Job ID = 6453761 SRX = SRX146992 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:30:41 prefetch.2.10.7: 1) Downloading 'SRR495366'... 2020-06-21T08:30:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:34:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:34:27 prefetch.2.10.7: 1) 'SRR495366' was downloaded successfully Read 29833522 spots for SRR495366/SRR495366.sra Written 29833522 spots for SRR495366/SRR495366.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: 00:06:14 29833522 reads; of these: 29833522 (100.00%) were unpaired; of these: 1231551 (4.13%) aligned 0 times 21803129 (73.08%) aligned exactly 1 time 6798842 (22.79%) aligned >1 times 95.87% overall alignment rate Time searching: 00:06:14 Overall time: 00:06:14 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] 6547243 / 28601971 = 0.2289 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 17:47:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.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 17:47:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:47:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:47:57: 1000000 INFO @ Sun, 21 Jun 2020 17:48:01: 2000000 INFO @ Sun, 21 Jun 2020 17:48:06: 3000000 INFO @ Sun, 21 Jun 2020 17:48:11: 4000000 INFO @ Sun, 21 Jun 2020 17:48:15: 5000000 INFO @ Sun, 21 Jun 2020 17:48:20: 6000000 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 17:48:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.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 17:48:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:48:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:48:25: 7000000 INFO @ Sun, 21 Jun 2020 17:48:27: 1000000 INFO @ Sun, 21 Jun 2020 17:48:30: 8000000 INFO @ Sun, 21 Jun 2020 17:48:32: 2000000 INFO @ Sun, 21 Jun 2020 17:48:35: 9000000 INFO @ Sun, 21 Jun 2020 17:48:37: 3000000 INFO @ Sun, 21 Jun 2020 17:48:39: 10000000 INFO @ Sun, 21 Jun 2020 17:48:42: 4000000 INFO @ Sun, 21 Jun 2020 17:48:44: 11000000 INFO @ Sun, 21 Jun 2020 17:48:47: 5000000 INFO @ Sun, 21 Jun 2020 17:48:49: 12000000 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 17:48:52: 6000000 INFO @ Sun, 21 Jun 2020 17:48:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.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 17:48:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:48:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:48:54: 13000000 INFO @ Sun, 21 Jun 2020 17:48:57: 7000000 INFO @ Sun, 21 Jun 2020 17:48:58: 1000000 INFO @ Sun, 21 Jun 2020 17:48:59: 14000000 INFO @ Sun, 21 Jun 2020 17:49:02: 8000000 INFO @ Sun, 21 Jun 2020 17:49:03: 2000000 INFO @ Sun, 21 Jun 2020 17:49:04: 15000000 INFO @ Sun, 21 Jun 2020 17:49:07: 9000000 INFO @ Sun, 21 Jun 2020 17:49:09: 3000000 INFO @ Sun, 21 Jun 2020 17:49:09: 16000000 INFO @ Sun, 21 Jun 2020 17:49:12: 10000000 INFO @ Sun, 21 Jun 2020 17:49:14: 4000000 INFO @ Sun, 21 Jun 2020 17:49:14: 17000000 INFO @ Sun, 21 Jun 2020 17:49:17: 11000000 INFO @ Sun, 21 Jun 2020 17:49:19: 18000000 INFO @ Sun, 21 Jun 2020 17:49:20: 5000000 INFO @ Sun, 21 Jun 2020 17:49:22: 12000000 INFO @ Sun, 21 Jun 2020 17:49:25: 19000000 INFO @ Sun, 21 Jun 2020 17:49:25: 6000000 INFO @ Sun, 21 Jun 2020 17:49:27: 13000000 INFO @ Sun, 21 Jun 2020 17:49:30: 20000000 INFO @ Sun, 21 Jun 2020 17:49:31: 7000000 INFO @ Sun, 21 Jun 2020 17:49:33: 14000000 INFO @ Sun, 21 Jun 2020 17:49:35: 21000000 INFO @ Sun, 21 Jun 2020 17:49:37: 8000000 INFO @ Sun, 21 Jun 2020 17:49:38: 15000000 INFO @ Sun, 21 Jun 2020 17:49:41: 22000000 INFO @ Sun, 21 Jun 2020 17:49:41: #1 tag size is determined as 38 bps INFO @ Sun, 21 Jun 2020 17:49:41: #1 tag size = 38 INFO @ Sun, 21 Jun 2020 17:49:41: #1 total tags in treatment: 22054728 INFO @ Sun, 21 Jun 2020 17:49:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:41: #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 17:49:42: #1 tags after filtering in treatment: 22054670 INFO @ Sun, 21 Jun 2020 17:49:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:42: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:42: 9000000 INFO @ Sun, 21 Jun 2020 17:49:43: 16000000 INFO @ Sun, 21 Jun 2020 17:49:43: #2 number of paired peaks: 835 WARNING @ Sun, 21 Jun 2020 17:49:43: Fewer paired peaks (835) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 835 pairs to build model! INFO @ Sun, 21 Jun 2020 17:49:43: start model_add_line... INFO @ Sun, 21 Jun 2020 17:49:44: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:44: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:44: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:44: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 17:49:44: #2 alternative fragment length(s) may be 4,106 bps INFO @ Sun, 21 Jun 2020 17:49:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.05_model.r INFO @ Sun, 21 Jun 2020 17:49:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:49:48: 17000000 INFO @ Sun, 21 Jun 2020 17:49:48: 10000000 INFO @ Sun, 21 Jun 2020 17:49:54: 18000000 INFO @ Sun, 21 Jun 2020 17:49:54: 11000000 INFO @ Sun, 21 Jun 2020 17:49:59: 19000000 INFO @ Sun, 21 Jun 2020 17:50:00: 12000000 INFO @ Sun, 21 Jun 2020 17:50:05: 20000000 INFO @ Sun, 21 Jun 2020 17:50:05: 13000000 INFO @ Sun, 21 Jun 2020 17:50:10: 21000000 INFO @ Sun, 21 Jun 2020 17:50:11: 14000000 INFO @ Sun, 21 Jun 2020 17:50:16: 22000000 INFO @ Sun, 21 Jun 2020 17:50:16: #1 tag size is determined as 38 bps INFO @ Sun, 21 Jun 2020 17:50:16: #1 tag size = 38 INFO @ Sun, 21 Jun 2020 17:50:16: #1 total tags in treatment: 22054728 INFO @ Sun, 21 Jun 2020 17:50:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:50:16: #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 17:50:16: 15000000 INFO @ Sun, 21 Jun 2020 17:50:17: #1 tags after filtering in treatment: 22054670 INFO @ Sun, 21 Jun 2020 17:50:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:50:17: #1 finished! INFO @ Sun, 21 Jun 2020 17:50:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:50:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:50:18: #2 number of paired peaks: 835 WARNING @ Sun, 21 Jun 2020 17:50:18: Fewer paired peaks (835) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 835 pairs to build model! INFO @ Sun, 21 Jun 2020 17:50:18: start model_add_line... INFO @ Sun, 21 Jun 2020 17:50:18: start X-correlation... INFO @ Sun, 21 Jun 2020 17:50:18: end of X-cor INFO @ Sun, 21 Jun 2020 17:50:18: #2 finished! INFO @ Sun, 21 Jun 2020 17:50:18: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 17:50:18: #2 alternative fragment length(s) may be 4,106 bps INFO @ Sun, 21 Jun 2020 17:50:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.10_model.r INFO @ Sun, 21 Jun 2020 17:50:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:50:18: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:50:21: 16000000 INFO @ Sun, 21 Jun 2020 17:50:27: 17000000 INFO @ Sun, 21 Jun 2020 17:50:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:50:32: 18000000 INFO @ Sun, 21 Jun 2020 17:50:38: 19000000 INFO @ Sun, 21 Jun 2020 17:50:43: 20000000 INFO @ Sun, 21 Jun 2020 17:50:49: 21000000 INFO @ Sun, 21 Jun 2020 17:50:54: 22000000 INFO @ Sun, 21 Jun 2020 17:50:55: #1 tag size is determined as 38 bps INFO @ Sun, 21 Jun 2020 17:50:55: #1 tag size = 38 INFO @ Sun, 21 Jun 2020 17:50:55: #1 total tags in treatment: 22054728 INFO @ Sun, 21 Jun 2020 17:50:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:50:55: #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 17:50:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.05_summits.bed INFO @ Sun, 21 Jun 2020 17:50:55: Done! INFO @ Sun, 21 Jun 2020 17:50:55: #1 tags after filtering in treatment: 22054670 INFO @ Sun, 21 Jun 2020 17:50:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:50:55: #1 finished! INFO @ Sun, 21 Jun 2020 17:50:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:50:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:50:57: #2 number of paired peaks: 835 WARNING @ Sun, 21 Jun 2020 17:50:57: Fewer paired peaks (835) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 835 pairs to build model! INFO @ Sun, 21 Jun 2020 17:50:57: start model_add_line... INFO @ Sun, 21 Jun 2020 17:50:57: start X-correlation... INFO @ Sun, 21 Jun 2020 17:50:57: end of X-cor INFO @ Sun, 21 Jun 2020 17:50:57: #2 finished! INFO @ Sun, 21 Jun 2020 17:50:57: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 17:50:57: #2 alternative fragment length(s) may be 4,106 bps INFO @ Sun, 21 Jun 2020 17:50:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.20_model.r INFO @ Sun, 21 Jun 2020 17:50:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:50:57: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (462 chroms): 3 millis pass2 - checking and writing primary data (19815 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:51:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:51:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:51:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:51:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.10_summits.bed INFO @ Sun, 21 Jun 2020 17:51:29: Done! pass1 - making usageList (402 chroms): 2 millis pass2 - checking and writing primary data (8315 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:51:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:52:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:52:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:52:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX146992/SRX146992.20_summits.bed INFO @ Sun, 21 Jun 2020 17:52:03: Done! pass1 - making usageList (311 chroms): 1 millis pass2 - checking and writing primary data (3292 records, 4 fields): 12 millis CompletedMACS2peakCalling