Job ID = 6454868 SRX = SRX2592459 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:30:44 prefetch.2.10.7: 1) Downloading 'SRR5289736'... 2020-06-21T09:30:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:34:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:34:40 prefetch.2.10.7: 1) 'SRR5289736' was downloaded successfully Read 20726827 spots for SRR5289736/SRR5289736.sra Written 20726827 spots for SRR5289736/SRR5289736.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: 00:04:08 20726827 reads; of these: 20726827 (100.00%) were unpaired; of these: 6862046 (33.11%) aligned 0 times 11106754 (53.59%) aligned exactly 1 time 2758027 (13.31%) aligned >1 times 66.89% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:08 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] 7505197 / 13864781 = 0.5413 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 18:43:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.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 18:43:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:16: 1000000 INFO @ Sun, 21 Jun 2020 18:43:23: 2000000 INFO @ Sun, 21 Jun 2020 18:43:30: 3000000 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 18:43:37: 4000000 INFO @ Sun, 21 Jun 2020 18:43:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.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 18:43:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:45: 5000000 INFO @ Sun, 21 Jun 2020 18:43:46: 1000000 INFO @ Sun, 21 Jun 2020 18:43:54: 6000000 INFO @ Sun, 21 Jun 2020 18:43:54: 2000000 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: 6359584 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: 6359432 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: #2 number of paired peaks: 3380 INFO @ Sun, 21 Jun 2020 18:43:58: start model_add_line... INFO @ Sun, 21 Jun 2020 18:43:58: start X-correlation... INFO @ Sun, 21 Jun 2020 18:43:58: end of X-cor INFO @ Sun, 21 Jun 2020 18:43:58: #2 finished! INFO @ Sun, 21 Jun 2020 18:43:58: #2 predicted fragment length is 200 bps INFO @ Sun, 21 Jun 2020 18:43:58: #2 alternative fragment length(s) may be 200 bps INFO @ Sun, 21 Jun 2020 18:43:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.05_model.r INFO @ Sun, 21 Jun 2020 18:43:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:43:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:44:01: 3000000 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 18:44:07: 4000000 INFO @ Sun, 21 Jun 2020 18:44:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.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 18:44:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:44:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:44:14: 5000000 INFO @ Sun, 21 Jun 2020 18:44:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:44:17: 1000000 INFO @ Sun, 21 Jun 2020 18:44:21: 6000000 INFO @ Sun, 21 Jun 2020 18:44:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:44:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:44:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.05_summits.bed INFO @ Sun, 21 Jun 2020 18:44:23: Done! INFO @ Sun, 21 Jun 2020 18:44:23: 2000000 pass1 - making usageList (465 chroms): 2 millis pass2 - checking and writing primary data (6664 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:44:24: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:44:24: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:44:24: #1 total tags in treatment: 6359584 INFO @ Sun, 21 Jun 2020 18:44:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:44:24: #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 18:44:24: #1 tags after filtering in treatment: 6359432 INFO @ Sun, 21 Jun 2020 18:44:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:44:24: #1 finished! INFO @ Sun, 21 Jun 2020 18:44:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:44:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:44:25: #2 number of paired peaks: 3380 INFO @ Sun, 21 Jun 2020 18:44:25: start model_add_line... INFO @ Sun, 21 Jun 2020 18:44:25: start X-correlation... INFO @ Sun, 21 Jun 2020 18:44:25: end of X-cor INFO @ Sun, 21 Jun 2020 18:44:25: #2 finished! INFO @ Sun, 21 Jun 2020 18:44:25: #2 predicted fragment length is 200 bps INFO @ Sun, 21 Jun 2020 18:44:25: #2 alternative fragment length(s) may be 200 bps INFO @ Sun, 21 Jun 2020 18:44:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.10_model.r INFO @ Sun, 21 Jun 2020 18:44:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:44:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:44:30: 3000000 INFO @ Sun, 21 Jun 2020 18:44:36: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:44:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:44:43: 5000000 INFO @ Sun, 21 Jun 2020 18:44:49: 6000000 INFO @ Sun, 21 Jun 2020 18:44:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:44:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:44:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.10_summits.bed INFO @ Sun, 21 Jun 2020 18:44:50: Done! pass1 - making usageList (329 chroms): 1 millis pass2 - checking and writing primary data (4988 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:44:51: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:44:51: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:44:51: #1 total tags in treatment: 6359584 INFO @ Sun, 21 Jun 2020 18:44:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:44:51: #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 18:44:51: #1 tags after filtering in treatment: 6359432 INFO @ Sun, 21 Jun 2020 18:44:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:44:51: #1 finished! INFO @ Sun, 21 Jun 2020 18:44:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:44:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:44:52: #2 number of paired peaks: 3380 INFO @ Sun, 21 Jun 2020 18:44:52: start model_add_line... INFO @ Sun, 21 Jun 2020 18:44:52: start X-correlation... INFO @ Sun, 21 Jun 2020 18:44:52: end of X-cor INFO @ Sun, 21 Jun 2020 18:44:52: #2 finished! INFO @ Sun, 21 Jun 2020 18:44:52: #2 predicted fragment length is 200 bps INFO @ Sun, 21 Jun 2020 18:44:52: #2 alternative fragment length(s) may be 200 bps INFO @ Sun, 21 Jun 2020 18:44:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.20_model.r INFO @ Sun, 21 Jun 2020 18:44:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:44:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:45:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:45:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:45:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:45:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592459/SRX2592459.20_summits.bed INFO @ Sun, 21 Jun 2020 18:45:17: Done! pass1 - making usageList (163 chroms): 1 millis pass2 - checking and writing primary data (3337 records, 4 fields): 8 millis CompletedMACS2peakCalling