Job ID = 6454063 SRX = SRX1794248 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:50:34 prefetch.2.10.7: 1) Downloading 'SRR3575292'... 2020-06-21T08:50:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:51:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:51:48 prefetch.2.10.7: 'SRR3575292' is valid 2020-06-21T08:51:48 prefetch.2.10.7: 1) 'SRR3575292' was downloaded successfully Read 10337172 spots for SRR3575292/SRR3575292.sra Written 10337172 spots for SRR3575292/SRR3575292.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 10337172 reads; of these: 10337172 (100.00%) were unpaired; of these: 611623 (5.92%) aligned 0 times 7830802 (75.75%) aligned exactly 1 time 1894747 (18.33%) aligned >1 times 94.08% 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_rmdupse_core] 1286258 / 9725549 = 0.1323 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 17:58:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.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 17:58:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:58:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:58:16: 1000000 INFO @ Sun, 21 Jun 2020 17:58:23: 2000000 INFO @ Sun, 21 Jun 2020 17:58:29: 3000000 INFO @ Sun, 21 Jun 2020 17:58:35: 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 17:58:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.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 17:58:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:58:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:58:41: 5000000 INFO @ Sun, 21 Jun 2020 17:58:47: 1000000 INFO @ Sun, 21 Jun 2020 17:58:48: 6000000 INFO @ Sun, 21 Jun 2020 17:58:54: 2000000 INFO @ Sun, 21 Jun 2020 17:58:55: 7000000 INFO @ Sun, 21 Jun 2020 17:59:01: 3000000 INFO @ Sun, 21 Jun 2020 17:59:02: 8000000 INFO @ Sun, 21 Jun 2020 17:59:05: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:59:05: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:59:05: #1 total tags in treatment: 8439291 INFO @ Sun, 21 Jun 2020 17:59:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:59:05: #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 17:59:05: #1 tags after filtering in treatment: 8439113 INFO @ Sun, 21 Jun 2020 17:59:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:59:05: #1 finished! INFO @ Sun, 21 Jun 2020 17:59:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:59:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:59:06: #2 number of paired peaks: 6440 INFO @ Sun, 21 Jun 2020 17:59:06: start model_add_line... INFO @ Sun, 21 Jun 2020 17:59:07: start X-correlation... INFO @ Sun, 21 Jun 2020 17:59:07: end of X-cor INFO @ Sun, 21 Jun 2020 17:59:07: #2 finished! INFO @ Sun, 21 Jun 2020 17:59:07: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 17:59:07: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 17:59:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.05_model.r INFO @ Sun, 21 Jun 2020 17:59:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:59:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:59:07: 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 17:59:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.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 17:59:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:59:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:59:14: 5000000 INFO @ Sun, 21 Jun 2020 17:59:17: 1000000 INFO @ Sun, 21 Jun 2020 17:59:20: 6000000 INFO @ Sun, 21 Jun 2020 17:59:24: 2000000 INFO @ Sun, 21 Jun 2020 17:59:27: 7000000 INFO @ Sun, 21 Jun 2020 17:59:30: 3000000 INFO @ Sun, 21 Jun 2020 17:59:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:59:35: 8000000 INFO @ Sun, 21 Jun 2020 17:59:36: 4000000 INFO @ Sun, 21 Jun 2020 17:59:38: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:59:38: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:59:38: #1 total tags in treatment: 8439291 INFO @ Sun, 21 Jun 2020 17:59:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:59:38: #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 17:59:38: #1 tags after filtering in treatment: 8439113 INFO @ Sun, 21 Jun 2020 17:59:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:59:38: #1 finished! INFO @ Sun, 21 Jun 2020 17:59:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:59:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:59:39: #2 number of paired peaks: 6440 INFO @ Sun, 21 Jun 2020 17:59:39: start model_add_line... INFO @ Sun, 21 Jun 2020 17:59:39: start X-correlation... INFO @ Sun, 21 Jun 2020 17:59:39: end of X-cor INFO @ Sun, 21 Jun 2020 17:59:39: #2 finished! INFO @ Sun, 21 Jun 2020 17:59:39: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 17:59:39: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 17:59:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.10_model.r INFO @ Sun, 21 Jun 2020 17:59:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:59:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:59:42: 5000000 INFO @ Sun, 21 Jun 2020 17:59:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:59:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:59:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.05_summits.bed INFO @ Sun, 21 Jun 2020 17:59:43: Done! pass1 - making usageList (319 chroms): 2 millis pass2 - checking and writing primary data (10285 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:59:48: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:59:54: 7000000 INFO @ Sun, 21 Jun 2020 17:59:59: 8000000 INFO @ Sun, 21 Jun 2020 18:00:02: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:00:02: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:00:02: #1 total tags in treatment: 8439291 INFO @ Sun, 21 Jun 2020 18:00:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:00:02: #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 18:00:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:00:02: #1 tags after filtering in treatment: 8439113 INFO @ Sun, 21 Jun 2020 18:00:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:00:02: #1 finished! INFO @ Sun, 21 Jun 2020 18:00:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:00:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:00:04: #2 number of paired peaks: 6440 INFO @ Sun, 21 Jun 2020 18:00:04: start model_add_line... INFO @ Sun, 21 Jun 2020 18:00:04: start X-correlation... INFO @ Sun, 21 Jun 2020 18:00:04: end of X-cor INFO @ Sun, 21 Jun 2020 18:00:04: #2 finished! INFO @ Sun, 21 Jun 2020 18:00:04: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 18:00:04: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 18:00:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.20_model.r INFO @ Sun, 21 Jun 2020 18:00:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:00:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:00:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:00:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:00:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.10_summits.bed INFO @ Sun, 21 Jun 2020 18:00:14: Done! pass1 - making usageList (198 chroms): 2 millis pass2 - checking and writing primary data (7069 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:00:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:00:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:00:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:00:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794248/SRX1794248.20_summits.bed INFO @ Sun, 21 Jun 2020 18:00:39: Done! pass1 - making usageList (147 chroms): 1 millis pass2 - checking and writing primary data (3582 records, 4 fields): 9 millis CompletedMACS2peakCalling