Job ID = 6367193 SRX = SRX2978697 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:21:46 prefetch.2.10.7: 1) Downloading 'SRR5799204'... 2020-06-15T23:21:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:33 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:33 prefetch.2.10.7: 1) 'SRR5799204' was downloaded successfully 2020-06-15T23:23:33 prefetch.2.10.7: 'SRR5799204' has 0 unresolved dependencies Read 18679435 spots for SRR5799204/SRR5799204.sra Written 18679435 spots for SRR5799204/SRR5799204.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: 00:16:30 18679435 reads; of these: 18679435 (100.00%) were paired; of these: 2901445 (15.53%) aligned concordantly 0 times 13261540 (71.00%) aligned concordantly exactly 1 time 2516450 (13.47%) aligned concordantly >1 times ---- 2901445 pairs aligned concordantly 0 times; of these: 1756921 (60.55%) aligned discordantly 1 time ---- 1144524 pairs aligned 0 times concordantly or discordantly; of these: 2289048 mates make up the pairs; of these: 1211387 (52.92%) aligned 0 times 615911 (26.91%) aligned exactly 1 time 461750 (20.17%) aligned >1 times 96.76% overall alignment rate Time searching: 00:16:30 Overall time: 00:16:30 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 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] 3307087 / 17525409 = 0.1887 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 08:50:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.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 08:50:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:15: 1000000 INFO @ Tue, 16 Jun 2020 08:50:21: 2000000 INFO @ Tue, 16 Jun 2020 08:50:27: 3000000 INFO @ Tue, 16 Jun 2020 08:50:32: 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 @ Tue, 16 Jun 2020 08:50:38: 5000000 INFO @ Tue, 16 Jun 2020 08:50:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.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 08:50:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:44: 6000000 INFO @ Tue, 16 Jun 2020 08:50:45: 1000000 INFO @ Tue, 16 Jun 2020 08:50:51: 7000000 INFO @ Tue, 16 Jun 2020 08:50:52: 2000000 INFO @ Tue, 16 Jun 2020 08:50:59: 8000000 INFO @ Tue, 16 Jun 2020 08:50:59: 3000000 INFO @ Tue, 16 Jun 2020 08:51:05: 4000000 INFO @ Tue, 16 Jun 2020 08:51:06: 9000000 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 08:51:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.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 08:51:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:51:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:51:12: 5000000 INFO @ Tue, 16 Jun 2020 08:51:14: 10000000 INFO @ Tue, 16 Jun 2020 08:51:16: 1000000 INFO @ Tue, 16 Jun 2020 08:51:19: 6000000 INFO @ Tue, 16 Jun 2020 08:51:22: 11000000 INFO @ Tue, 16 Jun 2020 08:51:23: 2000000 INFO @ Tue, 16 Jun 2020 08:51:27: 7000000 INFO @ Tue, 16 Jun 2020 08:51:30: 12000000 INFO @ Tue, 16 Jun 2020 08:51:31: 3000000 INFO @ Tue, 16 Jun 2020 08:51:34: 8000000 INFO @ Tue, 16 Jun 2020 08:51:37: 13000000 INFO @ Tue, 16 Jun 2020 08:51:38: 4000000 INFO @ Tue, 16 Jun 2020 08:51:41: 9000000 INFO @ Tue, 16 Jun 2020 08:51:45: 14000000 INFO @ Tue, 16 Jun 2020 08:51:45: 5000000 INFO @ Tue, 16 Jun 2020 08:51:48: 10000000 INFO @ Tue, 16 Jun 2020 08:51:53: 6000000 INFO @ Tue, 16 Jun 2020 08:51:53: 15000000 INFO @ Tue, 16 Jun 2020 08:51:55: 11000000 INFO @ Tue, 16 Jun 2020 08:52:00: 7000000 INFO @ Tue, 16 Jun 2020 08:52:01: 16000000 INFO @ Tue, 16 Jun 2020 08:52:03: 12000000 INFO @ Tue, 16 Jun 2020 08:52:07: 8000000 INFO @ Tue, 16 Jun 2020 08:52:09: 17000000 INFO @ Tue, 16 Jun 2020 08:52:10: 13000000 INFO @ Tue, 16 Jun 2020 08:52:15: 9000000 INFO @ Tue, 16 Jun 2020 08:52:17: 18000000 INFO @ Tue, 16 Jun 2020 08:52:17: 14000000 INFO @ Tue, 16 Jun 2020 08:52:23: 10000000 INFO @ Tue, 16 Jun 2020 08:52:24: 15000000 INFO @ Tue, 16 Jun 2020 08:52:25: 19000000 INFO @ Tue, 16 Jun 2020 08:52:30: 11000000 INFO @ Tue, 16 Jun 2020 08:52:31: 16000000 INFO @ Tue, 16 Jun 2020 08:52:33: 20000000 INFO @ Tue, 16 Jun 2020 08:52:37: 12000000 INFO @ Tue, 16 Jun 2020 08:52:39: 17000000 INFO @ Tue, 16 Jun 2020 08:52:41: 21000000 INFO @ Tue, 16 Jun 2020 08:52:45: 13000000 INFO @ Tue, 16 Jun 2020 08:52:46: 18000000 INFO @ Tue, 16 Jun 2020 08:52:49: 22000000 INFO @ Tue, 16 Jun 2020 08:52:53: 14000000 INFO @ Tue, 16 Jun 2020 08:52:53: 19000000 INFO @ Tue, 16 Jun 2020 08:52:56: 23000000 INFO @ Tue, 16 Jun 2020 08:53:00: 15000000 INFO @ Tue, 16 Jun 2020 08:53:00: 20000000 INFO @ Tue, 16 Jun 2020 08:53:05: 24000000 INFO @ Tue, 16 Jun 2020 08:53:08: 21000000 INFO @ Tue, 16 Jun 2020 08:53:08: 16000000 INFO @ Tue, 16 Jun 2020 08:53:13: 25000000 INFO @ Tue, 16 Jun 2020 08:53:15: 22000000 INFO @ Tue, 16 Jun 2020 08:53:16: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:53:21: 26000000 INFO @ Tue, 16 Jun 2020 08:53:22: 23000000 INFO @ Tue, 16 Jun 2020 08:53:23: 18000000 INFO @ Tue, 16 Jun 2020 08:53:29: 27000000 INFO @ Tue, 16 Jun 2020 08:53:29: 24000000 INFO @ Tue, 16 Jun 2020 08:53:31: 19000000 INFO @ Tue, 16 Jun 2020 08:53:36: 25000000 INFO @ Tue, 16 Jun 2020 08:53:37: 28000000 INFO @ Tue, 16 Jun 2020 08:53:38: 20000000 INFO @ Tue, 16 Jun 2020 08:53:43: 26000000 INFO @ Tue, 16 Jun 2020 08:53:45: 29000000 INFO @ Tue, 16 Jun 2020 08:53:46: 21000000 INFO @ Tue, 16 Jun 2020 08:53:49: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:53:49: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:53:49: #1 total tags in treatment: 12614226 INFO @ Tue, 16 Jun 2020 08:53:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:53:49: #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 08:53:49: #1 tags after filtering in treatment: 11514065 INFO @ Tue, 16 Jun 2020 08:53:49: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 08:53:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:53:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:53:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:53:50: #2 number of paired peaks: 481 WARNING @ Tue, 16 Jun 2020 08:53:50: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Tue, 16 Jun 2020 08:53:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:53:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:53:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:53:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:53:50: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 08:53:50: #2 alternative fragment length(s) may be 4,129 bps INFO @ Tue, 16 Jun 2020 08:53:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.05_model.r INFO @ Tue, 16 Jun 2020 08:53:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:53:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:53:51: 27000000 INFO @ Tue, 16 Jun 2020 08:53:53: 22000000 INFO @ Tue, 16 Jun 2020 08:53:58: 28000000 INFO @ Tue, 16 Jun 2020 08:54:01: 23000000 INFO @ Tue, 16 Jun 2020 08:54:05: 29000000 INFO @ Tue, 16 Jun 2020 08:54:08: 24000000 INFO @ Tue, 16 Jun 2020 08:54:09: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:54:09: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:54:09: #1 total tags in treatment: 12614226 INFO @ Tue, 16 Jun 2020 08:54:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:54:09: #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 08:54:09: #1 tags after filtering in treatment: 11514065 INFO @ Tue, 16 Jun 2020 08:54:09: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 08:54:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:54:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:54:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:54:10: #2 number of paired peaks: 481 WARNING @ Tue, 16 Jun 2020 08:54:10: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Tue, 16 Jun 2020 08:54:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:54:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:54:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:54:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:54:10: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 08:54:10: #2 alternative fragment length(s) may be 4,129 bps INFO @ Tue, 16 Jun 2020 08:54:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.10_model.r INFO @ Tue, 16 Jun 2020 08:54:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:54:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:54:15: 25000000 INFO @ Tue, 16 Jun 2020 08:54:15: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:54:22: 26000000 INFO @ Tue, 16 Jun 2020 08:54:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:54:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:54:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.05_summits.bed INFO @ Tue, 16 Jun 2020 08:54:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (449 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:54:29: 27000000 INFO @ Tue, 16 Jun 2020 08:54:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:54:35: 28000000 INFO @ Tue, 16 Jun 2020 08:54:42: 29000000 INFO @ Tue, 16 Jun 2020 08:54:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:54:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:54:46: #1 total tags in treatment: 12614226 INFO @ Tue, 16 Jun 2020 08:54:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:54:46: #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 08:54:46: #1 tags after filtering in treatment: 11514065 INFO @ Tue, 16 Jun 2020 08:54:46: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 08:54:46: #1 finished! INFO @ Tue, 16 Jun 2020 08:54:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:54:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:54:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:54:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:54:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.10_summits.bed INFO @ Tue, 16 Jun 2020 08:54:46: Done! INFO @ Tue, 16 Jun 2020 08:54:47: #2 number of paired peaks: 481 WARNING @ Tue, 16 Jun 2020 08:54:47: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Tue, 16 Jun 2020 08:54:47: start model_add_line... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (346 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:54:47: start X-correlation... INFO @ Tue, 16 Jun 2020 08:54:47: end of X-cor INFO @ Tue, 16 Jun 2020 08:54:47: #2 finished! INFO @ Tue, 16 Jun 2020 08:54:47: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 08:54:47: #2 alternative fragment length(s) may be 4,129 bps INFO @ Tue, 16 Jun 2020 08:54:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.20_model.r INFO @ Tue, 16 Jun 2020 08:54:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:54:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:55:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:55:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:55:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:55:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978697/SRX2978697.20_summits.bed INFO @ Tue, 16 Jun 2020 08:55:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (225 records, 4 fields): 1 millis CompletedMACS2peakCalling