Job ID = 6367198 SRX = SRX2978702 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:16:31 prefetch.2.10.7: 1) Downloading 'SRR5799209'... 2020-06-15T23:16:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:19:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:19:00 prefetch.2.10.7: 1) 'SRR5799209' was downloaded successfully 2020-06-15T23:19:00 prefetch.2.10.7: 'SRR5799209' has 0 unresolved dependencies Read 17929000 spots for SRR5799209/SRR5799209.sra Written 17929000 spots for SRR5799209/SRR5799209.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: 00:27:56 17929000 reads; of these: 17929000 (100.00%) were paired; of these: 854102 (4.76%) aligned concordantly 0 times 9193297 (51.28%) aligned concordantly exactly 1 time 7881601 (43.96%) aligned concordantly >1 times ---- 854102 pairs aligned concordantly 0 times; of these: 97325 (11.40%) aligned discordantly 1 time ---- 756777 pairs aligned 0 times concordantly or discordantly; of these: 1513554 mates make up the pairs; of these: 1214687 (80.25%) aligned 0 times 118712 (7.84%) aligned exactly 1 time 180155 (11.90%) aligned >1 times 96.61% overall alignment rate Time searching: 00:27:56 Overall time: 00:27:56 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] 6186949 / 17149106 = 0.3608 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 08:56:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.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 08:56:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:33: 1000000 INFO @ Tue, 16 Jun 2020 08:56:38: 2000000 INFO @ Tue, 16 Jun 2020 08:56:44: 3000000 INFO @ Tue, 16 Jun 2020 08:56:50: 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 08:56:55: 5000000 INFO @ Tue, 16 Jun 2020 08:56:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.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 08:56:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:57:01: 6000000 INFO @ Tue, 16 Jun 2020 08:57:04: 1000000 INFO @ Tue, 16 Jun 2020 08:57:08: 7000000 INFO @ Tue, 16 Jun 2020 08:57:11: 2000000 INFO @ Tue, 16 Jun 2020 08:57:14: 8000000 INFO @ Tue, 16 Jun 2020 08:57:18: 3000000 INFO @ Tue, 16 Jun 2020 08:57:21: 9000000 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 08:57:25: 4000000 INFO @ Tue, 16 Jun 2020 08:57:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.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 08:57:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:57:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:57:27: 10000000 INFO @ Tue, 16 Jun 2020 08:57:31: 5000000 INFO @ Tue, 16 Jun 2020 08:57:33: 1000000 INFO @ Tue, 16 Jun 2020 08:57:34: 11000000 INFO @ Tue, 16 Jun 2020 08:57:39: 6000000 INFO @ Tue, 16 Jun 2020 08:57:40: 12000000 INFO @ Tue, 16 Jun 2020 08:57:40: 2000000 INFO @ Tue, 16 Jun 2020 08:57:46: 7000000 INFO @ Tue, 16 Jun 2020 08:57:47: 13000000 INFO @ Tue, 16 Jun 2020 08:57:47: 3000000 INFO @ Tue, 16 Jun 2020 08:57:53: 8000000 INFO @ Tue, 16 Jun 2020 08:57:53: 14000000 INFO @ Tue, 16 Jun 2020 08:57:54: 4000000 INFO @ Tue, 16 Jun 2020 08:57:59: 15000000 INFO @ Tue, 16 Jun 2020 08:58:00: 9000000 INFO @ Tue, 16 Jun 2020 08:58:00: 5000000 INFO @ Tue, 16 Jun 2020 08:58:06: 16000000 INFO @ Tue, 16 Jun 2020 08:58:06: 6000000 INFO @ Tue, 16 Jun 2020 08:58:07: 10000000 INFO @ Tue, 16 Jun 2020 08:58:12: 17000000 INFO @ Tue, 16 Jun 2020 08:58:13: 7000000 INFO @ Tue, 16 Jun 2020 08:58:14: 11000000 INFO @ Tue, 16 Jun 2020 08:58:19: 18000000 INFO @ Tue, 16 Jun 2020 08:58:20: 8000000 INFO @ Tue, 16 Jun 2020 08:58:20: 12000000 INFO @ Tue, 16 Jun 2020 08:58:25: 19000000 INFO @ Tue, 16 Jun 2020 08:58:26: 9000000 INFO @ Tue, 16 Jun 2020 08:58:27: 13000000 INFO @ Tue, 16 Jun 2020 08:58:32: 20000000 INFO @ Tue, 16 Jun 2020 08:58:33: 10000000 INFO @ Tue, 16 Jun 2020 08:58:34: 14000000 INFO @ Tue, 16 Jun 2020 08:58:38: 21000000 INFO @ Tue, 16 Jun 2020 08:58:39: 11000000 INFO @ Tue, 16 Jun 2020 08:58:41: 15000000 INFO @ Tue, 16 Jun 2020 08:58:45: 22000000 INFO @ Tue, 16 Jun 2020 08:58:46: 12000000 INFO @ Tue, 16 Jun 2020 08:58:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:58:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:58:46: #1 total tags in treatment: 10900491 INFO @ Tue, 16 Jun 2020 08:58:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:58:46: #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 08:58:47: #1 tags after filtering in treatment: 6690628 INFO @ Tue, 16 Jun 2020 08:58:47: #1 Redundant rate of treatment: 0.39 INFO @ Tue, 16 Jun 2020 08:58:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:58:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:58:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:58:48: #2 number of paired peaks: 5141 INFO @ Tue, 16 Jun 2020 08:58:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:58:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:58:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:58:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:58:48: #2 predicted fragment length is 183 bps INFO @ Tue, 16 Jun 2020 08:58:48: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 16 Jun 2020 08:58:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.05_model.r INFO @ Tue, 16 Jun 2020 08:58:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:58:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:58:48: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:58:52: 13000000 INFO @ Tue, 16 Jun 2020 08:58:55: 17000000 INFO @ Tue, 16 Jun 2020 08:58:59: 14000000 INFO @ Tue, 16 Jun 2020 08:59:02: 18000000 INFO @ Tue, 16 Jun 2020 08:59:05: 15000000 INFO @ Tue, 16 Jun 2020 08:59:09: 19000000 INFO @ Tue, 16 Jun 2020 08:59:12: 16000000 INFO @ Tue, 16 Jun 2020 08:59:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:59:16: 20000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:59:18: 17000000 INFO @ Tue, 16 Jun 2020 08:59:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:59:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:59:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.05_summits.bed INFO @ Tue, 16 Jun 2020 08:59:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6323 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:59:23: 21000000 INFO @ Tue, 16 Jun 2020 08:59:25: 18000000 INFO @ Tue, 16 Jun 2020 08:59:30: 22000000 INFO @ Tue, 16 Jun 2020 08:59:31: 19000000 INFO @ Tue, 16 Jun 2020 08:59:32: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:59:32: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:59:32: #1 total tags in treatment: 10900491 INFO @ Tue, 16 Jun 2020 08:59:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:59:32: #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 08:59:33: #1 tags after filtering in treatment: 6690628 INFO @ Tue, 16 Jun 2020 08:59:33: #1 Redundant rate of treatment: 0.39 INFO @ Tue, 16 Jun 2020 08:59:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:59:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:59:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:59:33: #2 number of paired peaks: 5141 INFO @ Tue, 16 Jun 2020 08:59:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:59:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:59:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:59:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:59:34: #2 predicted fragment length is 183 bps INFO @ Tue, 16 Jun 2020 08:59:34: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 16 Jun 2020 08:59:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.10_model.r INFO @ Tue, 16 Jun 2020 08:59:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:59:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:59:37: 20000000 INFO @ Tue, 16 Jun 2020 08:59:43: 21000000 INFO @ Tue, 16 Jun 2020 08:59:48: 22000000 INFO @ Tue, 16 Jun 2020 08:59:50: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:59:50: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:59:50: #1 total tags in treatment: 10900491 INFO @ Tue, 16 Jun 2020 08:59:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:59:50: #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 08:59:50: #1 tags after filtering in treatment: 6690628 INFO @ Tue, 16 Jun 2020 08:59:50: #1 Redundant rate of treatment: 0.39 INFO @ Tue, 16 Jun 2020 08:59:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:59:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:59:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:59:51: #2 number of paired peaks: 5141 INFO @ Tue, 16 Jun 2020 08:59:51: start model_add_line... INFO @ Tue, 16 Jun 2020 08:59:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:59:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:59:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:59:51: #2 predicted fragment length is 183 bps INFO @ Tue, 16 Jun 2020 08:59:51: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 16 Jun 2020 08:59:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.20_model.r INFO @ Tue, 16 Jun 2020 08:59:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:59:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:59:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:00:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:00:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:00:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.10_summits.bed INFO @ Tue, 16 Jun 2020 09:00:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4123 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:00:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:00:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:00:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:00:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978702/SRX2978702.20_summits.bed INFO @ Tue, 16 Jun 2020 09:00:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2327 records, 4 fields): 3 millis CompletedMACS2peakCalling