Job ID = 6454067 SRX = SRX1794252 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:45:47 prefetch.2.10.7: 1) Downloading 'SRR3575296'... 2020-06-21T08:45:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:49:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:49:42 prefetch.2.10.7: 'SRR3575296' is valid 2020-06-21T08:49:42 prefetch.2.10.7: 1) 'SRR3575296' was downloaded successfully Read 11940468 spots for SRR3575296/SRR3575296.sra Written 11940468 spots for SRR3575296/SRR3575296.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: 00:02:40 11940468 reads; of these: 11940468 (100.00%) were unpaired; of these: 360632 (3.02%) aligned 0 times 9924528 (83.12%) aligned exactly 1 time 1655308 (13.86%) aligned >1 times 96.98% overall alignment rate Time searching: 00:02:40 Overall time: 00:02:40 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] 2742877 / 11579836 = 0.2369 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 17:56:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.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 17:56:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:56:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:56:20: 1000000 INFO @ Sun, 21 Jun 2020 17:56:25: 2000000 INFO @ Sun, 21 Jun 2020 17:56:30: 3000000 INFO @ Sun, 21 Jun 2020 17:56:35: 4000000 INFO @ Sun, 21 Jun 2020 17:56:40: 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 17:56:44: 6000000 INFO @ Sun, 21 Jun 2020 17:56:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.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 17:56:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:56:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:56:49: 7000000 INFO @ Sun, 21 Jun 2020 17:56:50: 1000000 INFO @ Sun, 21 Jun 2020 17:56:55: 8000000 INFO @ Sun, 21 Jun 2020 17:56:55: 2000000 INFO @ Sun, 21 Jun 2020 17:56:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:56:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:56:59: #1 total tags in treatment: 8836959 INFO @ Sun, 21 Jun 2020 17:56:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:56:59: #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 17:57:00: #1 tags after filtering in treatment: 8836766 INFO @ Sun, 21 Jun 2020 17:57:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:57:00: #1 finished! INFO @ Sun, 21 Jun 2020 17:57:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:57:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:57:00: 3000000 INFO @ Sun, 21 Jun 2020 17:57:01: #2 number of paired peaks: 11870 INFO @ Sun, 21 Jun 2020 17:57:01: start model_add_line... INFO @ Sun, 21 Jun 2020 17:57:01: start X-correlation... INFO @ Sun, 21 Jun 2020 17:57:01: end of X-cor INFO @ Sun, 21 Jun 2020 17:57:01: #2 finished! INFO @ Sun, 21 Jun 2020 17:57:01: #2 predicted fragment length is 180 bps INFO @ Sun, 21 Jun 2020 17:57:01: #2 alternative fragment length(s) may be 180 bps INFO @ Sun, 21 Jun 2020 17:57:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.05_model.r INFO @ Sun, 21 Jun 2020 17:57:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:57:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:57:05: 4000000 INFO @ Sun, 21 Jun 2020 17:57:10: 5000000 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 17:57:15: 6000000 INFO @ Sun, 21 Jun 2020 17:57:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.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 17:57:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:57:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:57:20: 7000000 INFO @ Sun, 21 Jun 2020 17:57:21: 1000000 INFO @ Sun, 21 Jun 2020 17:57:25: 8000000 INFO @ Sun, 21 Jun 2020 17:57:27: 2000000 INFO @ Sun, 21 Jun 2020 17:57:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:57:30: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:57:30: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:57:30: #1 total tags in treatment: 8836959 INFO @ Sun, 21 Jun 2020 17:57:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:57:30: #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 17:57:30: #1 tags after filtering in treatment: 8836766 INFO @ Sun, 21 Jun 2020 17:57:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:57:30: #1 finished! INFO @ Sun, 21 Jun 2020 17:57:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:57:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:57:31: #2 number of paired peaks: 11870 INFO @ Sun, 21 Jun 2020 17:57:31: start model_add_line... INFO @ Sun, 21 Jun 2020 17:57:32: start X-correlation... INFO @ Sun, 21 Jun 2020 17:57:32: end of X-cor INFO @ Sun, 21 Jun 2020 17:57:32: #2 finished! INFO @ Sun, 21 Jun 2020 17:57:32: #2 predicted fragment length is 180 bps INFO @ Sun, 21 Jun 2020 17:57:32: #2 alternative fragment length(s) may be 180 bps INFO @ Sun, 21 Jun 2020 17:57:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.10_model.r INFO @ Sun, 21 Jun 2020 17:57:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:57:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:57:33: 3000000 INFO @ Sun, 21 Jun 2020 17:57:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:57:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:57:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.05_summits.bed INFO @ Sun, 21 Jun 2020 17:57:38: Done! INFO @ Sun, 21 Jun 2020 17:57:38: 4000000 pass1 - making usageList (196 chroms): 2 millis pass2 - checking and writing primary data (8690 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:57:44: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:57:50: 6000000 INFO @ Sun, 21 Jun 2020 17:57:56: 7000000 INFO @ Sun, 21 Jun 2020 17:57:56: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:58:02: 8000000 INFO @ Sun, 21 Jun 2020 17:58:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:58:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:58:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.10_summits.bed INFO @ Sun, 21 Jun 2020 17:58:07: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:58:07: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:58:07: #1 total tags in treatment: 8836959 INFO @ Sun, 21 Jun 2020 17:58:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:58:07: #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 17:58:07: Done! INFO @ Sun, 21 Jun 2020 17:58:07: #1 tags after filtering in treatment: 8836766 INFO @ Sun, 21 Jun 2020 17:58:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:58:07: #1 finished! INFO @ Sun, 21 Jun 2020 17:58:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:58:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:58:09: #2 number of paired peaks: 11870 INFO @ Sun, 21 Jun 2020 17:58:09: start model_add_line... INFO @ Sun, 21 Jun 2020 17:58:09: start X-correlation... INFO @ Sun, 21 Jun 2020 17:58:09: end of X-cor INFO @ Sun, 21 Jun 2020 17:58:09: #2 finished! INFO @ Sun, 21 Jun 2020 17:58:09: #2 predicted fragment length is 180 bps INFO @ Sun, 21 Jun 2020 17:58:09: #2 alternative fragment length(s) may be 180 bps INFO @ Sun, 21 Jun 2020 17:58:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.20_model.r INFO @ Sun, 21 Jun 2020 17:58:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:58:09: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (155 chroms): 2 millis pass2 - checking and writing primary data (8182 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:58:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:58:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:58:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:58:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794252/SRX1794252.20_summits.bed INFO @ Sun, 21 Jun 2020 17:58:46: Done! pass1 - making usageList (114 chroms): 2 millis pass2 - checking and writing primary data (7338 records, 4 fields): 11 millis CompletedMACS2peakCalling