Job ID = 6455592 SRX = SRX287912 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:22:36 prefetch.2.10.7: 1) Downloading 'SRR870101'... 2020-06-21T10:22:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:25:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:25:28 prefetch.2.10.7: 'SRR870101' is valid 2020-06-21T10:25:28 prefetch.2.10.7: 1) 'SRR870101' was downloaded successfully Read 15514865 spots for SRR870101/SRR870101.sra Written 15514865 spots for SRR870101/SRR870101.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: 00:03:26 15514865 reads; of these: 15514865 (100.00%) were unpaired; of these: 1054554 (6.80%) aligned 0 times 12286823 (79.19%) aligned exactly 1 time 2173488 (14.01%) aligned >1 times 93.20% overall alignment rate Time searching: 00:03:26 Overall time: 00:03:26 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] 4498980 / 14460311 = 0.3111 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 19:33:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.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 19:33:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:33:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:33:20: 1000000 INFO @ Sun, 21 Jun 2020 19:33:26: 2000000 INFO @ Sun, 21 Jun 2020 19:33:31: 3000000 INFO @ Sun, 21 Jun 2020 19:33:36: 4000000 INFO @ Sun, 21 Jun 2020 19:33:41: 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 19:33:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.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 19:33:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:33:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:33:46: 6000000 INFO @ Sun, 21 Jun 2020 19:33:51: 1000000 INFO @ Sun, 21 Jun 2020 19:33:52: 7000000 INFO @ Sun, 21 Jun 2020 19:33:56: 2000000 INFO @ Sun, 21 Jun 2020 19:33:57: 8000000 INFO @ Sun, 21 Jun 2020 19:34:02: 3000000 INFO @ Sun, 21 Jun 2020 19:34:03: 9000000 INFO @ Sun, 21 Jun 2020 19:34:07: 4000000 INFO @ Sun, 21 Jun 2020 19:34:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:34:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:34:09: #1 total tags in treatment: 9961331 INFO @ Sun, 21 Jun 2020 19:34:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:34:09: #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 19:34:09: #1 tags after filtering in treatment: 9961329 INFO @ Sun, 21 Jun 2020 19:34:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:34:09: #1 finished! INFO @ Sun, 21 Jun 2020 19:34:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:34:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:34:10: #2 number of paired peaks: 4405 INFO @ Sun, 21 Jun 2020 19:34:10: start model_add_line... INFO @ Sun, 21 Jun 2020 19:34:10: start X-correlation... INFO @ Sun, 21 Jun 2020 19:34:10: end of X-cor INFO @ Sun, 21 Jun 2020 19:34:10: #2 finished! INFO @ Sun, 21 Jun 2020 19:34:10: #2 predicted fragment length is 300 bps INFO @ Sun, 21 Jun 2020 19:34:10: #2 alternative fragment length(s) may be 300 bps INFO @ Sun, 21 Jun 2020 19:34:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.05_model.r INFO @ Sun, 21 Jun 2020 19:34:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:34:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:34:13: 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 19:34:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.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 19:34:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:18: 6000000 INFO @ Sun, 21 Jun 2020 19:34:22: 1000000 INFO @ Sun, 21 Jun 2020 19:34:24: 7000000 INFO @ Sun, 21 Jun 2020 19:34:28: 2000000 INFO @ Sun, 21 Jun 2020 19:34:30: 8000000 INFO @ Sun, 21 Jun 2020 19:34:35: 3000000 INFO @ Sun, 21 Jun 2020 19:34:37: 9000000 INFO @ Sun, 21 Jun 2020 19:34:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:34:41: 4000000 INFO @ Sun, 21 Jun 2020 19:34:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:34:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:34:43: #1 total tags in treatment: 9961331 INFO @ Sun, 21 Jun 2020 19:34:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:34:43: #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 19:34:43: #1 tags after filtering in treatment: 9961329 INFO @ Sun, 21 Jun 2020 19:34:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:34:43: #1 finished! INFO @ Sun, 21 Jun 2020 19:34:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:34:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:34:44: #2 number of paired peaks: 4405 INFO @ Sun, 21 Jun 2020 19:34:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:34:44: start X-correlation... INFO @ Sun, 21 Jun 2020 19:34:44: end of X-cor INFO @ Sun, 21 Jun 2020 19:34:44: #2 finished! INFO @ Sun, 21 Jun 2020 19:34:44: #2 predicted fragment length is 300 bps INFO @ Sun, 21 Jun 2020 19:34:44: #2 alternative fragment length(s) may be 300 bps INFO @ Sun, 21 Jun 2020 19:34:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.10_model.r INFO @ Sun, 21 Jun 2020 19:34:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:34:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:34:47: 5000000 INFO @ Sun, 21 Jun 2020 19:34:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:34:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:34:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.05_summits.bed INFO @ Sun, 21 Jun 2020 19:34:53: Done! pass1 - making usageList (454 chroms): 2 millis pass2 - checking and writing primary data (7204 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:34:53: 6000000 INFO @ Sun, 21 Jun 2020 19:34:59: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:35:05: 8000000 INFO @ Sun, 21 Jun 2020 19:35:12: 9000000 INFO @ Sun, 21 Jun 2020 19:35:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:35:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:35:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:35:18: #1 total tags in treatment: 9961331 INFO @ Sun, 21 Jun 2020 19:35:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:35:18: #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 19:35:18: #1 tags after filtering in treatment: 9961329 INFO @ Sun, 21 Jun 2020 19:35:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:18: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:19: #2 number of paired peaks: 4405 INFO @ Sun, 21 Jun 2020 19:35:19: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:19: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:19: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:19: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:19: #2 predicted fragment length is 300 bps INFO @ Sun, 21 Jun 2020 19:35:19: #2 alternative fragment length(s) may be 300 bps INFO @ Sun, 21 Jun 2020 19:35:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.20_model.r INFO @ Sun, 21 Jun 2020 19:35:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:35:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.10_summits.bed INFO @ Sun, 21 Jun 2020 19:35:27: Done! pass1 - making usageList (397 chroms): 2 millis pass2 - checking and writing primary data (6008 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:35:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287912/SRX287912.20_summits.bed INFO @ Sun, 21 Jun 2020 19:36:02: Done! pass1 - making usageList (238 chroms): 1 millis pass2 - checking and writing primary data (4539 records, 4 fields): 11 millis CompletedMACS2peakCalling