Job ID = 6458272 SRX = SRX5011033 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:38:14 prefetch.2.10.7: 1) Downloading 'SRR8191482'... 2020-06-21T12:38:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:42:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:42:40 prefetch.2.10.7: 1) 'SRR8191482' was downloaded successfully 2020-06-21T12:42:40 prefetch.2.10.7: 'SRR8191482' has 0 unresolved dependencies Read 39832402 spots for SRR8191482/SRR8191482.sra Written 39832402 spots for SRR8191482/SRR8191482.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: 00:09:51 39832402 reads; of these: 39832402 (100.00%) were unpaired; of these: 2220174 (5.57%) aligned 0 times 30119549 (75.62%) aligned exactly 1 time 7492679 (18.81%) aligned >1 times 94.43% overall alignment rate Time searching: 00:09:51 Overall time: 00:09:51 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 16 files... [bam_rmdupse_core] 16714886 / 37612228 = 0.4444 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 22:00:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.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 22:00:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:00:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:00:07: 1000000 INFO @ Sun, 21 Jun 2020 22:00:12: 2000000 INFO @ Sun, 21 Jun 2020 22:00:17: 3000000 INFO @ Sun, 21 Jun 2020 22:00:22: 4000000 INFO @ Sun, 21 Jun 2020 22:00:27: 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 22:00:32: 6000000 INFO @ Sun, 21 Jun 2020 22:00:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.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 22:00:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:00:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:00:38: 1000000 INFO @ Sun, 21 Jun 2020 22:00:38: 7000000 INFO @ Sun, 21 Jun 2020 22:00:43: 2000000 INFO @ Sun, 21 Jun 2020 22:00:43: 8000000 INFO @ Sun, 21 Jun 2020 22:00:49: 3000000 INFO @ Sun, 21 Jun 2020 22:00:49: 9000000 INFO @ Sun, 21 Jun 2020 22:00:54: 10000000 INFO @ Sun, 21 Jun 2020 22:00:54: 4000000 INFO @ Sun, 21 Jun 2020 22:00:59: 11000000 INFO @ Sun, 21 Jun 2020 22:00:59: 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 22:01:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.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 22:01:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:01:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:01:05: 12000000 INFO @ Sun, 21 Jun 2020 22:01:05: 6000000 INFO @ Sun, 21 Jun 2020 22:01:08: 1000000 INFO @ Sun, 21 Jun 2020 22:01:10: 13000000 INFO @ Sun, 21 Jun 2020 22:01:10: 7000000 INFO @ Sun, 21 Jun 2020 22:01:13: 2000000 INFO @ Sun, 21 Jun 2020 22:01:15: 14000000 INFO @ Sun, 21 Jun 2020 22:01:16: 8000000 INFO @ Sun, 21 Jun 2020 22:01:19: 3000000 INFO @ Sun, 21 Jun 2020 22:01:21: 15000000 INFO @ Sun, 21 Jun 2020 22:01:21: 9000000 INFO @ Sun, 21 Jun 2020 22:01:25: 4000000 INFO @ Sun, 21 Jun 2020 22:01:26: 16000000 INFO @ Sun, 21 Jun 2020 22:01:26: 10000000 INFO @ Sun, 21 Jun 2020 22:01:30: 5000000 INFO @ Sun, 21 Jun 2020 22:01:32: 11000000 INFO @ Sun, 21 Jun 2020 22:01:32: 17000000 INFO @ Sun, 21 Jun 2020 22:01:36: 6000000 INFO @ Sun, 21 Jun 2020 22:01:37: 12000000 INFO @ Sun, 21 Jun 2020 22:01:38: 18000000 INFO @ Sun, 21 Jun 2020 22:01:41: 7000000 INFO @ Sun, 21 Jun 2020 22:01:43: 13000000 INFO @ Sun, 21 Jun 2020 22:01:43: 19000000 INFO @ Sun, 21 Jun 2020 22:01:47: 8000000 INFO @ Sun, 21 Jun 2020 22:01:48: 14000000 INFO @ Sun, 21 Jun 2020 22:01:49: 20000000 INFO @ Sun, 21 Jun 2020 22:01:52: 9000000 INFO @ Sun, 21 Jun 2020 22:01:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:01:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:01:54: #1 total tags in treatment: 20897342 INFO @ Sun, 21 Jun 2020 22:01:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:01:54: #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 22:01:54: 15000000 INFO @ Sun, 21 Jun 2020 22:01:54: #1 tags after filtering in treatment: 20897275 INFO @ Sun, 21 Jun 2020 22:01:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:01:54: #1 finished! INFO @ Sun, 21 Jun 2020 22:01:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:01:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:01:56: #2 number of paired peaks: 4668 INFO @ Sun, 21 Jun 2020 22:01:56: start model_add_line... INFO @ Sun, 21 Jun 2020 22:01:56: start X-correlation... INFO @ Sun, 21 Jun 2020 22:01:56: end of X-cor INFO @ Sun, 21 Jun 2020 22:01:56: #2 finished! INFO @ Sun, 21 Jun 2020 22:01:56: #2 predicted fragment length is 222 bps INFO @ Sun, 21 Jun 2020 22:01:56: #2 alternative fragment length(s) may be 222 bps INFO @ Sun, 21 Jun 2020 22:01:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.05_model.r INFO @ Sun, 21 Jun 2020 22:01:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:01:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:01:57: 10000000 INFO @ Sun, 21 Jun 2020 22:01:59: 16000000 INFO @ Sun, 21 Jun 2020 22:02:03: 11000000 INFO @ Sun, 21 Jun 2020 22:02:05: 17000000 INFO @ Sun, 21 Jun 2020 22:02:08: 12000000 INFO @ Sun, 21 Jun 2020 22:02:11: 18000000 INFO @ Sun, 21 Jun 2020 22:02:14: 13000000 INFO @ Sun, 21 Jun 2020 22:02:16: 19000000 INFO @ Sun, 21 Jun 2020 22:02:19: 14000000 INFO @ Sun, 21 Jun 2020 22:02:22: 20000000 INFO @ Sun, 21 Jun 2020 22:02:24: 15000000 INFO @ Sun, 21 Jun 2020 22:02:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:02:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:02:27: #1 total tags in treatment: 20897342 INFO @ Sun, 21 Jun 2020 22:02:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:02:27: #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 22:02:28: #1 tags after filtering in treatment: 20897275 INFO @ Sun, 21 Jun 2020 22:02:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:02:28: #1 finished! INFO @ Sun, 21 Jun 2020 22:02:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:02:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:02:29: #2 number of paired peaks: 4668 INFO @ Sun, 21 Jun 2020 22:02:29: start model_add_line... INFO @ Sun, 21 Jun 2020 22:02:30: start X-correlation... INFO @ Sun, 21 Jun 2020 22:02:30: end of X-cor INFO @ Sun, 21 Jun 2020 22:02:30: #2 finished! INFO @ Sun, 21 Jun 2020 22:02:30: #2 predicted fragment length is 222 bps INFO @ Sun, 21 Jun 2020 22:02:30: #2 alternative fragment length(s) may be 222 bps INFO @ Sun, 21 Jun 2020 22:02:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.10_model.r INFO @ Sun, 21 Jun 2020 22:02:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:02:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:02:30: 16000000 INFO @ Sun, 21 Jun 2020 22:02:35: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:02:40: 18000000 INFO @ Sun, 21 Jun 2020 22:02:45: 19000000 INFO @ Sun, 21 Jun 2020 22:02:51: 20000000 INFO @ Sun, 21 Jun 2020 22:02:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:02:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:02:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:02:55: #1 total tags in treatment: 20897342 INFO @ Sun, 21 Jun 2020 22:02:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:02:55: #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 22:02:56: #1 tags after filtering in treatment: 20897275 INFO @ Sun, 21 Jun 2020 22:02:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:02:56: #1 finished! INFO @ Sun, 21 Jun 2020 22:02:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:02:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:02:58: #2 number of paired peaks: 4668 INFO @ Sun, 21 Jun 2020 22:02:58: start model_add_line... INFO @ Sun, 21 Jun 2020 22:02:58: start X-correlation... INFO @ Sun, 21 Jun 2020 22:02:58: end of X-cor INFO @ Sun, 21 Jun 2020 22:02:58: #2 finished! INFO @ Sun, 21 Jun 2020 22:02:58: #2 predicted fragment length is 222 bps INFO @ Sun, 21 Jun 2020 22:02:58: #2 alternative fragment length(s) may be 222 bps INFO @ Sun, 21 Jun 2020 22:02:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.20_model.r INFO @ Sun, 21 Jun 2020 22:02:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:02:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:03:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:03:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:03:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.05_summits.bed INFO @ Sun, 21 Jun 2020 22:03:19: Done! pass1 - making usageList (604 chroms): 3 millis pass2 - checking and writing primary data (15150 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:03:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:03:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:03:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:03:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.10_summits.bed INFO @ Sun, 21 Jun 2020 22:03:52: Done! pass1 - making usageList (498 chroms): 2 millis pass2 - checking and writing primary data (12673 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:03:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:04:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:04:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:04:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011033/SRX5011033.20_summits.bed INFO @ Sun, 21 Jun 2020 22:04:20: Done! pass1 - making usageList (404 chroms): 2 millis pass2 - checking and writing primary data (9349 records, 4 fields): 21 millis CompletedMACS2peakCalling