Job ID = 6368454 SRX = SRX4996810 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:43:12 prefetch.2.10.7: 1) Downloading 'SRR8176696'... 2020-06-16T00:43:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:46:18 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:46:18 prefetch.2.10.7: 1) 'SRR8176696' was downloaded successfully 2020-06-16T00:46:18 prefetch.2.10.7: 'SRR8176696' has 0 unresolved dependencies Read 16829782 spots for SRR8176696/SRR8176696.sra Written 16829782 spots for SRR8176696/SRR8176696.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:19:39 16829782 reads; of these: 16829782 (100.00%) were paired; of these: 1039887 (6.18%) aligned concordantly 0 times 13261693 (78.80%) aligned concordantly exactly 1 time 2528202 (15.02%) aligned concordantly >1 times ---- 1039887 pairs aligned concordantly 0 times; of these: 413642 (39.78%) aligned discordantly 1 time ---- 626245 pairs aligned 0 times concordantly or discordantly; of these: 1252490 mates make up the pairs; of these: 913596 (72.94%) aligned 0 times 196917 (15.72%) aligned exactly 1 time 141977 (11.34%) aligned >1 times 97.29% overall alignment rate Time searching: 00:19:40 Overall time: 00:19:40 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 16 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] 5725021 / 16196255 = 0.3535 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 10:16:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.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 10:16:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:16:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:16:16: 1000000 INFO @ Tue, 16 Jun 2020 10:16:20: 2000000 INFO @ Tue, 16 Jun 2020 10:16:24: 3000000 INFO @ Tue, 16 Jun 2020 10:16:28: 4000000 INFO @ Tue, 16 Jun 2020 10:16:32: 5000000 INFO @ Tue, 16 Jun 2020 10:16:37: 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 @ Tue, 16 Jun 2020 10:16:41: 7000000 INFO @ Tue, 16 Jun 2020 10:16:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.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 10:16:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:16:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:16:45: 8000000 INFO @ Tue, 16 Jun 2020 10:16:46: 1000000 INFO @ Tue, 16 Jun 2020 10:16:49: 9000000 INFO @ Tue, 16 Jun 2020 10:16:50: 2000000 INFO @ Tue, 16 Jun 2020 10:16:53: 10000000 INFO @ Tue, 16 Jun 2020 10:16:54: 3000000 INFO @ Tue, 16 Jun 2020 10:16:58: 11000000 INFO @ Tue, 16 Jun 2020 10:16:59: 4000000 INFO @ Tue, 16 Jun 2020 10:17:02: 12000000 INFO @ Tue, 16 Jun 2020 10:17:03: 5000000 INFO @ Tue, 16 Jun 2020 10:17:06: 13000000 INFO @ Tue, 16 Jun 2020 10:17:08: 6000000 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 10:17:10: 14000000 INFO @ Tue, 16 Jun 2020 10:17:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.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 10:17:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:17:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:17:12: 7000000 INFO @ Tue, 16 Jun 2020 10:17:15: 15000000 INFO @ Tue, 16 Jun 2020 10:17:16: 1000000 INFO @ Tue, 16 Jun 2020 10:17:16: 8000000 INFO @ Tue, 16 Jun 2020 10:17:20: 16000000 INFO @ Tue, 16 Jun 2020 10:17:21: 9000000 INFO @ Tue, 16 Jun 2020 10:17:21: 2000000 INFO @ Tue, 16 Jun 2020 10:17:24: 17000000 INFO @ Tue, 16 Jun 2020 10:17:25: 10000000 INFO @ Tue, 16 Jun 2020 10:17:26: 3000000 INFO @ Tue, 16 Jun 2020 10:17:29: 18000000 INFO @ Tue, 16 Jun 2020 10:17:29: 11000000 INFO @ Tue, 16 Jun 2020 10:17:30: 4000000 INFO @ Tue, 16 Jun 2020 10:17:34: 19000000 INFO @ Tue, 16 Jun 2020 10:17:34: 12000000 INFO @ Tue, 16 Jun 2020 10:17:35: 5000000 INFO @ Tue, 16 Jun 2020 10:17:38: 13000000 INFO @ Tue, 16 Jun 2020 10:17:38: 20000000 INFO @ Tue, 16 Jun 2020 10:17:40: 6000000 INFO @ Tue, 16 Jun 2020 10:17:42: 14000000 INFO @ Tue, 16 Jun 2020 10:17:43: 21000000 INFO @ Tue, 16 Jun 2020 10:17:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:17:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:17:45: #1 total tags in treatment: 10136300 INFO @ Tue, 16 Jun 2020 10:17:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:17:45: #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 10:17:45: 7000000 INFO @ Tue, 16 Jun 2020 10:17:45: #1 tags after filtering in treatment: 9319282 INFO @ Tue, 16 Jun 2020 10:17:45: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 10:17:45: #1 finished! INFO @ Tue, 16 Jun 2020 10:17:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:17:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:17:45: #2 number of paired peaks: 542 WARNING @ Tue, 16 Jun 2020 10:17:45: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Tue, 16 Jun 2020 10:17:45: start model_add_line... INFO @ Tue, 16 Jun 2020 10:17:46: start X-correlation... INFO @ Tue, 16 Jun 2020 10:17:46: end of X-cor INFO @ Tue, 16 Jun 2020 10:17:46: #2 finished! INFO @ Tue, 16 Jun 2020 10:17:46: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 10:17:46: #2 alternative fragment length(s) may be 4,149 bps INFO @ Tue, 16 Jun 2020 10:17:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.05_model.r INFO @ Tue, 16 Jun 2020 10:17:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:17:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:17:47: 15000000 INFO @ Tue, 16 Jun 2020 10:17:49: 8000000 INFO @ Tue, 16 Jun 2020 10:17:51: 16000000 INFO @ Tue, 16 Jun 2020 10:17:53: 9000000 INFO @ Tue, 16 Jun 2020 10:17:55: 17000000 INFO @ Tue, 16 Jun 2020 10:17:58: 10000000 INFO @ Tue, 16 Jun 2020 10:17:59: 18000000 INFO @ Tue, 16 Jun 2020 10:18:02: 11000000 INFO @ Tue, 16 Jun 2020 10:18:04: 19000000 INFO @ Tue, 16 Jun 2020 10:18:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:18:06: 12000000 INFO @ Tue, 16 Jun 2020 10:18:08: 20000000 INFO @ Tue, 16 Jun 2020 10:18:11: 13000000 INFO @ Tue, 16 Jun 2020 10:18:12: 21000000 INFO @ Tue, 16 Jun 2020 10:18:13: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:18:13: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:18:13: #1 total tags in treatment: 10136300 INFO @ Tue, 16 Jun 2020 10:18:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:18:13: #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 10:18:14: #1 tags after filtering in treatment: 9319282 INFO @ Tue, 16 Jun 2020 10:18:14: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 10:18:14: #1 finished! INFO @ Tue, 16 Jun 2020 10:18:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:18:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:18:14: #2 number of paired peaks: 542 WARNING @ Tue, 16 Jun 2020 10:18:14: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Tue, 16 Jun 2020 10:18:14: start model_add_line... INFO @ Tue, 16 Jun 2020 10:18:14: start X-correlation... INFO @ Tue, 16 Jun 2020 10:18:14: end of X-cor INFO @ Tue, 16 Jun 2020 10:18:14: #2 finished! INFO @ Tue, 16 Jun 2020 10:18:14: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 10:18:14: #2 alternative fragment length(s) may be 4,149 bps INFO @ Tue, 16 Jun 2020 10:18:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.10_model.r INFO @ Tue, 16 Jun 2020 10:18:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:18:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:18:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:18:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:18:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.05_summits.bed INFO @ Tue, 16 Jun 2020 10:18:15: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (428 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:18:15: 14000000 INFO @ Tue, 16 Jun 2020 10:18:19: 15000000 INFO @ Tue, 16 Jun 2020 10:18:23: 16000000 INFO @ Tue, 16 Jun 2020 10:18:28: 17000000 INFO @ Tue, 16 Jun 2020 10:18:32: 18000000 INFO @ Tue, 16 Jun 2020 10:18:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:18:36: 19000000 INFO @ Tue, 16 Jun 2020 10:18:41: 20000000 INFO @ Tue, 16 Jun 2020 10:18:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:18:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:18:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.10_summits.bed INFO @ Tue, 16 Jun 2020 10:18:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (338 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:18:45: 21000000 INFO @ Tue, 16 Jun 2020 10:18:47: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:18:47: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:18:47: #1 total tags in treatment: 10136300 INFO @ Tue, 16 Jun 2020 10:18:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:18:47: #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 10:18:47: #1 tags after filtering in treatment: 9319282 INFO @ Tue, 16 Jun 2020 10:18:47: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 10:18:47: #1 finished! INFO @ Tue, 16 Jun 2020 10:18:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:18:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:18:47: #2 number of paired peaks: 542 WARNING @ Tue, 16 Jun 2020 10:18:47: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Tue, 16 Jun 2020 10:18:47: start model_add_line... INFO @ Tue, 16 Jun 2020 10:18:48: start X-correlation... INFO @ Tue, 16 Jun 2020 10:18:48: end of X-cor INFO @ Tue, 16 Jun 2020 10:18:48: #2 finished! INFO @ Tue, 16 Jun 2020 10:18:48: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 10:18:48: #2 alternative fragment length(s) may be 4,149 bps INFO @ Tue, 16 Jun 2020 10:18:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.20_model.r INFO @ Tue, 16 Jun 2020 10:18:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:18:48: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:19:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:19:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:19:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:19:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996810/SRX4996810.20_summits.bed INFO @ Tue, 16 Jun 2020 10:19:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (225 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。