INFO @ Sun, 21 Jun 2020 20:11:12: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:11:12: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:11:12: #1 total tags in treatment: 10889179 INFO @ Sun, 21 Jun 2020 20:11:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:11:12: #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 20:11:12: #1 tags after filtering in treatment: 10888965 INFO @ Sun, 21 Jun 2020 20:11:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:11:12: #1 finished! INFO @ Sun, 21 Jun 2020 20:11:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:11:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:11:13: #2 number of paired peaks: 2314 INFO @ Sun, 21 Jun 2020 20:11:13: start model_add_line... INFO @ Sun, 21 Jun 2020 20:11:13: start X-correlation... INFO @ Sun, 21 Jun 2020 20:11:13: end of X-cor INFO @ Sun, 21 Jun 2020 20:11:13: #2 finished! INFO @ Sun, 21 Jun 2020 20:11:13: #2 predicted fragment length is 251 bps INFO @ Sun, 21 Jun 2020 20:11:13: #2 alternative fragment length(s) may be 251 bps INFO @ Sun, 21 Jun 2020 20:11:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.20_model.r INFO @ Sun, 21 Jun 2020 20:11:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:11:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:11:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:11:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:11:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:11:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.10_summits.bed INFO @ Sun, 21 Jun 2020 20:11:34: Done! pass1 - making usageList (259 chroms): 2 millis pass2 - checking and writing primary data (10342 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:11:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:12:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:12:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:12:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404031/SRX3404031.20_summits.bed INFO @ Sun, 21 Jun 2020 20:12:05: Done! pass1 - making usageList (202 chroms): 1 millis pass2 - checking and writing primary data (3704 records, 4 fields): 12 millis CompletedMACS2peakCalling