Job ID = 6367401 SRX = SRX331160 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:24:46 prefetch.2.10.7: 1) Downloading 'SRR947392'... 2020-06-15T23:24:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:25:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:25:12 prefetch.2.10.7: 'SRR947392' is valid 2020-06-15T23:25:12 prefetch.2.10.7: 1) 'SRR947392' was downloaded successfully Read 6332462 spots for SRR947392/SRR947392.sra Written 6332462 spots for SRR947392/SRR947392.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: 00:00:39 6332462 reads; of these: 6332462 (100.00%) were unpaired; of these: 4185897 (66.10%) aligned 0 times 1828488 (28.87%) aligned exactly 1 time 318077 (5.02%) aligned >1 times 33.90% overall alignment rate Time searching: 00:00:39 Overall time: 00:00:39 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] 421023 / 2146565 = 0.1961 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 08:27:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.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 08:27:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:09: 1000000 INFO @ Tue, 16 Jun 2020 08:27:13: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:27:13: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:27:13: #1 total tags in treatment: 1725542 INFO @ Tue, 16 Jun 2020 08:27:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:13: #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 08:27:13: #1 tags after filtering in treatment: 1725542 INFO @ Tue, 16 Jun 2020 08:27:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:13: #2 number of paired peaks: 747 WARNING @ Tue, 16 Jun 2020 08:27:13: Fewer paired peaks (747) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 747 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:13: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 08:27:13: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 16 Jun 2020 08:27:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.05_model.r INFO @ Tue, 16 Jun 2020 08:27:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.05_summits.bed INFO @ Tue, 16 Jun 2020 08:27:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1217 records, 4 fields): 3 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 08:27:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.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 08:27:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:40: 1000000 INFO @ Tue, 16 Jun 2020 08:27:44: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:27:44: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:27:44: #1 total tags in treatment: 1725542 INFO @ Tue, 16 Jun 2020 08:27:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:44: #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 08:27:44: #1 tags after filtering in treatment: 1725542 INFO @ Tue, 16 Jun 2020 08:27:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:44: #2 number of paired peaks: 747 WARNING @ Tue, 16 Jun 2020 08:27:44: Fewer paired peaks (747) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 747 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:44: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:44: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:44: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:44: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:44: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 08:27:44: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 16 Jun 2020 08:27:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.10_model.r INFO @ Tue, 16 Jun 2020 08:27:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.10_summits.bed INFO @ Tue, 16 Jun 2020 08:27:50: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (479 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 08:28:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.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 08:28:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:09: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:28:13: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:28:13: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:28:13: #1 total tags in treatment: 1725542 INFO @ Tue, 16 Jun 2020 08:28:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:13: #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 08:28:13: #1 tags after filtering in treatment: 1725542 INFO @ Tue, 16 Jun 2020 08:28:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:13: #2 number of paired peaks: 747 WARNING @ Tue, 16 Jun 2020 08:28:13: Fewer paired peaks (747) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 747 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:13: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 08:28:13: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 16 Jun 2020 08:28:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.20_model.r INFO @ Tue, 16 Jun 2020 08:28:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:28:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331160/SRX331160.20_summits.bed INFO @ Tue, 16 Jun 2020 08:28:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (124 records, 4 fields): 1 millis CompletedMACS2peakCalling