Job ID = 6507880 SRX = SRX494965 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:38:57 prefetch.2.10.7: 1) Downloading 'SRR1198497'... 2020-06-26T13:38:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:40:00 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:40:01 prefetch.2.10.7: 'SRR1198497' is valid 2020-06-26T13:40:01 prefetch.2.10.7: 1) 'SRR1198497' was downloaded successfully Read 14251498 spots for SRR1198497/SRR1198497.sra Written 14251498 spots for SRR1198497/SRR1198497.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: 00:00:01 Multiseed full-index search: 00:03:35 14251498 reads; of these: 14251498 (100.00%) were unpaired; of these: 1246542 (8.75%) aligned 0 times 11665759 (81.86%) aligned exactly 1 time 1339197 (9.40%) aligned >1 times 91.25% overall alignment rate Time searching: 00:03:36 Overall time: 00:03:36 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] 9607510 / 13004956 = 0.7388 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 @ Fri, 26 Jun 2020 22:46:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.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 @ Fri, 26 Jun 2020 22:46:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:46:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:46:47: 1000000 INFO @ Fri, 26 Jun 2020 22:46:53: 2000000 INFO @ Fri, 26 Jun 2020 22:46:59: 3000000 INFO @ Fri, 26 Jun 2020 22:47:01: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:47:01: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:47:01: #1 total tags in treatment: 3397446 INFO @ Fri, 26 Jun 2020 22:47:01: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:47:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:47:01: #1 tags after filtering in treatment: 3397446 INFO @ Fri, 26 Jun 2020 22:47:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:47:01: #1 finished! INFO @ Fri, 26 Jun 2020 22:47:01: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:47:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:47:01: #2 number of paired peaks: 4837 INFO @ Fri, 26 Jun 2020 22:47:01: start model_add_line... INFO @ Fri, 26 Jun 2020 22:47:01: start X-correlation... INFO @ Fri, 26 Jun 2020 22:47:01: end of X-cor INFO @ Fri, 26 Jun 2020 22:47:01: #2 finished! INFO @ Fri, 26 Jun 2020 22:47:01: #2 predicted fragment length is 113 bps INFO @ Fri, 26 Jun 2020 22:47:01: #2 alternative fragment length(s) may be 113 bps INFO @ Fri, 26 Jun 2020 22:47:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.05_model.r INFO @ Fri, 26 Jun 2020 22:47:01: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:47:01: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 22:47:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:47:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.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 @ Fri, 26 Jun 2020 22:47:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:47:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:47:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:47:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:47:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.05_summits.bed INFO @ Fri, 26 Jun 2020 22:47:15: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7157 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:47:17: 1000000 INFO @ Fri, 26 Jun 2020 22:47:22: 2000000 INFO @ Fri, 26 Jun 2020 22:47:27: 3000000 INFO @ Fri, 26 Jun 2020 22:47:29: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:47:29: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:47:29: #1 total tags in treatment: 3397446 INFO @ Fri, 26 Jun 2020 22:47:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:47:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:47:29: #1 tags after filtering in treatment: 3397446 INFO @ Fri, 26 Jun 2020 22:47:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:47:29: #1 finished! INFO @ Fri, 26 Jun 2020 22:47:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:47:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:47:29: #2 number of paired peaks: 4837 INFO @ Fri, 26 Jun 2020 22:47:29: start model_add_line... INFO @ Fri, 26 Jun 2020 22:47:29: start X-correlation... INFO @ Fri, 26 Jun 2020 22:47:29: end of X-cor INFO @ Fri, 26 Jun 2020 22:47:29: #2 finished! INFO @ Fri, 26 Jun 2020 22:47:29: #2 predicted fragment length is 113 bps INFO @ Fri, 26 Jun 2020 22:47:29: #2 alternative fragment length(s) may be 113 bps INFO @ Fri, 26 Jun 2020 22:47:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.10_model.r INFO @ Fri, 26 Jun 2020 22:47:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:47:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:47:38: #3 Call peaks for each chromosome... 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 @ Fri, 26 Jun 2020 22:47:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.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 @ Fri, 26 Jun 2020 22:47:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:47:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:47:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:47:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:47:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.10_summits.bed INFO @ Fri, 26 Jun 2020 22:47:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5500 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:47:47: 1000000 INFO @ Fri, 26 Jun 2020 22:47:53: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:47:59: 3000000 INFO @ Fri, 26 Jun 2020 22:48:01: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:48:01: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:48:01: #1 total tags in treatment: 3397446 INFO @ Fri, 26 Jun 2020 22:48:01: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:48:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:48:01: #1 tags after filtering in treatment: 3397446 INFO @ Fri, 26 Jun 2020 22:48:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:48:01: #1 finished! INFO @ Fri, 26 Jun 2020 22:48:01: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:48:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:48:02: #2 number of paired peaks: 4837 INFO @ Fri, 26 Jun 2020 22:48:02: start model_add_line... INFO @ Fri, 26 Jun 2020 22:48:02: start X-correlation... INFO @ Fri, 26 Jun 2020 22:48:02: end of X-cor INFO @ Fri, 26 Jun 2020 22:48:02: #2 finished! INFO @ Fri, 26 Jun 2020 22:48:02: #2 predicted fragment length is 113 bps INFO @ Fri, 26 Jun 2020 22:48:02: #2 alternative fragment length(s) may be 113 bps INFO @ Fri, 26 Jun 2020 22:48:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.20_model.r INFO @ Fri, 26 Jun 2020 22:48:02: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:48:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:48:11: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:48:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:48:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:48:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494965/SRX494965.20_summits.bed INFO @ Fri, 26 Jun 2020 22:48:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3974 records, 4 fields): 6 millis CompletedMACS2peakCalling