Job ID = 6365869 SRX = SRX005626 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:41:29 prefetch.2.10.7: 1) Downloading 'SRR017595'... 2020-06-15T23:41:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:42:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:42:23 prefetch.2.10.7: 'SRR017595' is valid 2020-06-15T23:42:23 prefetch.2.10.7: 1) 'SRR017595' was downloaded successfully Read 4820475 spots for SRR017595/SRR017595.sra Written 4820475 spots for SRR017595/SRR017595.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: 00:00:36 4820475 reads; of these: 4820475 (100.00%) were unpaired; of these: 2091317 (43.38%) aligned 0 times 2348596 (48.72%) aligned exactly 1 time 380562 (7.89%) aligned >1 times 56.62% overall alignment rate Time searching: 00:00:36 Overall time: 00:00:36 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_rmdupse_core] 596899 / 2729158 = 0.2187 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 08:44:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.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 08:44:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:32: 1000000 INFO @ Tue, 16 Jun 2020 08:44:37: 2000000 INFO @ Tue, 16 Jun 2020 08:44:38: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 08:44:38: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 08:44:38: #1 total tags in treatment: 2132259 INFO @ Tue, 16 Jun 2020 08:44:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:44:38: #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 08:44:38: #1 tags after filtering in treatment: 2132259 INFO @ Tue, 16 Jun 2020 08:44:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:44:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:44:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:44:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:44:38: #2 number of paired peaks: 2329 INFO @ Tue, 16 Jun 2020 08:44:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:44:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:44:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:44:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:44:38: #2 predicted fragment length is 95 bps INFO @ Tue, 16 Jun 2020 08:44:38: #2 alternative fragment length(s) may be 95 bps INFO @ Tue, 16 Jun 2020 08:44:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.05_model.r INFO @ Tue, 16 Jun 2020 08:44:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:44:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:44:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:44:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:44:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:44:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.05_summits.bed INFO @ Tue, 16 Jun 2020 08:44:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1949 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 08:44:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.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 08:44:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:45:02: 1000000 INFO @ Tue, 16 Jun 2020 08:45:08: 2000000 INFO @ Tue, 16 Jun 2020 08:45:08: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 08:45:08: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 08:45:08: #1 total tags in treatment: 2132259 INFO @ Tue, 16 Jun 2020 08:45:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:08: #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 08:45:08: #1 tags after filtering in treatment: 2132259 INFO @ Tue, 16 Jun 2020 08:45:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:09: #2 number of paired peaks: 2329 INFO @ Tue, 16 Jun 2020 08:45:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:09: #2 predicted fragment length is 95 bps INFO @ Tue, 16 Jun 2020 08:45:09: #2 alternative fragment length(s) may be 95 bps INFO @ Tue, 16 Jun 2020 08:45:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.10_model.r INFO @ Tue, 16 Jun 2020 08:45:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:45:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.10_summits.bed INFO @ Tue, 16 Jun 2020 08:45:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (723 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 08:45:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.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 08:45:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:45:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:45:32: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:45:38: 2000000 INFO @ Tue, 16 Jun 2020 08:45:38: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 08:45:38: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 08:45:38: #1 total tags in treatment: 2132259 INFO @ Tue, 16 Jun 2020 08:45:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:38: #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 08:45:38: #1 tags after filtering in treatment: 2132259 INFO @ Tue, 16 Jun 2020 08:45:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:38: #2 number of paired peaks: 2329 INFO @ Tue, 16 Jun 2020 08:45:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:38: #2 predicted fragment length is 95 bps INFO @ Tue, 16 Jun 2020 08:45:38: #2 alternative fragment length(s) may be 95 bps INFO @ Tue, 16 Jun 2020 08:45:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.20_model.r INFO @ Tue, 16 Jun 2020 08:45:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:45:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX005626/SRX005626.20_summits.bed INFO @ Tue, 16 Jun 2020 08:45:46: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (218 records, 4 fields): 2 millis CompletedMACS2peakCalling