Job ID = 6453043 SRX = SRX101478 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:55:00 prefetch.2.10.7: 1) Downloading 'SRR353682'... 2020-06-21T07:55:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:57:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:57:55 prefetch.2.10.7: 1) 'SRR353682' was downloaded successfully Read 37703557 spots for SRR353682/SRR353682.sra Written 37703557 spots for SRR353682/SRR353682.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: 00:07:05 37703557 reads; of these: 37703557 (100.00%) were unpaired; of these: 8861333 (23.50%) aligned 0 times 23597356 (62.59%) aligned exactly 1 time 5244868 (13.91%) aligned >1 times 76.50% overall alignment rate Time searching: 00:07:05 Overall time: 00:07:05 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] 7766349 / 28842224 = 0.2693 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 17:12:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.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 17:12:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:12:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:12:43: 1000000 INFO @ Sun, 21 Jun 2020 17:12:48: 2000000 INFO @ Sun, 21 Jun 2020 17:12:54: 3000000 INFO @ Sun, 21 Jun 2020 17:12:59: 4000000 INFO @ Sun, 21 Jun 2020 17:13:05: 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 17:13:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.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 17:13:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:13:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:13:10: 6000000 INFO @ Sun, 21 Jun 2020 17:13:13: 1000000 INFO @ Sun, 21 Jun 2020 17:13:16: 7000000 INFO @ Sun, 21 Jun 2020 17:13:19: 2000000 INFO @ Sun, 21 Jun 2020 17:13:22: 8000000 INFO @ Sun, 21 Jun 2020 17:13:24: 3000000 INFO @ Sun, 21 Jun 2020 17:13:27: 9000000 INFO @ Sun, 21 Jun 2020 17:13:30: 4000000 INFO @ Sun, 21 Jun 2020 17:13:33: 10000000 INFO @ Sun, 21 Jun 2020 17:13:35: 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 17:13:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.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 17:13:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:13:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:13:39: 11000000 INFO @ Sun, 21 Jun 2020 17:13:41: 6000000 INFO @ Sun, 21 Jun 2020 17:13:44: 1000000 INFO @ Sun, 21 Jun 2020 17:13:45: 12000000 INFO @ Sun, 21 Jun 2020 17:13:46: 7000000 INFO @ Sun, 21 Jun 2020 17:13:50: 2000000 INFO @ Sun, 21 Jun 2020 17:13:51: 13000000 INFO @ Sun, 21 Jun 2020 17:13:51: 8000000 INFO @ Sun, 21 Jun 2020 17:13:56: 3000000 INFO @ Sun, 21 Jun 2020 17:13:57: 14000000 INFO @ Sun, 21 Jun 2020 17:13:57: 9000000 INFO @ Sun, 21 Jun 2020 17:14:02: 4000000 INFO @ Sun, 21 Jun 2020 17:14:03: 10000000 INFO @ Sun, 21 Jun 2020 17:14:03: 15000000 INFO @ Sun, 21 Jun 2020 17:14:08: 11000000 INFO @ Sun, 21 Jun 2020 17:14:08: 5000000 INFO @ Sun, 21 Jun 2020 17:14:09: 16000000 INFO @ Sun, 21 Jun 2020 17:14:14: 12000000 INFO @ Sun, 21 Jun 2020 17:14:15: 6000000 INFO @ Sun, 21 Jun 2020 17:14:15: 17000000 INFO @ Sun, 21 Jun 2020 17:14:19: 13000000 INFO @ Sun, 21 Jun 2020 17:14:21: 7000000 INFO @ Sun, 21 Jun 2020 17:14:21: 18000000 INFO @ Sun, 21 Jun 2020 17:14:24: 14000000 INFO @ Sun, 21 Jun 2020 17:14:27: 8000000 INFO @ Sun, 21 Jun 2020 17:14:28: 19000000 INFO @ Sun, 21 Jun 2020 17:14:30: 15000000 INFO @ Sun, 21 Jun 2020 17:14:33: 9000000 INFO @ Sun, 21 Jun 2020 17:14:34: 20000000 INFO @ Sun, 21 Jun 2020 17:14:35: 16000000 INFO @ Sun, 21 Jun 2020 17:14:39: 10000000 INFO @ Sun, 21 Jun 2020 17:14:40: 21000000 INFO @ Sun, 21 Jun 2020 17:14:41: 17000000 INFO @ Sun, 21 Jun 2020 17:14:41: #1 tag size is determined as 41 bps INFO @ Sun, 21 Jun 2020 17:14:41: #1 tag size = 41 INFO @ Sun, 21 Jun 2020 17:14:41: #1 total tags in treatment: 21075875 INFO @ Sun, 21 Jun 2020 17:14:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:14:41: #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 17:14:42: #1 tags after filtering in treatment: 21075824 INFO @ Sun, 21 Jun 2020 17:14:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:14:42: #1 finished! INFO @ Sun, 21 Jun 2020 17:14:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:14:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:14:43: #2 number of paired peaks: 451 WARNING @ Sun, 21 Jun 2020 17:14:43: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Sun, 21 Jun 2020 17:14:43: start model_add_line... INFO @ Sun, 21 Jun 2020 17:14:43: start X-correlation... INFO @ Sun, 21 Jun 2020 17:14:43: end of X-cor INFO @ Sun, 21 Jun 2020 17:14:43: #2 finished! INFO @ Sun, 21 Jun 2020 17:14:43: #2 predicted fragment length is 168 bps INFO @ Sun, 21 Jun 2020 17:14:43: #2 alternative fragment length(s) may be 168 bps INFO @ Sun, 21 Jun 2020 17:14:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.05_model.r INFO @ Sun, 21 Jun 2020 17:14:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:14:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:14:45: 11000000 INFO @ Sun, 21 Jun 2020 17:14:46: 18000000 INFO @ Sun, 21 Jun 2020 17:14:51: 12000000 INFO @ Sun, 21 Jun 2020 17:14:52: 19000000 INFO @ Sun, 21 Jun 2020 17:14:57: 13000000 INFO @ Sun, 21 Jun 2020 17:14:57: 20000000 INFO @ Sun, 21 Jun 2020 17:15:03: 21000000 INFO @ Sun, 21 Jun 2020 17:15:03: 14000000 INFO @ Sun, 21 Jun 2020 17:15:03: #1 tag size is determined as 41 bps INFO @ Sun, 21 Jun 2020 17:15:03: #1 tag size = 41 INFO @ Sun, 21 Jun 2020 17:15:03: #1 total tags in treatment: 21075875 INFO @ Sun, 21 Jun 2020 17:15:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:15:03: #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 17:15:04: #1 tags after filtering in treatment: 21075824 INFO @ Sun, 21 Jun 2020 17:15:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:15:04: #1 finished! INFO @ Sun, 21 Jun 2020 17:15:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:15:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:15:05: #2 number of paired peaks: 451 WARNING @ Sun, 21 Jun 2020 17:15:05: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Sun, 21 Jun 2020 17:15:05: start model_add_line... INFO @ Sun, 21 Jun 2020 17:15:05: start X-correlation... INFO @ Sun, 21 Jun 2020 17:15:05: end of X-cor INFO @ Sun, 21 Jun 2020 17:15:05: #2 finished! INFO @ Sun, 21 Jun 2020 17:15:05: #2 predicted fragment length is 168 bps INFO @ Sun, 21 Jun 2020 17:15:05: #2 alternative fragment length(s) may be 168 bps INFO @ Sun, 21 Jun 2020 17:15:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.10_model.r INFO @ Sun, 21 Jun 2020 17:15:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:15:05: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:15:08: 15000000 INFO @ Sun, 21 Jun 2020 17:15:14: 16000000 INFO @ Sun, 21 Jun 2020 17:15:20: 17000000 INFO @ Sun, 21 Jun 2020 17:15:25: 18000000 INFO @ Sun, 21 Jun 2020 17:15:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:15:31: 19000000 INFO @ Sun, 21 Jun 2020 17:15:37: 20000000 INFO @ Sun, 21 Jun 2020 17:15:42: 21000000 INFO @ Sun, 21 Jun 2020 17:15:43: #1 tag size is determined as 41 bps INFO @ Sun, 21 Jun 2020 17:15:43: #1 tag size = 41 INFO @ Sun, 21 Jun 2020 17:15:43: #1 total tags in treatment: 21075875 INFO @ Sun, 21 Jun 2020 17:15:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:15:43: #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 17:15:44: #1 tags after filtering in treatment: 21075824 INFO @ Sun, 21 Jun 2020 17:15:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:15:44: #1 finished! INFO @ Sun, 21 Jun 2020 17:15:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:15:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:15:45: #2 number of paired peaks: 451 WARNING @ Sun, 21 Jun 2020 17:15:45: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Sun, 21 Jun 2020 17:15:45: start model_add_line... INFO @ Sun, 21 Jun 2020 17:15:45: start X-correlation... INFO @ Sun, 21 Jun 2020 17:15:45: end of X-cor INFO @ Sun, 21 Jun 2020 17:15:45: #2 finished! INFO @ Sun, 21 Jun 2020 17:15:45: #2 predicted fragment length is 168 bps INFO @ Sun, 21 Jun 2020 17:15:45: #2 alternative fragment length(s) may be 168 bps INFO @ Sun, 21 Jun 2020 17:15:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.20_model.r INFO @ Sun, 21 Jun 2020 17:15:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:15:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:15:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:15:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:15:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.05_summits.bed INFO @ Sun, 21 Jun 2020 17:15:46: Done! pass1 - making usageList (578 chroms): 1 millis pass2 - checking and writing primary data (4059 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:15:48: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:16:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:16:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:16:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.10_summits.bed INFO @ Sun, 21 Jun 2020 17:16:10: Done! pass1 - making usageList (442 chroms): 1 millis pass2 - checking and writing primary data (2734 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:16:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:16:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:16:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:16:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX101478/SRX101478.20_summits.bed INFO @ Sun, 21 Jun 2020 17:16:47: Done! pass1 - making usageList (242 chroms): 1 millis pass2 - checking and writing primary data (1666 records, 4 fields): 9 millis CompletedMACS2peakCalling