Job ID = 6456966 SRX = SRX4158198 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:29:10 prefetch.2.10.7: 1) Downloading 'SRR7253478'... 2020-06-21T11:29:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:31:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:31:37 prefetch.2.10.7: 'SRR7253478' is valid 2020-06-21T11:31:37 prefetch.2.10.7: 1) 'SRR7253478' was downloaded successfully Read 18103892 spots for SRR7253478/SRR7253478.sra Written 18103892 spots for SRR7253478/SRR7253478.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: 00:05:20 18103892 reads; of these: 18103892 (100.00%) were unpaired; of these: 639046 (3.53%) aligned 0 times 9795177 (54.11%) aligned exactly 1 time 7669669 (42.36%) aligned >1 times 96.47% overall alignment rate Time searching: 00:05:20 Overall time: 00:05:20 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] 2788456 / 17464846 = 0.1597 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 20:42:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.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 20:42:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:42:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:42:35: 1000000 INFO @ Sun, 21 Jun 2020 20:42:40: 2000000 INFO @ Sun, 21 Jun 2020 20:42:45: 3000000 INFO @ Sun, 21 Jun 2020 20:42:49: 4000000 INFO @ Sun, 21 Jun 2020 20:42:55: 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 20:42:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.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 20:42:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:42:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:43:00: 6000000 INFO @ Sun, 21 Jun 2020 20:43:05: 1000000 INFO @ Sun, 21 Jun 2020 20:43:05: 7000000 INFO @ Sun, 21 Jun 2020 20:43:10: 2000000 INFO @ Sun, 21 Jun 2020 20:43:10: 8000000 INFO @ Sun, 21 Jun 2020 20:43:15: 3000000 INFO @ Sun, 21 Jun 2020 20:43:15: 9000000 INFO @ Sun, 21 Jun 2020 20:43:20: 4000000 INFO @ Sun, 21 Jun 2020 20:43:20: 10000000 INFO @ Sun, 21 Jun 2020 20:43:25: 5000000 INFO @ Sun, 21 Jun 2020 20:43:25: 11000000 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 20:43:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.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 20:43:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:43:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:43:30: 6000000 INFO @ Sun, 21 Jun 2020 20:43:31: 12000000 INFO @ Sun, 21 Jun 2020 20:43:35: 1000000 INFO @ Sun, 21 Jun 2020 20:43:35: 7000000 INFO @ Sun, 21 Jun 2020 20:43:36: 13000000 INFO @ Sun, 21 Jun 2020 20:43:39: 2000000 INFO @ Sun, 21 Jun 2020 20:43:40: 8000000 INFO @ Sun, 21 Jun 2020 20:43:41: 14000000 INFO @ Sun, 21 Jun 2020 20:43:44: 3000000 INFO @ Sun, 21 Jun 2020 20:43:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:43:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:43:45: #1 total tags in treatment: 14676390 INFO @ Sun, 21 Jun 2020 20:43:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:43:45: #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 20:43:45: #1 tags after filtering in treatment: 14676337 INFO @ Sun, 21 Jun 2020 20:43:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:43:45: #1 finished! INFO @ Sun, 21 Jun 2020 20:43:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:43:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:43:46: 9000000 INFO @ Sun, 21 Jun 2020 20:43:47: #2 number of paired peaks: 3846 INFO @ Sun, 21 Jun 2020 20:43:47: start model_add_line... INFO @ Sun, 21 Jun 2020 20:43:47: start X-correlation... INFO @ Sun, 21 Jun 2020 20:43:47: end of X-cor INFO @ Sun, 21 Jun 2020 20:43:47: #2 finished! INFO @ Sun, 21 Jun 2020 20:43:47: #2 predicted fragment length is 202 bps INFO @ Sun, 21 Jun 2020 20:43:47: #2 alternative fragment length(s) may be 4,202 bps INFO @ Sun, 21 Jun 2020 20:43:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.05_model.r INFO @ Sun, 21 Jun 2020 20:43:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:43:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:43:49: 4000000 INFO @ Sun, 21 Jun 2020 20:43:51: 10000000 INFO @ Sun, 21 Jun 2020 20:43:54: 5000000 INFO @ Sun, 21 Jun 2020 20:43:56: 11000000 INFO @ Sun, 21 Jun 2020 20:43:59: 6000000 INFO @ Sun, 21 Jun 2020 20:44:01: 12000000 INFO @ Sun, 21 Jun 2020 20:44:04: 7000000 INFO @ Sun, 21 Jun 2020 20:44:06: 13000000 INFO @ Sun, 21 Jun 2020 20:44:09: 8000000 INFO @ Sun, 21 Jun 2020 20:44:11: 14000000 INFO @ Sun, 21 Jun 2020 20:44:14: 9000000 INFO @ Sun, 21 Jun 2020 20:44:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:44:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:44:15: #1 total tags in treatment: 14676390 INFO @ Sun, 21 Jun 2020 20:44:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:44:15: #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 20:44:16: #1 tags after filtering in treatment: 14676337 INFO @ Sun, 21 Jun 2020 20:44:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:44:16: #1 finished! INFO @ Sun, 21 Jun 2020 20:44:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:44:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:44:17: #2 number of paired peaks: 3846 INFO @ Sun, 21 Jun 2020 20:44:17: start model_add_line... INFO @ Sun, 21 Jun 2020 20:44:17: start X-correlation... INFO @ Sun, 21 Jun 2020 20:44:17: end of X-cor INFO @ Sun, 21 Jun 2020 20:44:17: #2 finished! INFO @ Sun, 21 Jun 2020 20:44:17: #2 predicted fragment length is 202 bps INFO @ Sun, 21 Jun 2020 20:44:17: #2 alternative fragment length(s) may be 4,202 bps INFO @ Sun, 21 Jun 2020 20:44:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.10_model.r INFO @ Sun, 21 Jun 2020 20:44:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:44:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:44:19: 10000000 INFO @ Sun, 21 Jun 2020 20:44:24: 11000000 INFO @ Sun, 21 Jun 2020 20:44:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:44:29: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:44:34: 13000000 INFO @ Sun, 21 Jun 2020 20:44:39: 14000000 INFO @ Sun, 21 Jun 2020 20:44:42: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:44:42: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:44:42: #1 total tags in treatment: 14676390 INFO @ Sun, 21 Jun 2020 20:44:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:44:42: #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 20:44:43: #1 tags after filtering in treatment: 14676337 INFO @ Sun, 21 Jun 2020 20:44:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:44:43: #1 finished! INFO @ Sun, 21 Jun 2020 20:44:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:44:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:44:44: #2 number of paired peaks: 3846 INFO @ Sun, 21 Jun 2020 20:44:44: start model_add_line... INFO @ Sun, 21 Jun 2020 20:44:44: start X-correlation... INFO @ Sun, 21 Jun 2020 20:44:44: end of X-cor INFO @ Sun, 21 Jun 2020 20:44:44: #2 finished! INFO @ Sun, 21 Jun 2020 20:44:44: #2 predicted fragment length is 202 bps INFO @ Sun, 21 Jun 2020 20:44:44: #2 alternative fragment length(s) may be 4,202 bps INFO @ Sun, 21 Jun 2020 20:44:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.20_model.r INFO @ Sun, 21 Jun 2020 20:44:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:44:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:44:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:44:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:44:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.05_summits.bed INFO @ Sun, 21 Jun 2020 20:44:45: Done! pass1 - making usageList (844 chroms): 3 millis pass2 - checking and writing primary data (10334 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:44:56: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:45:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:45:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:45:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.10_summits.bed INFO @ Sun, 21 Jun 2020 20:45:13: Done! pass1 - making usageList (612 chroms): 2 millis pass2 - checking and writing primary data (5764 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:45:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:45:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:45:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:45:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158198/SRX4158198.20_summits.bed INFO @ Sun, 21 Jun 2020 20:45:39: Done! pass1 - making usageList (365 chroms): 1 millis pass2 - checking and writing primary data (2356 records, 4 fields): 13 millis CompletedMACS2peakCalling