Job ID = 6456646 SRX = SRX3873736 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:58:31 prefetch.2.10.7: 1) Downloading 'SRR6927801'... 2020-06-21T10:58:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:00:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:00:16 prefetch.2.10.7: 'SRR6927801' is valid 2020-06-21T11:00:16 prefetch.2.10.7: 1) 'SRR6927801' was downloaded successfully 2020-06-21T11:00:16 prefetch.2.10.7: 'SRR6927801' has 0 unresolved dependencies Read 13697497 spots for SRR6927801/SRR6927801.sra Written 13697497 spots for SRR6927801/SRR6927801.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: 00:02:45 13697497 reads; of these: 13697497 (100.00%) were unpaired; of these: 2769343 (20.22%) aligned 0 times 9201026 (67.17%) aligned exactly 1 time 1727128 (12.61%) aligned >1 times 79.78% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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] 2443876 / 10928154 = 0.2236 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 20:07:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.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 20:07:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:07:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:07:48: 1000000 INFO @ Sun, 21 Jun 2020 20:07:53: 2000000 INFO @ Sun, 21 Jun 2020 20:07:58: 3000000 INFO @ Sun, 21 Jun 2020 20:08:04: 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 20:08:10: 5000000 INFO @ Sun, 21 Jun 2020 20:08:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.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 20:08:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:08:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:08:17: 6000000 INFO @ Sun, 21 Jun 2020 20:08:19: 1000000 INFO @ Sun, 21 Jun 2020 20:08:24: 7000000 INFO @ Sun, 21 Jun 2020 20:08:25: 2000000 INFO @ Sun, 21 Jun 2020 20:08:30: 3000000 INFO @ Sun, 21 Jun 2020 20:08:31: 8000000 INFO @ Sun, 21 Jun 2020 20:08:34: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:08:34: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:08:34: #1 total tags in treatment: 8484278 INFO @ Sun, 21 Jun 2020 20:08:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:08:34: #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 20:08:35: #1 tags after filtering in treatment: 8483993 INFO @ Sun, 21 Jun 2020 20:08:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:08:35: #1 finished! INFO @ Sun, 21 Jun 2020 20:08:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:08:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:08:36: #2 number of paired peaks: 7259 INFO @ Sun, 21 Jun 2020 20:08:36: start model_add_line... INFO @ Sun, 21 Jun 2020 20:08:36: start X-correlation... INFO @ Sun, 21 Jun 2020 20:08:36: end of X-cor INFO @ Sun, 21 Jun 2020 20:08:36: #2 finished! INFO @ Sun, 21 Jun 2020 20:08:36: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 20:08:36: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 21 Jun 2020 20:08:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.05_model.r INFO @ Sun, 21 Jun 2020 20:08:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:08:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:08:36: 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 20:08:42: 5000000 INFO @ Sun, 21 Jun 2020 20:08:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.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 20:08:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:08:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:08:48: 6000000 INFO @ Sun, 21 Jun 2020 20:08:49: 1000000 INFO @ Sun, 21 Jun 2020 20:08:54: 7000000 INFO @ Sun, 21 Jun 2020 20:08:55: 2000000 INFO @ Sun, 21 Jun 2020 20:09:01: 3000000 INFO @ Sun, 21 Jun 2020 20:09:01: 8000000 INFO @ Sun, 21 Jun 2020 20:09:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:09:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:09:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:09:04: #1 total tags in treatment: 8484278 INFO @ Sun, 21 Jun 2020 20:09:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:09:04: #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 20:09:05: #1 tags after filtering in treatment: 8483993 INFO @ Sun, 21 Jun 2020 20:09:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:09:05: #1 finished! INFO @ Sun, 21 Jun 2020 20:09:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:09:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:09:06: #2 number of paired peaks: 7259 INFO @ Sun, 21 Jun 2020 20:09:06: start model_add_line... INFO @ Sun, 21 Jun 2020 20:09:06: start X-correlation... INFO @ Sun, 21 Jun 2020 20:09:06: end of X-cor INFO @ Sun, 21 Jun 2020 20:09:06: #2 finished! INFO @ Sun, 21 Jun 2020 20:09:06: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 20:09:06: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 21 Jun 2020 20:09:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.10_model.r INFO @ Sun, 21 Jun 2020 20:09:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:09:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:09:07: 4000000 INFO @ Sun, 21 Jun 2020 20:09:13: 5000000 INFO @ Sun, 21 Jun 2020 20:09:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:09:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:09:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.05_summits.bed INFO @ Sun, 21 Jun 2020 20:09:15: Done! pass1 - making usageList (164 chroms): 2 millis pass2 - checking and writing primary data (8389 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:09:19: 6000000 INFO @ Sun, 21 Jun 2020 20:09:25: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:09:31: 8000000 INFO @ Sun, 21 Jun 2020 20:09:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:09:34: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:09:34: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:09:34: #1 total tags in treatment: 8484278 INFO @ Sun, 21 Jun 2020 20:09:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:09:34: #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 20:09:34: #1 tags after filtering in treatment: 8483993 INFO @ Sun, 21 Jun 2020 20:09:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:09:34: #1 finished! INFO @ Sun, 21 Jun 2020 20:09:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:09:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:09:36: #2 number of paired peaks: 7259 INFO @ Sun, 21 Jun 2020 20:09:36: start model_add_line... INFO @ Sun, 21 Jun 2020 20:09:36: start X-correlation... INFO @ Sun, 21 Jun 2020 20:09:36: end of X-cor INFO @ Sun, 21 Jun 2020 20:09:36: #2 finished! INFO @ Sun, 21 Jun 2020 20:09:36: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 20:09:36: #2 alternative fragment length(s) may be 165 bps INFO @ Sun, 21 Jun 2020 20:09:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.20_model.r INFO @ Sun, 21 Jun 2020 20:09:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:09:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:09:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:09:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:09:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.10_summits.bed INFO @ Sun, 21 Jun 2020 20:09:44: Done! pass1 - making usageList (135 chroms): 1 millis pass2 - checking and writing primary data (6523 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:10:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:10:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:10:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:10:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3873736/SRX3873736.20_summits.bed INFO @ Sun, 21 Jun 2020 20:10:13: Done! pass1 - making usageList (111 chroms): 2 millis pass2 - checking and writing primary data (4377 records, 4 fields): 12 millis CompletedMACS2peakCalling