Job ID = 6456129 SRX = SRX318801 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:31:21 prefetch.2.10.7: 1) Downloading 'SRR927117'... 2020-06-21T10:31:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:34:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:34:40 prefetch.2.10.7: 1) 'SRR927117' was downloaded successfully Read 18513994 spots for SRR927117/SRR927117.sra Written 18513994 spots for SRR927117/SRR927117.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: 00:04:52 18513994 reads; of these: 18513994 (100.00%) were unpaired; of these: 776109 (4.19%) aligned 0 times 13413538 (72.45%) aligned exactly 1 time 4324347 (23.36%) aligned >1 times 95.81% overall alignment rate Time searching: 00:04:53 Overall time: 00:04:53 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] 4476853 / 17737885 = 0.2524 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 19:44:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.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 19:44:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:44:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:44:51: 1000000 INFO @ Sun, 21 Jun 2020 19:44:58: 2000000 INFO @ Sun, 21 Jun 2020 19:45:04: 3000000 INFO @ Sun, 21 Jun 2020 19:45:11: 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 19:45:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.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 19:45:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:45:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:45:18: 5000000 INFO @ Sun, 21 Jun 2020 19:45:21: 1000000 INFO @ Sun, 21 Jun 2020 19:45:25: 6000000 INFO @ Sun, 21 Jun 2020 19:45:28: 2000000 INFO @ Sun, 21 Jun 2020 19:45:32: 7000000 INFO @ Sun, 21 Jun 2020 19:45:35: 3000000 INFO @ Sun, 21 Jun 2020 19:45:40: 8000000 INFO @ Sun, 21 Jun 2020 19:45:43: 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 19:45:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.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 19:45:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:45:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:45:47: 9000000 INFO @ Sun, 21 Jun 2020 19:45:50: 5000000 INFO @ Sun, 21 Jun 2020 19:45:52: 1000000 INFO @ Sun, 21 Jun 2020 19:45:54: 10000000 INFO @ Sun, 21 Jun 2020 19:45:57: 6000000 INFO @ Sun, 21 Jun 2020 19:45:59: 2000000 INFO @ Sun, 21 Jun 2020 19:46:01: 11000000 INFO @ Sun, 21 Jun 2020 19:46:04: 7000000 INFO @ Sun, 21 Jun 2020 19:46:07: 3000000 INFO @ Sun, 21 Jun 2020 19:46:09: 12000000 INFO @ Sun, 21 Jun 2020 19:46:11: 8000000 INFO @ Sun, 21 Jun 2020 19:46:14: 4000000 INFO @ Sun, 21 Jun 2020 19:46:16: 13000000 INFO @ Sun, 21 Jun 2020 19:46:18: 9000000 INFO @ Sun, 21 Jun 2020 19:46:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:46:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:46:18: #1 total tags in treatment: 13261032 INFO @ Sun, 21 Jun 2020 19:46:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:46:18: #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 19:46:18: #1 tags after filtering in treatment: 13261028 INFO @ Sun, 21 Jun 2020 19:46:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:46:18: #1 finished! INFO @ Sun, 21 Jun 2020 19:46:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:46:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:46:20: #2 number of paired peaks: 5655 INFO @ Sun, 21 Jun 2020 19:46:20: start model_add_line... INFO @ Sun, 21 Jun 2020 19:46:20: start X-correlation... INFO @ Sun, 21 Jun 2020 19:46:20: end of X-cor INFO @ Sun, 21 Jun 2020 19:46:20: #2 finished! INFO @ Sun, 21 Jun 2020 19:46:20: #2 predicted fragment length is 225 bps INFO @ Sun, 21 Jun 2020 19:46:20: #2 alternative fragment length(s) may be 225 bps INFO @ Sun, 21 Jun 2020 19:46:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.05_model.r INFO @ Sun, 21 Jun 2020 19:46:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:46:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:46:21: 5000000 INFO @ Sun, 21 Jun 2020 19:46:25: 10000000 INFO @ Sun, 21 Jun 2020 19:46:29: 6000000 INFO @ Sun, 21 Jun 2020 19:46:32: 11000000 INFO @ Sun, 21 Jun 2020 19:46:36: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:46:39: 12000000 INFO @ Sun, 21 Jun 2020 19:46:43: 8000000 INFO @ Sun, 21 Jun 2020 19:46:46: 13000000 INFO @ Sun, 21 Jun 2020 19:46:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:46:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:46:48: #1 total tags in treatment: 13261032 INFO @ Sun, 21 Jun 2020 19:46:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:46:48: #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 19:46:48: #1 tags after filtering in treatment: 13261028 INFO @ Sun, 21 Jun 2020 19:46:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:46:48: #1 finished! INFO @ Sun, 21 Jun 2020 19:46:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:46:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:46:50: #2 number of paired peaks: 5655 INFO @ Sun, 21 Jun 2020 19:46:50: start model_add_line... INFO @ Sun, 21 Jun 2020 19:46:50: start X-correlation... INFO @ Sun, 21 Jun 2020 19:46:50: end of X-cor INFO @ Sun, 21 Jun 2020 19:46:50: #2 finished! INFO @ Sun, 21 Jun 2020 19:46:50: #2 predicted fragment length is 225 bps INFO @ Sun, 21 Jun 2020 19:46:50: #2 alternative fragment length(s) may be 225 bps INFO @ Sun, 21 Jun 2020 19:46:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.10_model.r INFO @ Sun, 21 Jun 2020 19:46:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:46:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:46:50: 9000000 INFO @ Sun, 21 Jun 2020 19:46:57: 10000000 INFO @ Sun, 21 Jun 2020 19:46:59: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:47:04: 11000000 INFO @ Sun, 21 Jun 2020 19:47:11: 12000000 INFO @ Sun, 21 Jun 2020 19:47:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:47:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:47:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.05_summits.bed INFO @ Sun, 21 Jun 2020 19:47:16: Done! pass1 - making usageList (449 chroms): 2 millis pass2 - checking and writing primary data (8710 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:47:18: 13000000 INFO @ Sun, 21 Jun 2020 19:47:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:47:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:47:20: #1 total tags in treatment: 13261032 INFO @ Sun, 21 Jun 2020 19:47:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:47:20: #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 19:47:21: #1 tags after filtering in treatment: 13261028 INFO @ Sun, 21 Jun 2020 19:47:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:47:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:47:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:47:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:47:22: #2 number of paired peaks: 5655 INFO @ Sun, 21 Jun 2020 19:47:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:47:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:47:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:47:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:47:22: #2 predicted fragment length is 225 bps INFO @ Sun, 21 Jun 2020 19:47:22: #2 alternative fragment length(s) may be 225 bps INFO @ Sun, 21 Jun 2020 19:47:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.20_model.r INFO @ Sun, 21 Jun 2020 19:47:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:47:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:47:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:47:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:47:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:47:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.10_summits.bed INFO @ Sun, 21 Jun 2020 19:47:46: Done! pass1 - making usageList (329 chroms): 2 millis pass2 - checking and writing primary data (6657 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:48:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:48:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:48:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:48:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318801/SRX318801.20_summits.bed INFO @ Sun, 21 Jun 2020 19:48:19: Done! pass1 - making usageList (211 chroms): 2 millis pass2 - checking and writing primary data (4503 records, 4 fields): 11 millis CompletedMACS2peakCalling