Job ID = 6455178 SRX = SRX2829095 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:42:10 prefetch.2.10.7: 1) Downloading 'SRR5569905'... 2020-06-21T09:42:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:45:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:45:10 prefetch.2.10.7: 1) 'SRR5569905' was downloaded successfully Read 19931452 spots for SRR5569905/SRR5569905.sra Written 19931452 spots for SRR5569905/SRR5569905.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: 00:00:01 Multiseed full-index search: 00:04:08 19931452 reads; of these: 19931452 (100.00%) were unpaired; of these: 3606241 (18.09%) aligned 0 times 13983853 (70.16%) aligned exactly 1 time 2341358 (11.75%) aligned >1 times 81.91% overall alignment rate Time searching: 00:04:09 Overall time: 00:04:09 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] 7135088 / 16325211 = 0.4371 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 18:54:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.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 18:54:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:54:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:54:08: 1000000 INFO @ Sun, 21 Jun 2020 18:54:14: 2000000 INFO @ Sun, 21 Jun 2020 18:54:21: 3000000 INFO @ Sun, 21 Jun 2020 18:54:27: 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 18:54:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.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 18:54:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:54:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:54:34: 5000000 INFO @ Sun, 21 Jun 2020 18:54:38: 1000000 INFO @ Sun, 21 Jun 2020 18:54:41: 6000000 INFO @ Sun, 21 Jun 2020 18:54:45: 2000000 INFO @ Sun, 21 Jun 2020 18:54:47: 7000000 INFO @ Sun, 21 Jun 2020 18:54:52: 3000000 INFO @ Sun, 21 Jun 2020 18:54:54: 8000000 INFO @ Sun, 21 Jun 2020 18:54:59: 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 18:55:00: 9000000 INFO @ Sun, 21 Jun 2020 18:55:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:55:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:55:01: #1 total tags in treatment: 9190123 INFO @ Sun, 21 Jun 2020 18:55:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:55:01: #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 18:55:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.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 18:55:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:55:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:55:02: #1 tags after filtering in treatment: 9190099 INFO @ Sun, 21 Jun 2020 18:55:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:55:02: #1 finished! INFO @ Sun, 21 Jun 2020 18:55:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:55:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:55:03: #2 number of paired peaks: 7075 INFO @ Sun, 21 Jun 2020 18:55:03: start model_add_line... INFO @ Sun, 21 Jun 2020 18:55:03: start X-correlation... INFO @ Sun, 21 Jun 2020 18:55:03: end of X-cor INFO @ Sun, 21 Jun 2020 18:55:03: #2 finished! INFO @ Sun, 21 Jun 2020 18:55:03: #2 predicted fragment length is 187 bps INFO @ Sun, 21 Jun 2020 18:55:03: #2 alternative fragment length(s) may be 4,187 bps INFO @ Sun, 21 Jun 2020 18:55:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.05_model.r INFO @ Sun, 21 Jun 2020 18:55:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:55:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:55:06: 5000000 INFO @ Sun, 21 Jun 2020 18:55:08: 1000000 INFO @ Sun, 21 Jun 2020 18:55:13: 6000000 INFO @ Sun, 21 Jun 2020 18:55:15: 2000000 INFO @ Sun, 21 Jun 2020 18:55:20: 7000000 INFO @ Sun, 21 Jun 2020 18:55:22: 3000000 INFO @ Sun, 21 Jun 2020 18:55:27: 8000000 INFO @ Sun, 21 Jun 2020 18:55:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:55:28: 4000000 INFO @ Sun, 21 Jun 2020 18:55:34: 9000000 INFO @ Sun, 21 Jun 2020 18:55:34: 5000000 INFO @ Sun, 21 Jun 2020 18:55:36: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:55:36: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:55:36: #1 total tags in treatment: 9190123 INFO @ Sun, 21 Jun 2020 18:55:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:55:36: #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 18:55:36: #1 tags after filtering in treatment: 9190099 INFO @ Sun, 21 Jun 2020 18:55:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:55:36: #1 finished! INFO @ Sun, 21 Jun 2020 18:55:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:55:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:55:37: #2 number of paired peaks: 7075 INFO @ Sun, 21 Jun 2020 18:55:37: start model_add_line... INFO @ Sun, 21 Jun 2020 18:55:37: start X-correlation... INFO @ Sun, 21 Jun 2020 18:55:37: end of X-cor INFO @ Sun, 21 Jun 2020 18:55:37: #2 finished! INFO @ Sun, 21 Jun 2020 18:55:37: #2 predicted fragment length is 187 bps INFO @ Sun, 21 Jun 2020 18:55:37: #2 alternative fragment length(s) may be 4,187 bps INFO @ Sun, 21 Jun 2020 18:55:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.10_model.r INFO @ Sun, 21 Jun 2020 18:55:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:55:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:55:40: 6000000 INFO @ Sun, 21 Jun 2020 18:55:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:55:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:55:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.05_summits.bed INFO @ Sun, 21 Jun 2020 18:55:41: Done! pass1 - making usageList (305 chroms): 1 millis pass2 - checking and writing primary data (7930 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:55:45: 7000000 INFO @ Sun, 21 Jun 2020 18:55:51: 8000000 INFO @ Sun, 21 Jun 2020 18:55:56: 9000000 INFO @ Sun, 21 Jun 2020 18:55:58: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:55:58: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:55:58: #1 total tags in treatment: 9190123 INFO @ Sun, 21 Jun 2020 18:55:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:55:58: #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 18:55:58: #1 tags after filtering in treatment: 9190099 INFO @ Sun, 21 Jun 2020 18:55:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:55:58: #1 finished! INFO @ Sun, 21 Jun 2020 18:55:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:55:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:55:59: #2 number of paired peaks: 7075 INFO @ Sun, 21 Jun 2020 18:55:59: start model_add_line... INFO @ Sun, 21 Jun 2020 18:55:59: start X-correlation... INFO @ Sun, 21 Jun 2020 18:55:59: end of X-cor INFO @ Sun, 21 Jun 2020 18:55:59: #2 finished! INFO @ Sun, 21 Jun 2020 18:55:59: #2 predicted fragment length is 187 bps INFO @ Sun, 21 Jun 2020 18:55:59: #2 alternative fragment length(s) may be 4,187 bps INFO @ Sun, 21 Jun 2020 18:55:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.20_model.r INFO @ Sun, 21 Jun 2020 18:55:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:55:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:56:01: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:56:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:56:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:56:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.10_summits.bed INFO @ Sun, 21 Jun 2020 18:56:13: Done! pass1 - making usageList (248 chroms): 2 millis pass2 - checking and writing primary data (5285 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:56:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:56:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:56:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:56:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2829095/SRX2829095.20_summits.bed INFO @ Sun, 21 Jun 2020 18:56:34: Done! pass1 - making usageList (180 chroms): 1 millis pass2 - checking and writing primary data (2190 records, 4 fields): 8 millis CompletedMACS2peakCalling