Job ID = 6454670 SRX = SRX2458931 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:27:59 prefetch.2.10.7: 1) Downloading 'SRR5140280'... 2020-06-21T09:27:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:30:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:30:04 prefetch.2.10.7: 'SRR5140280' is valid 2020-06-21T09:30:04 prefetch.2.10.7: 1) 'SRR5140280' was downloaded successfully 2020-06-21T09:30:04 prefetch.2.10.7: 'SRR5140280' has 0 unresolved dependencies Read 10678664 spots for SRR5140280/SRR5140280.sra Written 10678664 spots for SRR5140280/SRR5140280.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: 00:02:43 10678664 reads; of these: 10678664 (100.00%) were unpaired; of these: 527047 (4.94%) aligned 0 times 7730483 (72.39%) aligned exactly 1 time 2421134 (22.67%) aligned >1 times 95.06% overall alignment rate Time searching: 00:02:43 Overall time: 00:02:43 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] 6766043 / 10151617 = 0.6665 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 18:35:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.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 18:35:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:35:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:35:24: 1000000 INFO @ Sun, 21 Jun 2020 18:35:31: 2000000 INFO @ Sun, 21 Jun 2020 18:35:38: 3000000 INFO @ Sun, 21 Jun 2020 18:35:41: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:35:41: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:35:41: #1 total tags in treatment: 3385574 INFO @ Sun, 21 Jun 2020 18:35:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:35:41: #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 18:35:41: #1 tags after filtering in treatment: 3385350 INFO @ Sun, 21 Jun 2020 18:35:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:35:41: #1 finished! INFO @ Sun, 21 Jun 2020 18:35:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:35:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:35:41: #2 number of paired peaks: 3269 INFO @ Sun, 21 Jun 2020 18:35:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:35:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:35:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:35:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:35:41: #2 predicted fragment length is 136 bps INFO @ Sun, 21 Jun 2020 18:35:41: #2 alternative fragment length(s) may be 136,141 bps INFO @ Sun, 21 Jun 2020 18:35:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.05_model.r INFO @ Sun, 21 Jun 2020 18:35:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:35:41: #3 Pre-compute pvalue-qvalue table... 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 18:35:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.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 18:35:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:35:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:35:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:35:54: 1000000 INFO @ Sun, 21 Jun 2020 18:35:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:35:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:35:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.05_summits.bed INFO @ Sun, 21 Jun 2020 18:35:55: Done! pass1 - making usageList (351 chroms): 1 millis pass2 - checking and writing primary data (1855 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:36:01: 2000000 INFO @ Sun, 21 Jun 2020 18:36:09: 3000000 INFO @ Sun, 21 Jun 2020 18:36:12: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:36:12: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:36:12: #1 total tags in treatment: 3385574 INFO @ Sun, 21 Jun 2020 18:36:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:36:12: #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 18:36:12: #1 tags after filtering in treatment: 3385350 INFO @ Sun, 21 Jun 2020 18:36:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:36:12: #1 finished! INFO @ Sun, 21 Jun 2020 18:36:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:36:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:36:12: #2 number of paired peaks: 3269 INFO @ Sun, 21 Jun 2020 18:36:12: start model_add_line... INFO @ Sun, 21 Jun 2020 18:36:12: start X-correlation... INFO @ Sun, 21 Jun 2020 18:36:12: end of X-cor INFO @ Sun, 21 Jun 2020 18:36:12: #2 finished! INFO @ Sun, 21 Jun 2020 18:36:12: #2 predicted fragment length is 136 bps INFO @ Sun, 21 Jun 2020 18:36:12: #2 alternative fragment length(s) may be 136,141 bps INFO @ Sun, 21 Jun 2020 18:36:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.10_model.r INFO @ Sun, 21 Jun 2020 18:36:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:36:12: #3 Pre-compute pvalue-qvalue table... 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 18:36:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.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 18:36:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:36:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:36:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:36:24: 1000000 INFO @ Sun, 21 Jun 2020 18:36:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:36:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:36:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.10_summits.bed INFO @ Sun, 21 Jun 2020 18:36:26: Done! pass1 - making usageList (196 chroms): 1 millis pass2 - checking and writing primary data (602 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:36:31: 2000000 INFO @ Sun, 21 Jun 2020 18:36:38: 3000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:36:41: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:36:41: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:36:41: #1 total tags in treatment: 3385574 INFO @ Sun, 21 Jun 2020 18:36:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:36:41: #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 18:36:41: #1 tags after filtering in treatment: 3385350 INFO @ Sun, 21 Jun 2020 18:36:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:36:41: #1 finished! INFO @ Sun, 21 Jun 2020 18:36:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:36:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:36:42: #2 number of paired peaks: 3269 INFO @ Sun, 21 Jun 2020 18:36:42: start model_add_line... INFO @ Sun, 21 Jun 2020 18:36:42: start X-correlation... INFO @ Sun, 21 Jun 2020 18:36:42: end of X-cor INFO @ Sun, 21 Jun 2020 18:36:42: #2 finished! INFO @ Sun, 21 Jun 2020 18:36:42: #2 predicted fragment length is 136 bps INFO @ Sun, 21 Jun 2020 18:36:42: #2 alternative fragment length(s) may be 136,141 bps INFO @ Sun, 21 Jun 2020 18:36:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.20_model.r INFO @ Sun, 21 Jun 2020 18:36:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:36:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:36:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:36:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:36:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:36:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2458931/SRX2458931.20_summits.bed INFO @ Sun, 21 Jun 2020 18:36:55: Done! pass1 - making usageList (144 chroms): 1 millis pass2 - checking and writing primary data (308 records, 4 fields): 7 millis CompletedMACS2peakCalling