Job ID = 6497333 SRX = SRX1353658 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:21:00 prefetch.2.10.7: 1) Downloading 'SRR2722812'... 2020-06-25T22:21:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:23:45 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:23:45 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:41 15153821 reads; of these: 15153821 (100.00%) were paired; of these: 815772 (5.38%) aligned concordantly 0 times 12133778 (80.07%) aligned concordantly exactly 1 time 2204271 (14.55%) aligned concordantly >1 times ---- 815772 pairs aligned concordantly 0 times; of these: 468606 (57.44%) aligned discordantly 1 time ---- 347166 pairs aligned 0 times concordantly or discordantly; of these: 694332 mates make up the pairs; of these: 310119 (44.66%) aligned 0 times 203759 (29.35%) aligned exactly 1 time 180454 (25.99%) aligned >1 times 98.98% overall alignment rate Time searching: 00:13:42 Overall time: 00:13:42 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] 218142 / 14688033 = 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 07:49:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353658/SRX1353658.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353658/SRX1353658.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353658/SRX1353658.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:49:02: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:49:02: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:49:07: 1000000 INFO @ Fri, 26 Jun 2020 07:49:12: 2000000 INFO @ Fri, 26 Jun 2020 07:49:17: 3000000 INFO @ Fri, 26 Jun 2020 07:49:22: 4000000 INFO @ Fri, 26 Jun 2020 07:49:27: 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 07:49:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353658/SRX1353658.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353658/SRX1353658.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353658/SRX1353658.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:49:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:49:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:49:32: 6000000 INFO @ Fri, 26 Jun 2020 07:49:37: 7000000 INFO @ Fri, 26 Jun 2020 07:49:38: 1000000 INFO @ Fri, 26 Jun 2020 07:49:42: 8000000 INFO @ Fri, 26 Jun 2020 07:49:44: 2000000 INFO @ Fri, 26 Jun 2020 07:49:48: 9000000 INFO @ Fri, 26 Jun 2020 07:49:50: 3000000 INFO @ Fri, 26 Jun 2020 07:49:53: 10000000 INFO @ Fri, 26 Jun 2020 07:49:56: 4000000 INFO @ Fri, 26 Jun 2020 07:49:59: 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 @ Fri, 26 Jun 2020 07:50:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353658/SRX1353658.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353658/SRX1353658.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353658/SRX1353658.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:50:01: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:50:01: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:50:02: 5000000 INFO @ Fri, 26 Jun 2020 07:50:04: 12000000 INFO @ Fri, 26 Jun 2020 07:50:08: 1000000 INFO @ Fri, 26 Jun 2020 07:50:08: 6000000 INFO @ Fri, 26 Jun 2020 07:50:09: 13000000 INFO @ Fri, 26 Jun 2020 07:50:14: 2000000 INFO @ Fri, 26 Jun 2020 07:50:15: 7000000 INFO @ Fri, 26 Jun 2020 07:50:15: 14000000 INFO @ Fri, 26 Jun 2020 07:50:20: 3000000 INFO @ Fri, 26 Jun 2020 07:50:20: 15000000 INFO @ Fri, 26 Jun 2020 07:50:21: 8000000 INFO @ Fri, 26 Jun 2020 07:50:26: 16000000 INFO @ Fri, 26 Jun 2020 07:50:26: 4000000 INFO @ Fri, 26 Jun 2020 07:50:27: 9000000 INFO @ Fri, 26 Jun 2020 07:50:31: 17000000 INFO @ Fri, 26 Jun 2020 07:50:32: 5000000 INFO @ Fri, 26 Jun 2020 07:50:34: 10000000 INFO @ Fri, 26 Jun 2020 07:50:37: 18000000 INFO @ Fri, 26 Jun 2020 07:50:38: 6000000 INFO @ Fri, 26 Jun 2020 07:50:40: 11000000 INFO @ Fri, 26 Jun 2020 07:50:42: 19000000 INFO @ Fri, 26 Jun 2020 07:50:45: 7000000 INFO @ Fri, 26 Jun 2020 07:50:46: 12000000 INFO @ Fri, 26 Jun 2020 07:50:47: 20000000 INFO @ Fri, 26 Jun 2020 07:50:51: 8000000 INFO @ Fri, 26 Jun 2020 07:50:53: 13000000 INFO @ Fri, 26 Jun 2020 07:50:53: 21000000 INFO @ Fri, 26 Jun 2020 07:50:57: 9000000 INFO @ Fri, 26 Jun 2020 07:50:58: 22000000 INFO @ Fri, 26 Jun 2020 07:50:59: 14000000 INFO @ Fri, 26 Jun 2020 07:51:04: 23000000 INFO @ Fri, 26 Jun 2020 07:51:04: 10000000 INFO @ Fri, 26 Jun 2020 07:51:05: 15000000 INFO @ Fri, 26 Jun 2020 07:51:09: 24000000 INFO @ Fri, 26 Jun 2020 07:51:10: 11000000 INFO @ Fri, 26 Jun 2020 07:51:11: 16000000 INFO @ Fri, 26 Jun 2020 07:51:14: 25000000 INFO @ Fri, 26 Jun 2020 07:51:16: 12000000 INFO @ Fri, 26 Jun 2020 07:51:17: 17000000 INFO @ Fri, 26 Jun 2020 07:51:20: 26000000 INFO @ Fri, 26 Jun 2020 07:51:23: 13000000 INFO @ Fri, 26 Jun 2020 07:51:23: 18000000 INFO @ Fri, 26 Jun 2020 07:51:25: 27000000 INFO @ Fri, 26 Jun 2020 07:51:29: 14000000 INFO @ Fri, 26 Jun 2020 07:51:30: 19000000 INFO @ Fri, 26 Jun 2020 07:51:30: 28000000 INFO @ Fri, 26 Jun 2020 07:51:35: 15000000 INFO @ Fri, 26 Jun 2020 07:51:36: 20000000 INFO @ Fri, 26 Jun 2020 07:51:36: 29000000 INFO @ Fri, 26 Jun 2020 07:51:39: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:51:39: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:51:39: #1 total tags in treatment: 14121546 INFO @ Fri, 26 Jun 2020 07:51:39: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:51:39: #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 07:51:39: #1 tags after filtering in treatment: 12922856 INFO @ Fri, 26 Jun 2020 07:51:39: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 07:51:39: #1 finished! INFO @ Fri, 26 Jun 2020 07:51:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:51:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:51:40: #2 number of paired peaks: 327 WARNING @ Fri, 26 Jun 2020 07:51:40: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Fri, 26 Jun 2020 07:51:40: start model_add_line... INFO @ Fri, 26 Jun 2020 07:51:40: start X-correlation... INFO @ Fri, 26 Jun 2020 07:51:40: end of X-cor INFO @ Fri, 26 Jun 2020 07:51:40: #2 finished! INFO @ Fri, 26 Jun 2020 07:51:40: #2 predicted fragment length is 132 bps INFO @ Fri, 26 Jun 2020 07:51:40: #2 alternative fragment length(s) may be 4,132 bps INFO @ Fri, 26 Jun 2020 07:51:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353658/SRX1353658.05_model.r INFO @ Fri, 26 Jun 2020 07:51:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:51:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:51:41: 16000000 INFO @ Fri, 26 Jun 2020 07:51:42: 21000000 INFO @ Fri, 26 Jun 2020 07:51:47: 17000000 INFO @ Fri, 26 Jun 2020 07:51:48: 22000000 INFO @ Fri, 26 Jun 2020 07:51:53: 18000000 INFO @ Fri, 26 Jun 2020 07:51:54: 23000000 INFO @ Fri, 26 Jun 2020 07:51:59: 19000000 INFO @ Fri, 26 Jun 2020 07:52:00: 24000000 INFO @ Fri, 26 Jun 2020 07:52:06: 20000000 INFO @ Fri, 26 Jun 2020 07:52:06: 25000000 INFO @ Fri, 26 Jun 2020 07:52:09: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:52:12: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:52:12: 26000000 INFO @ Fri, 26 Jun 2020 07:52:17: 22000000 INFO @ Fri, 26 Jun 2020 07:52:18: 27000000 INFO @ Fri, 26 Jun 2020 07:52:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353658/SRX1353658.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:52:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353658/SRX1353658.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:52:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353658/SRX1353658.05_summits.bed INFO @ Fri, 26 Jun 2020 07:52:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (704 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:52:23: 23000000 INFO @ Fri, 26 Jun 2020 07:52:24: 28000000 INFO @ Fri, 26 Jun 2020 07:52:29: 24000000 INFO @ Fri, 26 Jun 2020 07:52:30: 29000000 INFO @ Fri, 26 Jun 2020 07:52:34: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:52:34: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:52:34: #1 total tags in treatment: 14121546 INFO @ Fri, 26 Jun 2020 07:52:34: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:52:34: #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 07:52:34: #1 tags after filtering in treatment: 12922856 INFO @ Fri, 26 Jun 2020 07:52:34: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 07:52:34: #1 finished! INFO @ Fri, 26 Jun 2020 07:52:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:52:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:52:35: #2 number of paired peaks: 327 WARNING @ Fri, 26 Jun 2020 07:52:35: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Fri, 26 Jun 2020 07:52:35: start model_add_line... INFO @ Fri, 26 Jun 2020 07:52:35: start X-correlation... INFO @ Fri, 26 Jun 2020 07:52:35: end of X-cor INFO @ Fri, 26 Jun 2020 07:52:35: #2 finished! INFO @ Fri, 26 Jun 2020 07:52:35: #2 predicted fragment length is 132 bps INFO @ Fri, 26 Jun 2020 07:52:35: #2 alternative fragment length(s) may be 4,132 bps INFO @ Fri, 26 Jun 2020 07:52:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353658/SRX1353658.10_model.r INFO @ Fri, 26 Jun 2020 07:52:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:52:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:52:35: 25000000 INFO @ Fri, 26 Jun 2020 07:52:41: 26000000 INFO @ Fri, 26 Jun 2020 07:52:47: 27000000 INFO @ Fri, 26 Jun 2020 07:52:53: 28000000 INFO @ Fri, 26 Jun 2020 07:52:59: 29000000 INFO @ Fri, 26 Jun 2020 07:53:03: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:53:03: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:53:03: #1 total tags in treatment: 14121546 INFO @ Fri, 26 Jun 2020 07:53:03: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:53:03: #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 07:53:03: #1 tags after filtering in treatment: 12922856 INFO @ Fri, 26 Jun 2020 07:53:03: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 07:53:03: #1 finished! INFO @ Fri, 26 Jun 2020 07:53:03: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:53:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:53:04: #2 number of paired peaks: 327 WARNING @ Fri, 26 Jun 2020 07:53:04: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Fri, 26 Jun 2020 07:53:04: start model_add_line... INFO @ Fri, 26 Jun 2020 07:53:04: start X-correlation... INFO @ Fri, 26 Jun 2020 07:53:04: end of X-cor INFO @ Fri, 26 Jun 2020 07:53:04: #2 finished! INFO @ Fri, 26 Jun 2020 07:53:04: #2 predicted fragment length is 132 bps INFO @ Fri, 26 Jun 2020 07:53:04: #2 alternative fragment length(s) may be 4,132 bps INFO @ Fri, 26 Jun 2020 07:53:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353658/SRX1353658.20_model.r INFO @ Fri, 26 Jun 2020 07:53:04: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:53:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:53:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:53:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353658/SRX1353658.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:53:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353658/SRX1353658.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:53:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353658/SRX1353658.10_summits.bed INFO @ Fri, 26 Jun 2020 07:53:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (322 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:53:33: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:53:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353658/SRX1353658.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:53:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353658/SRX1353658.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:53:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353658/SRX1353658.20_summits.bed INFO @ Fri, 26 Jun 2020 07:53:46: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (213 records, 4 fields): 1 millis CompletedMACS2peakCalling