Job ID = 6366698 SRX = SRX2228854 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:58:08 prefetch.2.10.7: 1) Downloading 'SRR4380310'... 2020-06-15T22:58:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:58:47 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:58:47 prefetch.2.10.7: 'SRR4380310' is valid 2020-06-15T22:58:47 prefetch.2.10.7: 1) 'SRR4380310' was downloaded successfully Read 5119300 spots for SRR4380310/SRR4380310.sra Written 5119300 spots for SRR4380310/SRR4380310.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: 00:01:11 5119300 reads; of these: 5119300 (100.00%) were unpaired; of these: 236776 (4.63%) aligned 0 times 4056370 (79.24%) aligned exactly 1 time 826154 (16.14%) aligned >1 times 95.37% overall alignment rate Time searching: 00:01:11 Overall time: 00:01:11 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] 608177 / 4882524 = 0.1246 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 08:01:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.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 08:01:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:04: 1000000 INFO @ Tue, 16 Jun 2020 08:02:09: 2000000 INFO @ Tue, 16 Jun 2020 08:02:14: 3000000 INFO @ Tue, 16 Jun 2020 08:02:19: 4000000 INFO @ Tue, 16 Jun 2020 08:02:20: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:02:20: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:02:20: #1 total tags in treatment: 4274347 INFO @ Tue, 16 Jun 2020 08:02:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:20: #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 08:02:20: #1 tags after filtering in treatment: 4274347 INFO @ Tue, 16 Jun 2020 08:02:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:21: #2 number of paired peaks: 474 WARNING @ Tue, 16 Jun 2020 08:02:21: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Tue, 16 Jun 2020 08:02:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:21: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 08:02:21: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 16 Jun 2020 08:02:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.05_model.r INFO @ Tue, 16 Jun 2020 08:02:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:21: #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 @ Tue, 16 Jun 2020 08:02:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.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 08:02:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:34: 1000000 INFO @ Tue, 16 Jun 2020 08:02:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.05_summits.bed INFO @ Tue, 16 Jun 2020 08:02:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (528 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:02:39: 2000000 INFO @ Tue, 16 Jun 2020 08:02:44: 3000000 INFO @ Tue, 16 Jun 2020 08:02:49: 4000000 INFO @ Tue, 16 Jun 2020 08:02:50: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:02:50: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:02:50: #1 total tags in treatment: 4274347 INFO @ Tue, 16 Jun 2020 08:02:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:50: #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 08:02:51: #1 tags after filtering in treatment: 4274347 INFO @ Tue, 16 Jun 2020 08:02:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:51: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:51: #2 number of paired peaks: 474 WARNING @ Tue, 16 Jun 2020 08:02:51: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Tue, 16 Jun 2020 08:02:51: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:51: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 08:02:51: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 16 Jun 2020 08:02:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.10_model.r INFO @ Tue, 16 Jun 2020 08:02:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:51: #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 08:02:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.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 08:02:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:05: 1000000 INFO @ Tue, 16 Jun 2020 08:03:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.10_summits.bed INFO @ Tue, 16 Jun 2020 08:03:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (351 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:03:10: 2000000 INFO @ Tue, 16 Jun 2020 08:03:15: 3000000 INFO @ Tue, 16 Jun 2020 08:03:19: 4000000 INFO @ Tue, 16 Jun 2020 08:03:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:03:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:03:21: #1 total tags in treatment: 4274347 INFO @ Tue, 16 Jun 2020 08:03:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:21: #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 08:03:21: #1 tags after filtering in treatment: 4274347 INFO @ Tue, 16 Jun 2020 08:03:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:21: #2 number of paired peaks: 474 WARNING @ Tue, 16 Jun 2020 08:03:21: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Tue, 16 Jun 2020 08:03:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:21: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 08:03:21: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 16 Jun 2020 08:03:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.20_model.r INFO @ Tue, 16 Jun 2020 08:03:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:21: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:03:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:03:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228854/SRX2228854.20_summits.bed INFO @ Tue, 16 Jun 2020 08:03:35: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (194 records, 4 fields): 2 millis CompletedMACS2peakCalling