Job ID = 6367197 SRX = SRX2978701 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:43:14 prefetch.2.10.7: 1) Downloading 'SRR5799208'... 2020-06-15T23:43:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:48:15 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:48:15 prefetch.2.10.7: 1) 'SRR5799208' was downloaded successfully 2020-06-15T23:48:15 prefetch.2.10.7: 'SRR5799208' has 0 unresolved dependencies Read 17969658 spots for SRR5799208/SRR5799208.sra Written 17969658 spots for SRR5799208/SRR5799208.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: 00:37:41 17969658 reads; of these: 17969658 (100.00%) were paired; of these: 849840 (4.73%) aligned concordantly 0 times 9227131 (51.35%) aligned concordantly exactly 1 time 7892687 (43.92%) aligned concordantly >1 times ---- 849840 pairs aligned concordantly 0 times; of these: 98475 (11.59%) aligned discordantly 1 time ---- 751365 pairs aligned 0 times concordantly or discordantly; of these: 1502730 mates make up the pairs; of these: 1206984 (80.32%) aligned 0 times 117475 (7.82%) aligned exactly 1 time 178271 (11.86%) aligned >1 times 96.64% overall alignment rate Time searching: 00:37:41 Overall time: 00:37:41 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] 6216915 / 17194991 = 0.3616 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 09:37:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.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 09:37:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:17: 1000000 INFO @ Tue, 16 Jun 2020 09:37:23: 2000000 INFO @ Tue, 16 Jun 2020 09:37:28: 3000000 INFO @ Tue, 16 Jun 2020 09:37:33: 4000000 INFO @ Tue, 16 Jun 2020 09:37:38: 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 09:37:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.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 09:37:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:43: 6000000 INFO @ Tue, 16 Jun 2020 09:37:48: 1000000 INFO @ Tue, 16 Jun 2020 09:37:49: 7000000 INFO @ Tue, 16 Jun 2020 09:37:54: 2000000 INFO @ Tue, 16 Jun 2020 09:37:55: 8000000 INFO @ Tue, 16 Jun 2020 09:38:00: 3000000 INFO @ Tue, 16 Jun 2020 09:38:01: 9000000 INFO @ Tue, 16 Jun 2020 09:38:06: 4000000 INFO @ Tue, 16 Jun 2020 09:38:06: 10000000 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 09:38:12: 5000000 INFO @ Tue, 16 Jun 2020 09:38:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.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 09:38:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:12: 11000000 INFO @ Tue, 16 Jun 2020 09:38:18: 6000000 INFO @ Tue, 16 Jun 2020 09:38:19: 1000000 INFO @ Tue, 16 Jun 2020 09:38:19: 12000000 INFO @ Tue, 16 Jun 2020 09:38:25: 7000000 INFO @ Tue, 16 Jun 2020 09:38:25: 2000000 INFO @ Tue, 16 Jun 2020 09:38:26: 13000000 INFO @ Tue, 16 Jun 2020 09:38:31: 8000000 INFO @ Tue, 16 Jun 2020 09:38:32: 3000000 INFO @ Tue, 16 Jun 2020 09:38:32: 14000000 INFO @ Tue, 16 Jun 2020 09:38:38: 9000000 INFO @ Tue, 16 Jun 2020 09:38:38: 4000000 INFO @ Tue, 16 Jun 2020 09:38:39: 15000000 INFO @ Tue, 16 Jun 2020 09:38:44: 10000000 INFO @ Tue, 16 Jun 2020 09:38:45: 5000000 INFO @ Tue, 16 Jun 2020 09:38:45: 16000000 INFO @ Tue, 16 Jun 2020 09:38:51: 11000000 INFO @ Tue, 16 Jun 2020 09:38:51: 6000000 INFO @ Tue, 16 Jun 2020 09:38:52: 17000000 INFO @ Tue, 16 Jun 2020 09:38:58: 12000000 INFO @ Tue, 16 Jun 2020 09:38:58: 7000000 INFO @ Tue, 16 Jun 2020 09:38:58: 18000000 INFO @ Tue, 16 Jun 2020 09:39:04: 8000000 INFO @ Tue, 16 Jun 2020 09:39:04: 13000000 INFO @ Tue, 16 Jun 2020 09:39:05: 19000000 INFO @ Tue, 16 Jun 2020 09:39:11: 9000000 INFO @ Tue, 16 Jun 2020 09:39:11: 14000000 INFO @ Tue, 16 Jun 2020 09:39:11: 20000000 INFO @ Tue, 16 Jun 2020 09:39:17: 10000000 INFO @ Tue, 16 Jun 2020 09:39:18: 15000000 INFO @ Tue, 16 Jun 2020 09:39:18: 21000000 INFO @ Tue, 16 Jun 2020 09:39:24: 11000000 INFO @ Tue, 16 Jun 2020 09:39:24: 22000000 INFO @ Tue, 16 Jun 2020 09:39:24: 16000000 INFO @ Tue, 16 Jun 2020 09:39:26: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:39:26: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:39:26: #1 total tags in treatment: 10915752 INFO @ Tue, 16 Jun 2020 09:39:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:26: #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 09:39:26: #1 tags after filtering in treatment: 6705154 INFO @ Tue, 16 Jun 2020 09:39:26: #1 Redundant rate of treatment: 0.39 INFO @ Tue, 16 Jun 2020 09:39:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:27: #2 number of paired peaks: 5180 INFO @ Tue, 16 Jun 2020 09:39:27: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:27: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:27: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:27: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:27: #2 predicted fragment length is 185 bps INFO @ Tue, 16 Jun 2020 09:39:27: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 16 Jun 2020 09:39:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.05_model.r INFO @ Tue, 16 Jun 2020 09:39:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:39:30: 12000000 INFO @ Tue, 16 Jun 2020 09:39:30: 17000000 INFO @ Tue, 16 Jun 2020 09:39:36: 13000000 INFO @ Tue, 16 Jun 2020 09:39:36: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:39:42: 14000000 INFO @ Tue, 16 Jun 2020 09:39:42: 19000000 INFO @ Tue, 16 Jun 2020 09:39:48: 15000000 INFO @ Tue, 16 Jun 2020 09:39:48: 20000000 INFO @ Tue, 16 Jun 2020 09:39:54: 16000000 INFO @ Tue, 16 Jun 2020 09:39:54: 21000000 INFO @ Tue, 16 Jun 2020 09:39:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:00: 17000000 INFO @ Tue, 16 Jun 2020 09:40:00: 22000000 INFO @ Tue, 16 Jun 2020 09:40:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:02: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:40:02: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:40:02: #1 total tags in treatment: 10915752 INFO @ Tue, 16 Jun 2020 09:40:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:02: #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 09:40:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.05_summits.bed INFO @ Tue, 16 Jun 2020 09:40:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6192 records, 4 fields): 9 millis INFO @ Tue, 16 Jun 2020 09:40:02: #1 tags after filtering in treatment: 6705154 INFO @ Tue, 16 Jun 2020 09:40:02: #1 Redundant rate of treatment: 0.39 INFO @ Tue, 16 Jun 2020 09:40:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:02: #2 looking for paired plus/minus strand peaks... CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:40:03: #2 number of paired peaks: 5180 INFO @ Tue, 16 Jun 2020 09:40:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:03: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:03: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:03: #2 predicted fragment length is 185 bps INFO @ Tue, 16 Jun 2020 09:40:03: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 16 Jun 2020 09:40:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.10_model.r INFO @ Tue, 16 Jun 2020 09:40:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:05: 18000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:40:10: 19000000 INFO @ Tue, 16 Jun 2020 09:40:15: 20000000 INFO @ Tue, 16 Jun 2020 09:40:21: 21000000 INFO @ Tue, 16 Jun 2020 09:40:26: 22000000 INFO @ Tue, 16 Jun 2020 09:40:28: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:40:28: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:40:28: #1 total tags in treatment: 10915752 INFO @ Tue, 16 Jun 2020 09:40:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:28: #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 09:40:29: #1 tags after filtering in treatment: 6705154 INFO @ Tue, 16 Jun 2020 09:40:29: #1 Redundant rate of treatment: 0.39 INFO @ Tue, 16 Jun 2020 09:40:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:29: #2 number of paired peaks: 5180 INFO @ Tue, 16 Jun 2020 09:40:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:30: #2 predicted fragment length is 185 bps INFO @ Tue, 16 Jun 2020 09:40:30: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 16 Jun 2020 09:40:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.20_model.r INFO @ Tue, 16 Jun 2020 09:40:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.10_summits.bed INFO @ Tue, 16 Jun 2020 09:40:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4140 records, 4 fields): 61 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:40:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978701/SRX2978701.20_summits.bed INFO @ Tue, 16 Jun 2020 09:41:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2357 records, 4 fields): 5 millis CompletedMACS2peakCalling