Job ID = 6368449 SRX = SRX4996805 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:10:21 prefetch.2.10.7: 1) Downloading 'SRR8176691'... 2020-06-16T00:10:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:13:32 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:13:32 prefetch.2.10.7: 1) 'SRR8176691' was downloaded successfully 2020-06-16T00:13:32 prefetch.2.10.7: 'SRR8176691' has 0 unresolved dependencies Read 13986985 spots for SRR8176691/SRR8176691.sra Written 13986985 spots for SRR8176691/SRR8176691.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: 00:13:30 13986985 reads; of these: 13986985 (100.00%) were paired; of these: 2050812 (14.66%) aligned concordantly 0 times 9693493 (69.30%) aligned concordantly exactly 1 time 2242680 (16.03%) aligned concordantly >1 times ---- 2050812 pairs aligned concordantly 0 times; of these: 1027474 (50.10%) aligned discordantly 1 time ---- 1023338 pairs aligned 0 times concordantly or discordantly; of these: 2046676 mates make up the pairs; of these: 1398969 (68.35%) aligned 0 times 309962 (15.14%) aligned exactly 1 time 337745 (16.50%) aligned >1 times 95.00% overall alignment rate Time searching: 00:13:30 Overall time: 00:13:30 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] 5266219 / 12955663 = 0.4065 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 09:33:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.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 09:33:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:53: 1000000 INFO @ Tue, 16 Jun 2020 09:33:59: 2000000 INFO @ Tue, 16 Jun 2020 09:34:04: 3000000 INFO @ Tue, 16 Jun 2020 09:34:09: 4000000 INFO @ Tue, 16 Jun 2020 09:34:14: 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 09:34:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.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 09:34:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:19: 6000000 INFO @ Tue, 16 Jun 2020 09:34:24: 1000000 INFO @ Tue, 16 Jun 2020 09:34:25: 7000000 INFO @ Tue, 16 Jun 2020 09:34:29: 2000000 INFO @ Tue, 16 Jun 2020 09:34:30: 8000000 INFO @ Tue, 16 Jun 2020 09:34:34: 3000000 INFO @ Tue, 16 Jun 2020 09:34:35: 9000000 INFO @ Tue, 16 Jun 2020 09:34:39: 4000000 INFO @ Tue, 16 Jun 2020 09:34:40: 10000000 INFO @ Tue, 16 Jun 2020 09:34:44: 5000000 INFO @ Tue, 16 Jun 2020 09:34:45: 11000000 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 09:34:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.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 09:34:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:49: 6000000 INFO @ Tue, 16 Jun 2020 09:34:50: 12000000 INFO @ Tue, 16 Jun 2020 09:34:53: 1000000 INFO @ Tue, 16 Jun 2020 09:34:54: 7000000 INFO @ Tue, 16 Jun 2020 09:34:55: 13000000 INFO @ Tue, 16 Jun 2020 09:34:58: 2000000 INFO @ Tue, 16 Jun 2020 09:34:59: 8000000 INFO @ Tue, 16 Jun 2020 09:35:01: 14000000 INFO @ Tue, 16 Jun 2020 09:35:02: 3000000 INFO @ Tue, 16 Jun 2020 09:35:04: 9000000 INFO @ Tue, 16 Jun 2020 09:35:06: 15000000 INFO @ Tue, 16 Jun 2020 09:35:07: 4000000 INFO @ Tue, 16 Jun 2020 09:35:09: 10000000 INFO @ Tue, 16 Jun 2020 09:35:11: 16000000 INFO @ Tue, 16 Jun 2020 09:35:11: 5000000 INFO @ Tue, 16 Jun 2020 09:35:11: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:35:11: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:35:11: #1 total tags in treatment: 6896874 INFO @ Tue, 16 Jun 2020 09:35:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:11: #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 09:35:11: #1 tags after filtering in treatment: 6243028 INFO @ Tue, 16 Jun 2020 09:35:11: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 09:35:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:12: #2 number of paired peaks: 709 WARNING @ Tue, 16 Jun 2020 09:35:12: Fewer paired peaks (709) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 709 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:12: #2 predicted fragment length is 162 bps INFO @ Tue, 16 Jun 2020 09:35:12: #2 alternative fragment length(s) may be 4,162 bps INFO @ Tue, 16 Jun 2020 09:35:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.05_model.r INFO @ Tue, 16 Jun 2020 09:35:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:14: 11000000 INFO @ Tue, 16 Jun 2020 09:35:16: 6000000 INFO @ Tue, 16 Jun 2020 09:35:19: 12000000 INFO @ Tue, 16 Jun 2020 09:35:20: 7000000 INFO @ Tue, 16 Jun 2020 09:35:24: 13000000 INFO @ Tue, 16 Jun 2020 09:35:24: 8000000 INFO @ Tue, 16 Jun 2020 09:35:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:29: 9000000 INFO @ Tue, 16 Jun 2020 09:35:30: 14000000 INFO @ Tue, 16 Jun 2020 09:35:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.05_summits.bed INFO @ Tue, 16 Jun 2020 09:35:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (435 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:35:33: 10000000 INFO @ Tue, 16 Jun 2020 09:35:35: 15000000 INFO @ Tue, 16 Jun 2020 09:35:38: 11000000 INFO @ Tue, 16 Jun 2020 09:35:40: 16000000 INFO @ Tue, 16 Jun 2020 09:35:40: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:35:40: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:35:40: #1 total tags in treatment: 6896874 INFO @ Tue, 16 Jun 2020 09:35:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:40: #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 09:35:40: #1 tags after filtering in treatment: 6243028 INFO @ Tue, 16 Jun 2020 09:35:40: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 09:35:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:40: #2 number of paired peaks: 709 WARNING @ Tue, 16 Jun 2020 09:35:40: Fewer paired peaks (709) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 709 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:40: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:40: #2 predicted fragment length is 162 bps INFO @ Tue, 16 Jun 2020 09:35:40: #2 alternative fragment length(s) may be 4,162 bps INFO @ Tue, 16 Jun 2020 09:35:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.10_model.r INFO @ Tue, 16 Jun 2020 09:35:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:42: 12000000 INFO @ Tue, 16 Jun 2020 09:35:46: 13000000 INFO @ Tue, 16 Jun 2020 09:35:51: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:35:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:55: 15000000 INFO @ Tue, 16 Jun 2020 09:35:59: 16000000 INFO @ Tue, 16 Jun 2020 09:35:59: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:35:59: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:35:59: #1 total tags in treatment: 6896874 INFO @ Tue, 16 Jun 2020 09:35:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:59: #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 09:36:00: #1 tags after filtering in treatment: 6243028 INFO @ Tue, 16 Jun 2020 09:36:00: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 09:36:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:00: #2 number of paired peaks: 709 WARNING @ Tue, 16 Jun 2020 09:36:00: Fewer paired peaks (709) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 709 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:00: #2 predicted fragment length is 162 bps INFO @ Tue, 16 Jun 2020 09:36:00: #2 alternative fragment length(s) may be 4,162 bps INFO @ Tue, 16 Jun 2020 09:36:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.20_model.r INFO @ Tue, 16 Jun 2020 09:36:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.10_summits.bed INFO @ Tue, 16 Jun 2020 09:36:01: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (318 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996805/SRX4996805.20_summits.bed INFO @ Tue, 16 Jun 2020 09:36:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (209 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。