Job ID = 6367192 SRX = SRX2978696 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:25:02 prefetch.2.10.7: 1) Downloading 'SRR5799203'... 2020-06-15T23:25:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:32:48 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:32:48 prefetch.2.10.7: 1) 'SRR5799203' was downloaded successfully 2020-06-15T23:32:48 prefetch.2.10.7: 'SRR5799203' has 0 unresolved dependencies Read 28765215 spots for SRR5799203/SRR5799203.sra Written 28765215 spots for SRR5799203/SRR5799203.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: 00:17:39 28765215 reads; of these: 28765215 (100.00%) were paired; of these: 11740793 (40.82%) aligned concordantly 0 times 14150008 (49.19%) aligned concordantly exactly 1 time 2874414 (9.99%) aligned concordantly >1 times ---- 11740793 pairs aligned concordantly 0 times; of these: 294704 (2.51%) aligned discordantly 1 time ---- 11446089 pairs aligned 0 times concordantly or discordantly; of these: 22892178 mates make up the pairs; of these: 22040873 (96.28%) aligned 0 times 585516 (2.56%) aligned exactly 1 time 265789 (1.16%) aligned >1 times 61.69% overall alignment rate Time searching: 00:17:39 Overall time: 00:17:39 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] 12624409 / 17305005 = 0.7295 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 09:00:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.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 09:00:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:00:25: 1000000 INFO @ Tue, 16 Jun 2020 09:00:30: 2000000 INFO @ Tue, 16 Jun 2020 09:00:36: 3000000 INFO @ Tue, 16 Jun 2020 09:00:41: 4000000 INFO @ Tue, 16 Jun 2020 09:00:47: 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 @ Tue, 16 Jun 2020 09:00:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.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 09:00:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:00:53: 6000000 INFO @ Tue, 16 Jun 2020 09:00:57: 1000000 INFO @ Tue, 16 Jun 2020 09:00:59: 7000000 INFO @ Tue, 16 Jun 2020 09:01:05: 2000000 INFO @ Tue, 16 Jun 2020 09:01:06: 8000000 INFO @ Tue, 16 Jun 2020 09:01:12: 9000000 INFO @ Tue, 16 Jun 2020 09:01:13: 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 09:01:18: 10000000 INFO @ Tue, 16 Jun 2020 09:01:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.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 09:01:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:20: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:01:20: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:01:20: #1 total tags in treatment: 4593121 INFO @ Tue, 16 Jun 2020 09:01:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:01:20: #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 09:01:20: #1 tags after filtering in treatment: 4121860 INFO @ Tue, 16 Jun 2020 09:01:20: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 09:01:20: #1 finished! INFO @ Tue, 16 Jun 2020 09:01:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:01:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:01:20: #2 number of paired peaks: 1659 INFO @ Tue, 16 Jun 2020 09:01:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:01:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:01:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:01:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:01:21: #2 predicted fragment length is 168 bps INFO @ Tue, 16 Jun 2020 09:01:21: #2 alternative fragment length(s) may be 4,168 bps INFO @ Tue, 16 Jun 2020 09:01:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.05_model.r INFO @ Tue, 16 Jun 2020 09:01:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:01:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:01:21: 4000000 INFO @ Tue, 16 Jun 2020 09:01:27: 1000000 INFO @ Tue, 16 Jun 2020 09:01:28: 5000000 INFO @ Tue, 16 Jun 2020 09:01:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:01:34: 2000000 INFO @ Tue, 16 Jun 2020 09:01:36: 6000000 INFO @ Tue, 16 Jun 2020 09:01:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:01:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:01:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.05_summits.bed INFO @ Tue, 16 Jun 2020 09:01:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1052 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:01:41: 3000000 INFO @ Tue, 16 Jun 2020 09:01:44: 7000000 INFO @ Tue, 16 Jun 2020 09:01:49: 4000000 INFO @ Tue, 16 Jun 2020 09:01:52: 8000000 INFO @ Tue, 16 Jun 2020 09:01:56: 5000000 INFO @ Tue, 16 Jun 2020 09:02:00: 9000000 INFO @ Tue, 16 Jun 2020 09:02:03: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:02:08: 10000000 INFO @ Tue, 16 Jun 2020 09:02:09: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:02:09: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:02:09: #1 total tags in treatment: 4593121 INFO @ Tue, 16 Jun 2020 09:02:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:09: #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 09:02:09: #1 tags after filtering in treatment: 4121860 INFO @ Tue, 16 Jun 2020 09:02:09: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 09:02:09: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:10: #2 number of paired peaks: 1659 INFO @ Tue, 16 Jun 2020 09:02:10: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:10: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:10: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:10: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:10: #2 predicted fragment length is 168 bps INFO @ Tue, 16 Jun 2020 09:02:10: #2 alternative fragment length(s) may be 4,168 bps INFO @ Tue, 16 Jun 2020 09:02:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.10_model.r INFO @ Tue, 16 Jun 2020 09:02:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:11: 7000000 INFO @ Tue, 16 Jun 2020 09:02:18: 8000000 INFO @ Tue, 16 Jun 2020 09:02:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:02:25: 9000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:02:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:02:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:02:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.10_summits.bed INFO @ Tue, 16 Jun 2020 09:02:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (581 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:02:32: 10000000 INFO @ Tue, 16 Jun 2020 09:02:33: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:02:33: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:02:33: #1 total tags in treatment: 4593121 INFO @ Tue, 16 Jun 2020 09:02:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:33: #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 09:02:33: #1 tags after filtering in treatment: 4121860 INFO @ Tue, 16 Jun 2020 09:02:33: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 09:02:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:34: #2 number of paired peaks: 1659 INFO @ Tue, 16 Jun 2020 09:02:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:34: #2 predicted fragment length is 168 bps INFO @ Tue, 16 Jun 2020 09:02:34: #2 alternative fragment length(s) may be 4,168 bps INFO @ Tue, 16 Jun 2020 09:02:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.20_model.r INFO @ Tue, 16 Jun 2020 09:02:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:02:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:02:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:02:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978696/SRX2978696.20_summits.bed INFO @ Tue, 16 Jun 2020 09:02:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (310 records, 4 fields): 1 millis CompletedMACS2peakCalling