Job ID = 6455740 SRX = SRX288034 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:24:06 prefetch.2.10.7: 1) Downloading 'SRR870223'... 2020-06-21T10:24:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:27:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:27:34 prefetch.2.10.7: 1) 'SRR870223' was downloaded successfully Read 24734451 spots for SRR870223/SRR870223.sra Written 24734451 spots for SRR870223/SRR870223.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: 00:05:49 24734451 reads; of these: 24734451 (100.00%) were unpaired; of these: 2270245 (9.18%) aligned 0 times 17293603 (69.92%) aligned exactly 1 time 5170603 (20.90%) aligned >1 times 90.82% overall alignment rate Time searching: 00:05:49 Overall time: 00:05:49 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 12 files... [bam_rmdupse_core] 4005517 / 22464206 = 0.1783 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 19:42:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.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 19:42:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:42:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:42:08: 1000000 INFO @ Sun, 21 Jun 2020 19:42:14: 2000000 INFO @ Sun, 21 Jun 2020 19:42:19: 3000000 INFO @ Sun, 21 Jun 2020 19:42:25: 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 19:42:30: 5000000 INFO @ Sun, 21 Jun 2020 19:42:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.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 19:42:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:42:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:42:36: 6000000 INFO @ Sun, 21 Jun 2020 19:42:39: 1000000 INFO @ Sun, 21 Jun 2020 19:42:43: 7000000 INFO @ Sun, 21 Jun 2020 19:42:45: 2000000 INFO @ Sun, 21 Jun 2020 19:42:49: 8000000 INFO @ Sun, 21 Jun 2020 19:42:51: 3000000 INFO @ Sun, 21 Jun 2020 19:42:55: 9000000 INFO @ Sun, 21 Jun 2020 19:42:57: 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 19:43:02: 10000000 INFO @ Sun, 21 Jun 2020 19:43:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.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 19:43:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:43:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:43:03: 5000000 INFO @ Sun, 21 Jun 2020 19:43:08: 11000000 INFO @ Sun, 21 Jun 2020 19:43:09: 6000000 INFO @ Sun, 21 Jun 2020 19:43:10: 1000000 INFO @ Sun, 21 Jun 2020 19:43:14: 12000000 INFO @ Sun, 21 Jun 2020 19:43:15: 7000000 INFO @ Sun, 21 Jun 2020 19:43:17: 2000000 INFO @ Sun, 21 Jun 2020 19:43:21: 13000000 INFO @ Sun, 21 Jun 2020 19:43:22: 8000000 INFO @ Sun, 21 Jun 2020 19:43:23: 3000000 INFO @ Sun, 21 Jun 2020 19:43:27: 14000000 INFO @ Sun, 21 Jun 2020 19:43:28: 9000000 INFO @ Sun, 21 Jun 2020 19:43:30: 4000000 INFO @ Sun, 21 Jun 2020 19:43:34: 15000000 INFO @ Sun, 21 Jun 2020 19:43:35: 10000000 INFO @ Sun, 21 Jun 2020 19:43:36: 5000000 INFO @ Sun, 21 Jun 2020 19:43:41: 11000000 INFO @ Sun, 21 Jun 2020 19:43:42: 16000000 INFO @ Sun, 21 Jun 2020 19:43:42: 6000000 INFO @ Sun, 21 Jun 2020 19:43:48: 12000000 INFO @ Sun, 21 Jun 2020 19:43:48: 7000000 INFO @ Sun, 21 Jun 2020 19:43:48: 17000000 INFO @ Sun, 21 Jun 2020 19:43:54: 13000000 INFO @ Sun, 21 Jun 2020 19:43:54: 8000000 INFO @ Sun, 21 Jun 2020 19:43:55: 18000000 INFO @ Sun, 21 Jun 2020 19:43:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:43:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:43:58: #1 total tags in treatment: 18458689 INFO @ Sun, 21 Jun 2020 19:43:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:43:58: #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 19:43:59: #1 tags after filtering in treatment: 18458689 INFO @ Sun, 21 Jun 2020 19:43:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:43:59: #1 finished! INFO @ Sun, 21 Jun 2020 19:43:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:43:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:44:00: 14000000 INFO @ Sun, 21 Jun 2020 19:44:00: #2 number of paired peaks: 774 WARNING @ Sun, 21 Jun 2020 19:44:00: Fewer paired peaks (774) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 774 pairs to build model! INFO @ Sun, 21 Jun 2020 19:44:00: start model_add_line... INFO @ Sun, 21 Jun 2020 19:44:01: start X-correlation... INFO @ Sun, 21 Jun 2020 19:44:01: end of X-cor INFO @ Sun, 21 Jun 2020 19:44:01: #2 finished! INFO @ Sun, 21 Jun 2020 19:44:01: #2 predicted fragment length is 178 bps INFO @ Sun, 21 Jun 2020 19:44:01: #2 alternative fragment length(s) may be 178 bps INFO @ Sun, 21 Jun 2020 19:44:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.05_model.r INFO @ Sun, 21 Jun 2020 19:44:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:44:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:44:01: 9000000 INFO @ Sun, 21 Jun 2020 19:44:06: 15000000 INFO @ Sun, 21 Jun 2020 19:44:07: 10000000 INFO @ Sun, 21 Jun 2020 19:44:12: 16000000 INFO @ Sun, 21 Jun 2020 19:44:13: 11000000 INFO @ Sun, 21 Jun 2020 19:44:18: 17000000 INFO @ Sun, 21 Jun 2020 19:44:19: 12000000 INFO @ Sun, 21 Jun 2020 19:44:24: 18000000 INFO @ Sun, 21 Jun 2020 19:44:25: 13000000 INFO @ Sun, 21 Jun 2020 19:44:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:44:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:44:27: #1 total tags in treatment: 18458689 INFO @ Sun, 21 Jun 2020 19:44:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:44:27: #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 19:44:28: #1 tags after filtering in treatment: 18458689 INFO @ Sun, 21 Jun 2020 19:44:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:44:28: #1 finished! INFO @ Sun, 21 Jun 2020 19:44:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:44:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:44:29: #2 number of paired peaks: 774 WARNING @ Sun, 21 Jun 2020 19:44:29: Fewer paired peaks (774) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 774 pairs to build model! INFO @ Sun, 21 Jun 2020 19:44:29: start model_add_line... INFO @ Sun, 21 Jun 2020 19:44:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:44:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:44:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:44:30: #2 predicted fragment length is 178 bps INFO @ Sun, 21 Jun 2020 19:44:30: #2 alternative fragment length(s) may be 178 bps INFO @ Sun, 21 Jun 2020 19:44:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.10_model.r INFO @ Sun, 21 Jun 2020 19:44:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:44:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:44:31: 14000000 INFO @ Sun, 21 Jun 2020 19:44:37: 15000000 INFO @ Sun, 21 Jun 2020 19:44:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:44:44: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:44:50: 17000000 INFO @ Sun, 21 Jun 2020 19:44:56: 18000000 INFO @ Sun, 21 Jun 2020 19:44:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:44:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:44:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.05_summits.bed INFO @ Sun, 21 Jun 2020 19:44:57: Done! pass1 - making usageList (686 chroms): 2 millis pass2 - checking and writing primary data (7933 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:44:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:44:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:44:59: #1 total tags in treatment: 18458689 INFO @ Sun, 21 Jun 2020 19:44:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:44:59: #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 19:45:00: #1 tags after filtering in treatment: 18458689 INFO @ Sun, 21 Jun 2020 19:45:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:45:00: #1 finished! INFO @ Sun, 21 Jun 2020 19:45:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:45:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:45:01: #2 number of paired peaks: 774 WARNING @ Sun, 21 Jun 2020 19:45:01: Fewer paired peaks (774) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 774 pairs to build model! INFO @ Sun, 21 Jun 2020 19:45:01: start model_add_line... INFO @ Sun, 21 Jun 2020 19:45:01: start X-correlation... INFO @ Sun, 21 Jun 2020 19:45:01: end of X-cor INFO @ Sun, 21 Jun 2020 19:45:01: #2 finished! INFO @ Sun, 21 Jun 2020 19:45:01: #2 predicted fragment length is 178 bps INFO @ Sun, 21 Jun 2020 19:45:01: #2 alternative fragment length(s) may be 178 bps INFO @ Sun, 21 Jun 2020 19:45:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.20_model.r INFO @ Sun, 21 Jun 2020 19:45:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:45:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:45:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:45:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:45:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:45:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.10_summits.bed INFO @ Sun, 21 Jun 2020 19:45:24: Done! pass1 - making usageList (583 chroms): 2 millis pass2 - checking and writing primary data (5815 records, 4 fields): 36 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:45:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:45:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:45:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:45:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288034/SRX288034.20_summits.bed INFO @ Sun, 21 Jun 2020 19:45:55: Done! pass1 - making usageList (467 chroms): 1 millis pass2 - checking and writing primary data (3726 records, 4 fields): 30 millis CompletedMACS2peakCalling