Job ID = 6507720 SRX = SRX1353658 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:38:17 prefetch.2.10.7: 1) Downloading 'SRR2722812'... 2020-06-26T13:38:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:41:32 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:41:32 prefetch.2.10.7: 1) 'SRR2722812' was downloaded successfully Read 15153821 spots for SRR2722812/SRR2722812.sra Written 15153821 spots for SRR2722812/SRR2722812.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: 00:15:58 15153821 reads; of these: 15153821 (100.00%) were paired; of these: 815670 (5.38%) aligned concordantly 0 times 12133775 (80.07%) aligned concordantly exactly 1 time 2204376 (14.55%) aligned concordantly >1 times ---- 815670 pairs aligned concordantly 0 times; of these: 468615 (57.45%) aligned discordantly 1 time ---- 347055 pairs aligned 0 times concordantly or discordantly; of these: 694110 mates make up the pairs; of these: 309931 (44.65%) aligned 0 times 203735 (29.35%) aligned exactly 1 time 180444 (26.00%) aligned >1 times 98.98% overall alignment rate Time searching: 00:15:58 Overall time: 00:15:58 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] 218151 / 14688149 = 0.0149 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 @ Fri, 26 Jun 2020 23:09:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.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 @ Fri, 26 Jun 2020 23:09:32: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:09:32: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:09:37: 1000000 INFO @ Fri, 26 Jun 2020 23:09:43: 2000000 INFO @ Fri, 26 Jun 2020 23:09:48: 3000000 INFO @ Fri, 26 Jun 2020 23:09:54: 4000000 INFO @ Fri, 26 Jun 2020 23:09:59: 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 @ Fri, 26 Jun 2020 23:10:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.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 @ Fri, 26 Jun 2020 23:10:02: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:10:02: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:10:05: 6000000 INFO @ Fri, 26 Jun 2020 23:10:09: 1000000 INFO @ Fri, 26 Jun 2020 23:10:11: 7000000 INFO @ Fri, 26 Jun 2020 23:10:15: 2000000 INFO @ Fri, 26 Jun 2020 23:10:17: 8000000 INFO @ Fri, 26 Jun 2020 23:10:22: 3000000 INFO @ Fri, 26 Jun 2020 23:10:23: 9000000 INFO @ Fri, 26 Jun 2020 23:10:29: 10000000 INFO @ Fri, 26 Jun 2020 23:10:30: 4000000 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 @ Fri, 26 Jun 2020 23:10:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.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 @ Fri, 26 Jun 2020 23:10:32: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:10:32: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:10:35: 11000000 INFO @ Fri, 26 Jun 2020 23:10:37: 5000000 INFO @ Fri, 26 Jun 2020 23:10:38: 1000000 INFO @ Fri, 26 Jun 2020 23:10:41: 12000000 INFO @ Fri, 26 Jun 2020 23:10:44: 2000000 INFO @ Fri, 26 Jun 2020 23:10:44: 6000000 INFO @ Fri, 26 Jun 2020 23:10:46: 13000000 INFO @ Fri, 26 Jun 2020 23:10:50: 3000000 INFO @ Fri, 26 Jun 2020 23:10:50: 7000000 INFO @ Fri, 26 Jun 2020 23:10:52: 14000000 INFO @ Fri, 26 Jun 2020 23:10:55: 4000000 INFO @ Fri, 26 Jun 2020 23:10:57: 8000000 INFO @ Fri, 26 Jun 2020 23:10:58: 15000000 INFO @ Fri, 26 Jun 2020 23:11:01: 5000000 INFO @ Fri, 26 Jun 2020 23:11:03: 16000000 INFO @ Fri, 26 Jun 2020 23:11:04: 9000000 INFO @ Fri, 26 Jun 2020 23:11:07: 6000000 INFO @ Fri, 26 Jun 2020 23:11:09: 17000000 INFO @ Fri, 26 Jun 2020 23:11:10: 10000000 INFO @ Fri, 26 Jun 2020 23:11:13: 7000000 INFO @ Fri, 26 Jun 2020 23:11:14: 18000000 INFO @ Fri, 26 Jun 2020 23:11:17: 11000000 INFO @ Fri, 26 Jun 2020 23:11:18: 8000000 INFO @ Fri, 26 Jun 2020 23:11:20: 19000000 INFO @ Fri, 26 Jun 2020 23:11:23: 12000000 INFO @ Fri, 26 Jun 2020 23:11:24: 9000000 INFO @ Fri, 26 Jun 2020 23:11:26: 20000000 INFO @ Fri, 26 Jun 2020 23:11:29: 13000000 INFO @ Fri, 26 Jun 2020 23:11:30: 10000000 INFO @ Fri, 26 Jun 2020 23:11:32: 21000000 INFO @ Fri, 26 Jun 2020 23:11:35: 11000000 INFO @ Fri, 26 Jun 2020 23:11:35: 14000000 INFO @ Fri, 26 Jun 2020 23:11:37: 22000000 INFO @ Fri, 26 Jun 2020 23:11:41: 12000000 INFO @ Fri, 26 Jun 2020 23:11:41: 15000000 INFO @ Fri, 26 Jun 2020 23:11:43: 23000000 INFO @ Fri, 26 Jun 2020 23:11:46: 13000000 INFO @ Fri, 26 Jun 2020 23:11:47: 16000000 INFO @ Fri, 26 Jun 2020 23:11:48: 24000000 INFO @ Fri, 26 Jun 2020 23:11:52: 14000000 INFO @ Fri, 26 Jun 2020 23:11:53: 17000000 INFO @ Fri, 26 Jun 2020 23:11:54: 25000000 INFO @ Fri, 26 Jun 2020 23:11:58: 15000000 INFO @ Fri, 26 Jun 2020 23:11:59: 18000000 INFO @ Fri, 26 Jun 2020 23:11:59: 26000000 INFO @ Fri, 26 Jun 2020 23:12:03: 16000000 INFO @ Fri, 26 Jun 2020 23:12:05: 27000000 INFO @ Fri, 26 Jun 2020 23:12:05: 19000000 INFO @ Fri, 26 Jun 2020 23:12:09: 17000000 INFO @ Fri, 26 Jun 2020 23:12:11: 28000000 INFO @ Fri, 26 Jun 2020 23:12:11: 20000000 INFO @ Fri, 26 Jun 2020 23:12:14: 18000000 INFO @ Fri, 26 Jun 2020 23:12:16: 29000000 INFO @ Fri, 26 Jun 2020 23:12:17: 21000000 INFO @ Fri, 26 Jun 2020 23:12:19: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:12:19: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:12:19: #1 total tags in treatment: 14121639 INFO @ Fri, 26 Jun 2020 23:12:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:12:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:12:20: #1 tags after filtering in treatment: 12922936 INFO @ Fri, 26 Jun 2020 23:12:20: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 23:12:20: #1 finished! INFO @ Fri, 26 Jun 2020 23:12:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:12:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:12:20: 19000000 INFO @ Fri, 26 Jun 2020 23:12:20: #2 number of paired peaks: 328 WARNING @ Fri, 26 Jun 2020 23:12:20: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Fri, 26 Jun 2020 23:12:20: start model_add_line... INFO @ Fri, 26 Jun 2020 23:12:21: start X-correlation... INFO @ Fri, 26 Jun 2020 23:12:21: end of X-cor INFO @ Fri, 26 Jun 2020 23:12:21: #2 finished! INFO @ Fri, 26 Jun 2020 23:12:21: #2 predicted fragment length is 132 bps INFO @ Fri, 26 Jun 2020 23:12:21: #2 alternative fragment length(s) may be 4,132 bps INFO @ Fri, 26 Jun 2020 23:12:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.05_model.r INFO @ Fri, 26 Jun 2020 23:12:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:12:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:12:23: 22000000 INFO @ Fri, 26 Jun 2020 23:12:25: 20000000 INFO @ Fri, 26 Jun 2020 23:12:30: 23000000 INFO @ Fri, 26 Jun 2020 23:12:31: 21000000 INFO @ Fri, 26 Jun 2020 23:12:36: 24000000 INFO @ Fri, 26 Jun 2020 23:12:36: 22000000 INFO @ Fri, 26 Jun 2020 23:12:42: 23000000 INFO @ Fri, 26 Jun 2020 23:12:42: 25000000 INFO @ Fri, 26 Jun 2020 23:12:47: 24000000 INFO @ Fri, 26 Jun 2020 23:12:48: 26000000 INFO @ Fri, 26 Jun 2020 23:12:49: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:12:52: 25000000 INFO @ Fri, 26 Jun 2020 23:12:54: 27000000 INFO @ Fri, 26 Jun 2020 23:12:58: 26000000 INFO @ Fri, 26 Jun 2020 23:13:00: 28000000 INFO @ Fri, 26 Jun 2020 23:13:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:13:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:13:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.05_summits.bed INFO @ Fri, 26 Jun 2020 23:13:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (704 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:13:03: 27000000 INFO @ Fri, 26 Jun 2020 23:13:06: 29000000 INFO @ Fri, 26 Jun 2020 23:13:08: 28000000 INFO @ Fri, 26 Jun 2020 23:13:10: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:13:10: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:13:10: #1 total tags in treatment: 14121639 INFO @ Fri, 26 Jun 2020 23:13:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:13:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:13:10: #1 tags after filtering in treatment: 12922936 INFO @ Fri, 26 Jun 2020 23:13:10: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 23:13:10: #1 finished! INFO @ Fri, 26 Jun 2020 23:13:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:13:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:13:11: #2 number of paired peaks: 328 WARNING @ Fri, 26 Jun 2020 23:13:11: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Fri, 26 Jun 2020 23:13:11: start model_add_line... INFO @ Fri, 26 Jun 2020 23:13:11: start X-correlation... INFO @ Fri, 26 Jun 2020 23:13:11: end of X-cor INFO @ Fri, 26 Jun 2020 23:13:11: #2 finished! INFO @ Fri, 26 Jun 2020 23:13:11: #2 predicted fragment length is 132 bps INFO @ Fri, 26 Jun 2020 23:13:11: #2 alternative fragment length(s) may be 4,132 bps INFO @ Fri, 26 Jun 2020 23:13:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.10_model.r INFO @ Fri, 26 Jun 2020 23:13:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:13:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:13:14: 29000000 INFO @ Fri, 26 Jun 2020 23:13:16: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:13:16: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:13:16: #1 total tags in treatment: 14121639 INFO @ Fri, 26 Jun 2020 23:13:16: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:13:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:13:17: #1 tags after filtering in treatment: 12922936 INFO @ Fri, 26 Jun 2020 23:13:17: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 23:13:17: #1 finished! INFO @ Fri, 26 Jun 2020 23:13:17: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:13:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:13:18: #2 number of paired peaks: 328 WARNING @ Fri, 26 Jun 2020 23:13:18: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Fri, 26 Jun 2020 23:13:18: start model_add_line... INFO @ Fri, 26 Jun 2020 23:13:18: start X-correlation... INFO @ Fri, 26 Jun 2020 23:13:18: end of X-cor INFO @ Fri, 26 Jun 2020 23:13:18: #2 finished! INFO @ Fri, 26 Jun 2020 23:13:18: #2 predicted fragment length is 132 bps INFO @ Fri, 26 Jun 2020 23:13:18: #2 alternative fragment length(s) may be 4,132 bps INFO @ Fri, 26 Jun 2020 23:13:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.20_model.r INFO @ Fri, 26 Jun 2020 23:13:18: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:13:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:13:41: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:13:47: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:13:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:13:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:13:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.10_summits.bed INFO @ Fri, 26 Jun 2020 23:13:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (322 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:14:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:14:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:14:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353658/SRX1353658.20_summits.bed INFO @ Fri, 26 Jun 2020 23:14:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (213 records, 4 fields): 2 millis CompletedMACS2peakCalling