Job ID = 6368455 SRX = SRX4996811 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:10:09 prefetch.2.10.7: 1) Downloading 'SRR8176697'... 2020-06-16T00:10:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:13:13 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:13:13 prefetch.2.10.7: 1) 'SRR8176697' was downloaded successfully 2020-06-16T00:13:13 prefetch.2.10.7: 'SRR8176697' has 0 unresolved dependencies Read 17088064 spots for SRR8176697/SRR8176697.sra Written 17088064 spots for SRR8176697/SRR8176697.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: 00:14:04 17088064 reads; of these: 17088064 (100.00%) were paired; of these: 3945718 (23.09%) aligned concordantly 0 times 11063347 (64.74%) aligned concordantly exactly 1 time 2078999 (12.17%) aligned concordantly >1 times ---- 3945718 pairs aligned concordantly 0 times; of these: 910536 (23.08%) aligned discordantly 1 time ---- 3035182 pairs aligned 0 times concordantly or discordantly; of these: 6070364 mates make up the pairs; of these: 5513929 (90.83%) aligned 0 times 298927 (4.92%) aligned exactly 1 time 257508 (4.24%) aligned >1 times 83.87% overall alignment rate Time searching: 00:14:04 Overall time: 00:14:04 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 4135137 / 14042938 = 0.2945 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 @ Tue, 16 Jun 2020 09:35:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:35:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:20: 1000000 INFO @ Tue, 16 Jun 2020 09:35:25: 2000000 INFO @ Tue, 16 Jun 2020 09:35:30: 3000000 INFO @ Tue, 16 Jun 2020 09:35:35: 4000000 INFO @ Tue, 16 Jun 2020 09:35:40: 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 @ Tue, 16 Jun 2020 09:35:45: 6000000 INFO @ Tue, 16 Jun 2020 09:35:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:35:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:51: 7000000 INFO @ Tue, 16 Jun 2020 09:35:51: 1000000 INFO @ Tue, 16 Jun 2020 09:35:56: 8000000 INFO @ Tue, 16 Jun 2020 09:35:57: 2000000 INFO @ Tue, 16 Jun 2020 09:36:02: 9000000 INFO @ Tue, 16 Jun 2020 09:36:02: 3000000 INFO @ Tue, 16 Jun 2020 09:36:07: 10000000 INFO @ Tue, 16 Jun 2020 09:36:08: 4000000 INFO @ Tue, 16 Jun 2020 09:36:13: 11000000 INFO @ Tue, 16 Jun 2020 09:36:13: 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 @ Tue, 16 Jun 2020 09:36:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:36:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:18: 12000000 INFO @ Tue, 16 Jun 2020 09:36:19: 6000000 INFO @ Tue, 16 Jun 2020 09:36:21: 1000000 INFO @ Tue, 16 Jun 2020 09:36:24: 13000000 INFO @ Tue, 16 Jun 2020 09:36:25: 7000000 INFO @ Tue, 16 Jun 2020 09:36:27: 2000000 INFO @ Tue, 16 Jun 2020 09:36:30: 14000000 INFO @ Tue, 16 Jun 2020 09:36:30: 8000000 INFO @ Tue, 16 Jun 2020 09:36:33: 3000000 INFO @ Tue, 16 Jun 2020 09:36:35: 15000000 INFO @ Tue, 16 Jun 2020 09:36:36: 9000000 INFO @ Tue, 16 Jun 2020 09:36:39: 4000000 INFO @ Tue, 16 Jun 2020 09:36:41: 16000000 INFO @ Tue, 16 Jun 2020 09:36:41: 10000000 INFO @ Tue, 16 Jun 2020 09:36:44: 5000000 INFO @ Tue, 16 Jun 2020 09:36:46: 17000000 INFO @ Tue, 16 Jun 2020 09:36:47: 11000000 INFO @ Tue, 16 Jun 2020 09:36:50: 6000000 INFO @ Tue, 16 Jun 2020 09:36:52: 18000000 INFO @ Tue, 16 Jun 2020 09:36:53: 12000000 INFO @ Tue, 16 Jun 2020 09:36:56: 7000000 INFO @ Tue, 16 Jun 2020 09:36:58: 19000000 INFO @ Tue, 16 Jun 2020 09:36:58: 13000000 INFO @ Tue, 16 Jun 2020 09:37:01: 8000000 INFO @ Tue, 16 Jun 2020 09:37:04: 20000000 INFO @ Tue, 16 Jun 2020 09:37:04: 14000000 INFO @ Tue, 16 Jun 2020 09:37:06: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:37:06: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:37:06: #1 total tags in treatment: 9128197 INFO @ Tue, 16 Jun 2020 09:37:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:37:06: #1 tags after filtering in treatment: 8458709 INFO @ Tue, 16 Jun 2020 09:37:06: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 09:37:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:06: #2 number of paired peaks: 560 WARNING @ Tue, 16 Jun 2020 09:37:06: Fewer paired peaks (560) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 560 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:07: #2 predicted fragment length is 161 bps INFO @ Tue, 16 Jun 2020 09:37:07: #2 alternative fragment length(s) may be 4,161 bps INFO @ Tue, 16 Jun 2020 09:37:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.05_model.r INFO @ Tue, 16 Jun 2020 09:37:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:07: 9000000 INFO @ Tue, 16 Jun 2020 09:37:10: 15000000 INFO @ Tue, 16 Jun 2020 09:37:13: 10000000 INFO @ Tue, 16 Jun 2020 09:37:16: 16000000 INFO @ Tue, 16 Jun 2020 09:37:19: 11000000 INFO @ Tue, 16 Jun 2020 09:37:22: 17000000 INFO @ Tue, 16 Jun 2020 09:37:25: 12000000 INFO @ Tue, 16 Jun 2020 09:37:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:28: 18000000 INFO @ Tue, 16 Jun 2020 09:37:31: 13000000 INFO @ Tue, 16 Jun 2020 09:37:34: 19000000 INFO @ Tue, 16 Jun 2020 09:37:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.05_summits.bed INFO @ Tue, 16 Jun 2020 09:37:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (434 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:37:37: 14000000 INFO @ Tue, 16 Jun 2020 09:37:40: 20000000 INFO @ Tue, 16 Jun 2020 09:37:42: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:37:42: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:37:42: #1 total tags in treatment: 9128197 INFO @ Tue, 16 Jun 2020 09:37:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:37:42: #1 tags after filtering in treatment: 8458709 INFO @ Tue, 16 Jun 2020 09:37:42: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 09:37:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:42: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:37:43: 15000000 INFO @ Tue, 16 Jun 2020 09:37:43: #2 number of paired peaks: 560 WARNING @ Tue, 16 Jun 2020 09:37:43: Fewer paired peaks (560) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 560 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:43: #2 predicted fragment length is 161 bps INFO @ Tue, 16 Jun 2020 09:37:43: #2 alternative fragment length(s) may be 4,161 bps INFO @ Tue, 16 Jun 2020 09:37:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.10_model.r INFO @ Tue, 16 Jun 2020 09:37:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:49: 16000000 INFO @ Tue, 16 Jun 2020 09:37:54: 17000000 INFO @ Tue, 16 Jun 2020 09:37:59: 18000000 INFO @ Tue, 16 Jun 2020 09:38:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:38:04: 19000000 INFO @ Tue, 16 Jun 2020 09:38:10: 20000000 INFO @ Tue, 16 Jun 2020 09:38:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:38:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:38:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.10_summits.bed INFO @ Tue, 16 Jun 2020 09:38:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (319 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:38:12: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:38:12: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:38:12: #1 total tags in treatment: 9128197 INFO @ Tue, 16 Jun 2020 09:38:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:38:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:38:12: #1 tags after filtering in treatment: 8458709 INFO @ Tue, 16 Jun 2020 09:38:12: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 09:38:12: #1 finished! INFO @ Tue, 16 Jun 2020 09:38:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:38:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:38:13: #2 number of paired peaks: 560 WARNING @ Tue, 16 Jun 2020 09:38:13: Fewer paired peaks (560) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 560 pairs to build model! INFO @ Tue, 16 Jun 2020 09:38:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:38:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:38:13: end of X-cor INFO @ Tue, 16 Jun 2020 09:38:13: #2 finished! INFO @ Tue, 16 Jun 2020 09:38:13: #2 predicted fragment length is 161 bps INFO @ Tue, 16 Jun 2020 09:38:13: #2 alternative fragment length(s) may be 4,161 bps INFO @ Tue, 16 Jun 2020 09:38:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.20_model.r INFO @ Tue, 16 Jun 2020 09:38:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:38:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:38:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:38:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:38:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:38:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996811/SRX4996811.20_summits.bed INFO @ Tue, 16 Jun 2020 09:38:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (211 records, 4 fields): 1 millis CompletedMACS2peakCalling