Job ID = 6454882 SRX = SRX2592470 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:31:29 prefetch.2.10.7: 1) Downloading 'SRR5289747'... 2020-06-21T09:31:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:34:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:34:05 prefetch.2.10.7: 1) 'SRR5289747' was downloaded successfully Read 17532108 spots for SRR5289747/SRR5289747.sra Written 17532108 spots for SRR5289747/SRR5289747.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: 00:03:44 17532108 reads; of these: 17532108 (100.00%) were unpaired; of these: 1637403 (9.34%) aligned 0 times 13069550 (74.55%) aligned exactly 1 time 2825155 (16.11%) aligned >1 times 90.66% overall alignment rate Time searching: 00:03:44 Overall time: 00:03:44 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] 5869762 / 15894705 = 0.3693 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 18:42:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.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 18:42:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:42:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:42:37: 1000000 INFO @ Sun, 21 Jun 2020 18:42:42: 2000000 INFO @ Sun, 21 Jun 2020 18:42:47: 3000000 INFO @ Sun, 21 Jun 2020 18:42:52: 4000000 INFO @ Sun, 21 Jun 2020 18:42:57: 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 18:43:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.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 18:43:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:02: 6000000 INFO @ Sun, 21 Jun 2020 18:43:08: 7000000 INFO @ Sun, 21 Jun 2020 18:43:08: 1000000 INFO @ Sun, 21 Jun 2020 18:43:13: 8000000 INFO @ Sun, 21 Jun 2020 18:43:13: 2000000 INFO @ Sun, 21 Jun 2020 18:43:19: 9000000 INFO @ Sun, 21 Jun 2020 18:43:19: 3000000 INFO @ Sun, 21 Jun 2020 18:43:24: 10000000 INFO @ Sun, 21 Jun 2020 18:43:24: 4000000 INFO @ Sun, 21 Jun 2020 18:43:24: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:43:24: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:43:24: #1 total tags in treatment: 10024943 INFO @ Sun, 21 Jun 2020 18:43:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:43:24: #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 18:43:25: #1 tags after filtering in treatment: 10024746 INFO @ Sun, 21 Jun 2020 18:43:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:43:25: #1 finished! INFO @ Sun, 21 Jun 2020 18:43:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:43:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:43:26: #2 number of paired peaks: 8716 INFO @ Sun, 21 Jun 2020 18:43:26: start model_add_line... INFO @ Sun, 21 Jun 2020 18:43:26: start X-correlation... INFO @ Sun, 21 Jun 2020 18:43:26: end of X-cor INFO @ Sun, 21 Jun 2020 18:43:26: #2 finished! INFO @ Sun, 21 Jun 2020 18:43:26: #2 predicted fragment length is 204 bps INFO @ Sun, 21 Jun 2020 18:43:26: #2 alternative fragment length(s) may be 204 bps INFO @ Sun, 21 Jun 2020 18:43:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.05_model.r INFO @ Sun, 21 Jun 2020 18:43:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:43:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:43:30: 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 18:43:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.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 18:43:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:35: 6000000 INFO @ Sun, 21 Jun 2020 18:43:37: 1000000 INFO @ Sun, 21 Jun 2020 18:43:40: 7000000 INFO @ Sun, 21 Jun 2020 18:43:43: 2000000 INFO @ Sun, 21 Jun 2020 18:43:46: 8000000 INFO @ Sun, 21 Jun 2020 18:43:48: 3000000 INFO @ Sun, 21 Jun 2020 18:43:51: 9000000 INFO @ Sun, 21 Jun 2020 18:43:53: 4000000 INFO @ Sun, 21 Jun 2020 18:43:57: 10000000 INFO @ Sun, 21 Jun 2020 18:43:57: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:43:57: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:43:57: #1 total tags in treatment: 10024943 INFO @ Sun, 21 Jun 2020 18:43:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:43:57: #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 18:43:57: #1 tags after filtering in treatment: 10024746 INFO @ Sun, 21 Jun 2020 18:43:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:43:57: #1 finished! INFO @ Sun, 21 Jun 2020 18:43:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:43:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:43:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:43:59: #2 number of paired peaks: 8716 INFO @ Sun, 21 Jun 2020 18:43:59: start model_add_line... INFO @ Sun, 21 Jun 2020 18:43:59: start X-correlation... INFO @ Sun, 21 Jun 2020 18:43:59: 5000000 INFO @ Sun, 21 Jun 2020 18:43:59: end of X-cor INFO @ Sun, 21 Jun 2020 18:43:59: #2 finished! INFO @ Sun, 21 Jun 2020 18:43:59: #2 predicted fragment length is 204 bps INFO @ Sun, 21 Jun 2020 18:43:59: #2 alternative fragment length(s) may be 204 bps INFO @ Sun, 21 Jun 2020 18:43:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.10_model.r INFO @ Sun, 21 Jun 2020 18:43:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:43:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:44:04: 6000000 INFO @ Sun, 21 Jun 2020 18:44:09: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:44:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:44:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:44:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.05_summits.bed INFO @ Sun, 21 Jun 2020 18:44:12: Done! pass1 - making usageList (183 chroms): 1 millis pass2 - checking and writing primary data (9171 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:44:14: 8000000 INFO @ Sun, 21 Jun 2020 18:44:20: 9000000 INFO @ Sun, 21 Jun 2020 18:44:25: 10000000 INFO @ Sun, 21 Jun 2020 18:44:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:44:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:44:25: #1 total tags in treatment: 10024943 INFO @ Sun, 21 Jun 2020 18:44:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:44:25: #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 18:44:25: #1 tags after filtering in treatment: 10024746 INFO @ Sun, 21 Jun 2020 18:44:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:44:25: #1 finished! INFO @ Sun, 21 Jun 2020 18:44:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:44:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:44:27: #2 number of paired peaks: 8716 INFO @ Sun, 21 Jun 2020 18:44:27: start model_add_line... INFO @ Sun, 21 Jun 2020 18:44:27: start X-correlation... INFO @ Sun, 21 Jun 2020 18:44:27: end of X-cor INFO @ Sun, 21 Jun 2020 18:44:27: #2 finished! INFO @ Sun, 21 Jun 2020 18:44:27: #2 predicted fragment length is 204 bps INFO @ Sun, 21 Jun 2020 18:44:27: #2 alternative fragment length(s) may be 204 bps INFO @ Sun, 21 Jun 2020 18:44:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.20_model.r INFO @ Sun, 21 Jun 2020 18:44:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:44:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:44:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:44:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:44:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:44:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.10_summits.bed INFO @ Sun, 21 Jun 2020 18:44:44: Done! pass1 - making usageList (142 chroms): 2 millis pass2 - checking and writing primary data (7461 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:44:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:45:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:45:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:45:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592470/SRX2592470.20_summits.bed INFO @ Sun, 21 Jun 2020 18:45:12: Done! pass1 - making usageList (111 chroms): 1 millis pass2 - checking and writing primary data (5799 records, 4 fields): 10 millis CompletedMACS2peakCalling