Job ID = 6366586 SRX = SRX2035133 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T22:43:22 prefetch.2.10.7: 1) Downloading 'SRR4044257'... 2020-06-15T22:43:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:46:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:46:46 prefetch.2.10.7: 1) 'SRR4044257' was downloaded successfully Read 7076912 spots for SRR4044257/SRR4044257.sra Written 7076912 spots for SRR4044257/SRR4044257.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: 00:08:15 7076912 reads; of these: 7076912 (100.00%) were paired; of these: 1059126 (14.97%) aligned concordantly 0 times 5482416 (77.47%) aligned concordantly exactly 1 time 535370 (7.57%) aligned concordantly >1 times ---- 1059126 pairs aligned concordantly 0 times; of these: 485278 (45.82%) aligned discordantly 1 time ---- 573848 pairs aligned 0 times concordantly or discordantly; of these: 1147696 mates make up the pairs; of these: 980048 (85.39%) aligned 0 times 76784 (6.69%) aligned exactly 1 time 90864 (7.92%) aligned >1 times 93.08% overall alignment rate Time searching: 00:08:15 Overall time: 00:08:15 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 8 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] 208522 / 6490639 = 0.0321 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 08:01:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.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 08:01:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:54: 1000000 INFO @ Tue, 16 Jun 2020 08:02:00: 2000000 INFO @ Tue, 16 Jun 2020 08:02:07: 3000000 INFO @ Tue, 16 Jun 2020 08:02:13: 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 08:02:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.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 08:02:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:19: 5000000 INFO @ Tue, 16 Jun 2020 08:02:27: 1000000 INFO @ Tue, 16 Jun 2020 08:02:27: 6000000 INFO @ Tue, 16 Jun 2020 08:02:34: 7000000 INFO @ Tue, 16 Jun 2020 08:02:35: 2000000 INFO @ Tue, 16 Jun 2020 08:02:41: 8000000 INFO @ Tue, 16 Jun 2020 08:02:44: 3000000 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 08:02:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.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 08:02:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:49: 9000000 INFO @ Tue, 16 Jun 2020 08:02:53: 4000000 INFO @ Tue, 16 Jun 2020 08:02:56: 10000000 INFO @ Tue, 16 Jun 2020 08:02:57: 1000000 INFO @ Tue, 16 Jun 2020 08:03:01: 5000000 INFO @ Tue, 16 Jun 2020 08:03:04: 11000000 INFO @ Tue, 16 Jun 2020 08:03:06: 2000000 INFO @ Tue, 16 Jun 2020 08:03:10: 6000000 INFO @ Tue, 16 Jun 2020 08:03:12: 12000000 INFO @ Tue, 16 Jun 2020 08:03:14: 3000000 INFO @ Tue, 16 Jun 2020 08:03:17: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:03:17: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:03:17: #1 total tags in treatment: 5813944 INFO @ Tue, 16 Jun 2020 08:03:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:17: #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 08:03:17: #1 tags after filtering in treatment: 5187054 INFO @ Tue, 16 Jun 2020 08:03:17: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 16 Jun 2020 08:03:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:18: #2 number of paired peaks: 4873 INFO @ Tue, 16 Jun 2020 08:03:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:18: #2 predicted fragment length is 269 bps INFO @ Tue, 16 Jun 2020 08:03:18: #2 alternative fragment length(s) may be 269 bps INFO @ Tue, 16 Jun 2020 08:03:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.05_model.r INFO @ Tue, 16 Jun 2020 08:03:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:03:19: 7000000 INFO @ Tue, 16 Jun 2020 08:03:23: 4000000 INFO @ Tue, 16 Jun 2020 08:03:27: 8000000 INFO @ Tue, 16 Jun 2020 08:03:32: 5000000 INFO @ Tue, 16 Jun 2020 08:03:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:36: 9000000 INFO @ Tue, 16 Jun 2020 08:03:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.05_summits.bed INFO @ Tue, 16 Jun 2020 08:03:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4390 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:03:40: 6000000 INFO @ Tue, 16 Jun 2020 08:03:45: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:03:49: 7000000 INFO @ Tue, 16 Jun 2020 08:03:54: 11000000 INFO @ Tue, 16 Jun 2020 08:03:58: 8000000 INFO @ Tue, 16 Jun 2020 08:04:02: 12000000 INFO @ Tue, 16 Jun 2020 08:04:07: 9000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:04:09: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:04:09: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:04:09: #1 total tags in treatment: 5813944 INFO @ Tue, 16 Jun 2020 08:04:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:09: #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 08:04:09: #1 tags after filtering in treatment: 5187054 INFO @ Tue, 16 Jun 2020 08:04:09: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 16 Jun 2020 08:04:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:10: #2 number of paired peaks: 4873 INFO @ Tue, 16 Jun 2020 08:04:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:10: #2 predicted fragment length is 269 bps INFO @ Tue, 16 Jun 2020 08:04:10: #2 alternative fragment length(s) may be 269 bps INFO @ Tue, 16 Jun 2020 08:04:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.10_model.r INFO @ Tue, 16 Jun 2020 08:04:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:15: 10000000 INFO @ Tue, 16 Jun 2020 08:04:23: 11000000 INFO @ Tue, 16 Jun 2020 08:04:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.10_summits.bed INFO @ Tue, 16 Jun 2020 08:04:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3483 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:04:31: 12000000 INFO @ Tue, 16 Jun 2020 08:04:37: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:04:37: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:04:37: #1 total tags in treatment: 5813944 INFO @ Tue, 16 Jun 2020 08:04:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:37: #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 08:04:38: #1 tags after filtering in treatment: 5187054 INFO @ Tue, 16 Jun 2020 08:04:38: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 16 Jun 2020 08:04:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:38: #2 number of paired peaks: 4873 INFO @ Tue, 16 Jun 2020 08:04:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:38: #2 predicted fragment length is 269 bps INFO @ Tue, 16 Jun 2020 08:04:38: #2 alternative fragment length(s) may be 269 bps INFO @ Tue, 16 Jun 2020 08:04:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.20_model.r INFO @ Tue, 16 Jun 2020 08:04:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2035133/SRX2035133.20_summits.bed INFO @ Tue, 16 Jun 2020 08:04:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (2699 records, 4 fields): 4 millis CompletedMACS2peakCalling