Job ID = 6367562 SRX = SRX331318 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:34:35 prefetch.2.10.7: 1) Downloading 'SRR947555'... 2020-06-15T23:34:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:35:10 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:35:10 prefetch.2.10.7: 'SRR947555' is valid 2020-06-15T23:35:10 prefetch.2.10.7: 1) 'SRR947555' was downloaded successfully Read 3566568 spots for SRR947555/SRR947555.sra Written 3566568 spots for SRR947555/SRR947555.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: 00:00:33 3566568 reads; of these: 3566568 (100.00%) were unpaired; of these: 489983 (13.74%) aligned 0 times 2530728 (70.96%) aligned exactly 1 time 545857 (15.30%) aligned >1 times 86.26% overall alignment rate Time searching: 00:00:33 Overall time: 00:00:33 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] 544648 / 3076585 = 0.1770 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 08:36:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.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 08:36:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:02: 1000000 INFO @ Tue, 16 Jun 2020 08:37:09: 2000000 INFO @ Tue, 16 Jun 2020 08:37:12: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:37:12: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:37:12: #1 total tags in treatment: 2531937 INFO @ Tue, 16 Jun 2020 08:37:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:12: #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 08:37:12: #1 tags after filtering in treatment: 2531937 INFO @ Tue, 16 Jun 2020 08:37:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:12: #2 number of paired peaks: 443 WARNING @ Tue, 16 Jun 2020 08:37:12: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Tue, 16 Jun 2020 08:37:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:12: #2 predicted fragment length is 98 bps INFO @ Tue, 16 Jun 2020 08:37:12: #2 alternative fragment length(s) may be 39,98,538,559 bps INFO @ Tue, 16 Jun 2020 08:37:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.05_model.r INFO @ Tue, 16 Jun 2020 08:37:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.05_summits.bed INFO @ Tue, 16 Jun 2020 08:37:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (546 records, 4 fields): 1 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 08:37:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.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 08:37:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:37:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:32: 1000000 INFO @ Tue, 16 Jun 2020 08:37:39: 2000000 INFO @ Tue, 16 Jun 2020 08:37:43: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:37:43: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:37:43: #1 total tags in treatment: 2531937 INFO @ Tue, 16 Jun 2020 08:37:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:43: #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 08:37:43: #1 tags after filtering in treatment: 2531937 INFO @ Tue, 16 Jun 2020 08:37:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:43: #2 number of paired peaks: 443 WARNING @ Tue, 16 Jun 2020 08:37:43: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Tue, 16 Jun 2020 08:37:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:43: #2 predicted fragment length is 98 bps INFO @ Tue, 16 Jun 2020 08:37:43: #2 alternative fragment length(s) may be 39,98,538,559 bps INFO @ Tue, 16 Jun 2020 08:37:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.10_model.r INFO @ Tue, 16 Jun 2020 08:37:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.10_summits.bed INFO @ Tue, 16 Jun 2020 08:37:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (300 records, 4 fields): 1 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 08:37:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.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 08:37:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:37:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:38:01: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:38:07: 2000000 INFO @ Tue, 16 Jun 2020 08:38:10: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:38:10: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:38:10: #1 total tags in treatment: 2531937 INFO @ Tue, 16 Jun 2020 08:38:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:38:10: #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 08:38:10: #1 tags after filtering in treatment: 2531937 INFO @ Tue, 16 Jun 2020 08:38:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:38:10: #1 finished! INFO @ Tue, 16 Jun 2020 08:38:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:38:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:38:10: #2 number of paired peaks: 443 WARNING @ Tue, 16 Jun 2020 08:38:10: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Tue, 16 Jun 2020 08:38:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:38:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:38:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:38:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:38:10: #2 predicted fragment length is 98 bps INFO @ Tue, 16 Jun 2020 08:38:10: #2 alternative fragment length(s) may be 39,98,538,559 bps INFO @ Tue, 16 Jun 2020 08:38:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.20_model.r INFO @ Tue, 16 Jun 2020 08:38:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:38:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:38:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:38:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:38:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:38:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331318/SRX331318.20_summits.bed INFO @ Tue, 16 Jun 2020 08:38:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (122 records, 4 fields): 0 millis CompletedMACS2peakCalling