Job ID = 6366311 SRX = SRX1099838 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:35:21 prefetch.2.10.7: 1) Downloading 'SRR2105908'... 2020-06-15T22:35:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:36:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:36:04 prefetch.2.10.7: 'SRR2105908' is valid 2020-06-15T22:36:04 prefetch.2.10.7: 1) 'SRR2105908' was downloaded successfully Read 5816551 spots for SRR2105908/SRR2105908.sra Written 5816551 spots for SRR2105908/SRR2105908.sra 2020-06-15T22:36:32 prefetch.2.10.7: 1) Downloading 'SRR2105909'... 2020-06-15T22:36:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:37:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:37:24 prefetch.2.10.7: 'SRR2105909' is valid 2020-06-15T22:37:24 prefetch.2.10.7: 1) 'SRR2105909' was downloaded successfully Read 7162624 spots for SRR2105909/SRR2105909.sra Written 7162624 spots for SRR2105909/SRR2105909.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: 00:02:50 12979175 reads; of these: 12979175 (100.00%) were unpaired; of these: 741887 (5.72%) aligned 0 times 10331662 (79.60%) aligned exactly 1 time 1905626 (14.68%) aligned >1 times 94.28% overall alignment rate Time searching: 00:02:51 Overall time: 00:02:51 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_rmdupse_core] 8052030 / 12237288 = 0.6580 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 07:43:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.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 07:43:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:40: 1000000 INFO @ Tue, 16 Jun 2020 07:43:47: 2000000 INFO @ Tue, 16 Jun 2020 07:43:54: 3000000 INFO @ Tue, 16 Jun 2020 07:44:00: 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 07:44:02: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:44:02: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:44:02: #1 total tags in treatment: 4185258 INFO @ Tue, 16 Jun 2020 07:44:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:02: #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 07:44:02: #1 tags after filtering in treatment: 4185258 INFO @ Tue, 16 Jun 2020 07:44:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:02: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:02: #2 number of paired peaks: 1684 INFO @ Tue, 16 Jun 2020 07:44:02: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:02: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:02: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:02: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:02: #2 predicted fragment length is 231 bps INFO @ Tue, 16 Jun 2020 07:44:02: #2 alternative fragment length(s) may be 231 bps INFO @ Tue, 16 Jun 2020 07:44:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.05_model.r INFO @ Tue, 16 Jun 2020 07:44:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:44:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.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 07:44:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:44:09: 1000000 INFO @ Tue, 16 Jun 2020 07:44:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:44:14: 2000000 INFO @ Tue, 16 Jun 2020 07:44:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.05_summits.bed INFO @ Tue, 16 Jun 2020 07:44:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3282 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:44:20: 3000000 INFO @ Tue, 16 Jun 2020 07:44:26: 4000000 INFO @ Tue, 16 Jun 2020 07:44:27: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:44:27: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:44:27: #1 total tags in treatment: 4185258 INFO @ Tue, 16 Jun 2020 07:44:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:27: #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 07:44:27: #1 tags after filtering in treatment: 4185258 INFO @ Tue, 16 Jun 2020 07:44:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:27: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:27: #2 number of paired peaks: 1684 INFO @ Tue, 16 Jun 2020 07:44:27: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:27: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:27: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:27: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:27: #2 predicted fragment length is 231 bps INFO @ Tue, 16 Jun 2020 07:44:27: #2 alternative fragment length(s) may be 231 bps INFO @ Tue, 16 Jun 2020 07:44:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.10_model.r INFO @ Tue, 16 Jun 2020 07:44:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:27: #3 Pre-compute pvalue-qvalue table... 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 07:44:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.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 07:44:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:44:39: 1000000 INFO @ Tue, 16 Jun 2020 07:44:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:44:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.10_summits.bed INFO @ Tue, 16 Jun 2020 07:44:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1280 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:44:46: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:44:52: 3000000 INFO @ Tue, 16 Jun 2020 07:44:58: 4000000 INFO @ Tue, 16 Jun 2020 07:44:59: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:44:59: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:44:59: #1 total tags in treatment: 4185258 INFO @ Tue, 16 Jun 2020 07:44:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:59: #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 07:44:59: #1 tags after filtering in treatment: 4185258 INFO @ Tue, 16 Jun 2020 07:44:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:59: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:59: #2 number of paired peaks: 1684 INFO @ Tue, 16 Jun 2020 07:44:59: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:00: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:00: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:00: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:00: #2 predicted fragment length is 231 bps INFO @ Tue, 16 Jun 2020 07:45:00: #2 alternative fragment length(s) may be 231 bps INFO @ Tue, 16 Jun 2020 07:45:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.20_model.r INFO @ Tue, 16 Jun 2020 07:45:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:45:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1099838/SRX1099838.20_summits.bed INFO @ Tue, 16 Jun 2020 07:45:18: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (441 records, 4 fields): 2 millis CompletedMACS2peakCalling