Job ID = 6454243 SRX = SRX193319 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:06:09 prefetch.2.10.7: 1) Downloading 'SRR585052'... 2020-06-21T09:06:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:08:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:08:09 prefetch.2.10.7: 'SRR585052' is valid 2020-06-21T09:08:09 prefetch.2.10.7: 1) 'SRR585052' was downloaded successfully Read 11006122 spots for SRR585052/SRR585052.sra Written 11006122 spots for SRR585052/SRR585052.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: 00:02:34 11006122 reads; of these: 11006122 (100.00%) were unpaired; of these: 630426 (5.73%) aligned 0 times 8755824 (79.55%) aligned exactly 1 time 1619872 (14.72%) aligned >1 times 94.27% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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] 1925850 / 10375696 = 0.1856 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 18:14:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.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 18:14:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:14:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:14:29: 1000000 INFO @ Sun, 21 Jun 2020 18:14:34: 2000000 INFO @ Sun, 21 Jun 2020 18:14:40: 3000000 INFO @ Sun, 21 Jun 2020 18:14:45: 4000000 INFO @ Sun, 21 Jun 2020 18:14:50: 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 18:14:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.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 18:14:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:14:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:14:56: 6000000 INFO @ Sun, 21 Jun 2020 18:15:00: 1000000 INFO @ Sun, 21 Jun 2020 18:15:02: 7000000 INFO @ Sun, 21 Jun 2020 18:15:06: 2000000 INFO @ Sun, 21 Jun 2020 18:15:08: 8000000 INFO @ Sun, 21 Jun 2020 18:15:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:15:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:15:11: #1 total tags in treatment: 8449846 INFO @ Sun, 21 Jun 2020 18:15:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:15:11: #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 18:15:11: #1 tags after filtering in treatment: 8449493 INFO @ Sun, 21 Jun 2020 18:15:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:15:11: #1 finished! INFO @ Sun, 21 Jun 2020 18:15:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:15:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:15:12: 3000000 INFO @ Sun, 21 Jun 2020 18:15:13: #2 number of paired peaks: 10831 INFO @ Sun, 21 Jun 2020 18:15:13: start model_add_line... INFO @ Sun, 21 Jun 2020 18:15:13: start X-correlation... INFO @ Sun, 21 Jun 2020 18:15:13: end of X-cor INFO @ Sun, 21 Jun 2020 18:15:13: #2 finished! INFO @ Sun, 21 Jun 2020 18:15:13: #2 predicted fragment length is 138 bps INFO @ Sun, 21 Jun 2020 18:15:13: #2 alternative fragment length(s) may be 138 bps INFO @ Sun, 21 Jun 2020 18:15:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.05_model.r INFO @ Sun, 21 Jun 2020 18:15:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:15:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:15:18: 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 18:15:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.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 18:15:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:15:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:15:23: 5000000 INFO @ Sun, 21 Jun 2020 18:15:30: 6000000 INFO @ Sun, 21 Jun 2020 18:15:30: 1000000 INFO @ Sun, 21 Jun 2020 18:15:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:15:36: 7000000 INFO @ Sun, 21 Jun 2020 18:15:37: 2000000 INFO @ Sun, 21 Jun 2020 18:15:43: 8000000 INFO @ Sun, 21 Jun 2020 18:15:44: 3000000 INFO @ Sun, 21 Jun 2020 18:15:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:15:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:15:46: #1 total tags in treatment: 8449846 INFO @ Sun, 21 Jun 2020 18:15:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:15:46: #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 18:15:46: #1 tags after filtering in treatment: 8449493 INFO @ Sun, 21 Jun 2020 18:15:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:15:46: #1 finished! INFO @ Sun, 21 Jun 2020 18:15:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:15:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:15:47: #2 number of paired peaks: 10831 INFO @ Sun, 21 Jun 2020 18:15:47: start model_add_line... INFO @ Sun, 21 Jun 2020 18:15:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:15:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:15:47: start X-correlation... INFO @ Sun, 21 Jun 2020 18:15:47: end of X-cor INFO @ Sun, 21 Jun 2020 18:15:47: #2 finished! INFO @ Sun, 21 Jun 2020 18:15:47: #2 predicted fragment length is 138 bps INFO @ Sun, 21 Jun 2020 18:15:47: #2 alternative fragment length(s) may be 138 bps INFO @ Sun, 21 Jun 2020 18:15:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.10_model.r INFO @ Sun, 21 Jun 2020 18:15:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:15:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:15:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.05_summits.bed INFO @ Sun, 21 Jun 2020 18:15:48: Done! pass1 - making usageList (155 chroms): 2 millis pass2 - checking and writing primary data (13163 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:15:50: 4000000 INFO @ Sun, 21 Jun 2020 18:15:56: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:16:03: 6000000 INFO @ Sun, 21 Jun 2020 18:16:10: 7000000 INFO @ Sun, 21 Jun 2020 18:16:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:16:16: 8000000 INFO @ Sun, 21 Jun 2020 18:16:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:16:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:16:19: #1 total tags in treatment: 8449846 INFO @ Sun, 21 Jun 2020 18:16:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:16:19: #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 18:16:20: #1 tags after filtering in treatment: 8449493 INFO @ Sun, 21 Jun 2020 18:16:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:16:20: #1 finished! INFO @ Sun, 21 Jun 2020 18:16:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:16:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:16:21: #2 number of paired peaks: 10831 INFO @ Sun, 21 Jun 2020 18:16:21: start model_add_line... INFO @ Sun, 21 Jun 2020 18:16:21: start X-correlation... INFO @ Sun, 21 Jun 2020 18:16:21: end of X-cor INFO @ Sun, 21 Jun 2020 18:16:21: #2 finished! INFO @ Sun, 21 Jun 2020 18:16:21: #2 predicted fragment length is 138 bps INFO @ Sun, 21 Jun 2020 18:16:21: #2 alternative fragment length(s) may be 138 bps INFO @ Sun, 21 Jun 2020 18:16:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.20_model.r INFO @ Sun, 21 Jun 2020 18:16:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:16:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:16:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:16:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:16:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.10_summits.bed INFO @ Sun, 21 Jun 2020 18:16:23: Done! pass1 - making usageList (123 chroms): 2 millis pass2 - checking and writing primary data (9484 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:16:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:16:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:16:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:16:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193319/SRX193319.20_summits.bed INFO @ Sun, 21 Jun 2020 18:16:56: Done! pass1 - making usageList (102 chroms): 1 millis pass2 - checking and writing primary data (5325 records, 4 fields): 9 millis CompletedMACS2peakCalling