Job ID = 6367618 SRX = SRX341786 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:04:30 prefetch.2.10.7: 1) Downloading 'SRR959927'... 2020-06-16T00:04:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:06:08 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:06:09 prefetch.2.10.7: 'SRR959927' is valid 2020-06-16T00:06:09 prefetch.2.10.7: 1) 'SRR959927' was downloaded successfully Read 13505880 spots for SRR959927/SRR959927.sra Written 13505880 spots for SRR959927/SRR959927.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: 00:03:52 13505880 reads; of these: 13505880 (100.00%) were unpaired; of these: 1944825 (14.40%) aligned 0 times 10177358 (75.36%) aligned exactly 1 time 1383697 (10.25%) aligned >1 times 85.60% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 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] 5188683 / 11561055 = 0.4488 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 09:14:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.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 09:14:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:00: 1000000 INFO @ Tue, 16 Jun 2020 09:15:07: 2000000 INFO @ Tue, 16 Jun 2020 09:15:13: 3000000 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 09:15:20: 4000000 INFO @ Tue, 16 Jun 2020 09:15:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.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 09:15:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:15:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:27: 5000000 INFO @ Tue, 16 Jun 2020 09:15:30: 1000000 INFO @ Tue, 16 Jun 2020 09:15:34: 6000000 INFO @ Tue, 16 Jun 2020 09:15:37: 2000000 INFO @ Tue, 16 Jun 2020 09:15:37: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:15:37: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:15:37: #1 total tags in treatment: 6372372 INFO @ Tue, 16 Jun 2020 09:15:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:15:37: #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 09:15:37: #1 tags after filtering in treatment: 6372372 INFO @ Tue, 16 Jun 2020 09:15:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:15:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:15:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:15:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:15:37: #2 number of paired peaks: 282 WARNING @ Tue, 16 Jun 2020 09:15:37: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Tue, 16 Jun 2020 09:15:37: start model_add_line... INFO @ Tue, 16 Jun 2020 09:15:37: start X-correlation... INFO @ Tue, 16 Jun 2020 09:15:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:15:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:15:38: #2 predicted fragment length is 224 bps INFO @ Tue, 16 Jun 2020 09:15:38: #2 alternative fragment length(s) may be 3,224,240,268 bps INFO @ Tue, 16 Jun 2020 09:15:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.05_model.r INFO @ Tue, 16 Jun 2020 09:15:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:15:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:15:44: 3000000 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 09:15:51: 4000000 INFO @ Tue, 16 Jun 2020 09:15:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:15:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.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 09:15:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:15:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:58: 5000000 INFO @ Tue, 16 Jun 2020 09:16:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.05_summits.bed INFO @ Tue, 16 Jun 2020 09:16:00: Done! INFO @ Tue, 16 Jun 2020 09:16:00: 1000000 pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (669 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:16:05: 6000000 INFO @ Tue, 16 Jun 2020 09:16:07: 2000000 INFO @ Tue, 16 Jun 2020 09:16:08: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:16:08: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:16:08: #1 total tags in treatment: 6372372 INFO @ Tue, 16 Jun 2020 09:16:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:08: #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 09:16:08: #1 tags after filtering in treatment: 6372372 INFO @ Tue, 16 Jun 2020 09:16:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:16:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:08: #2 number of paired peaks: 282 WARNING @ Tue, 16 Jun 2020 09:16:08: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:08: #2 predicted fragment length is 224 bps INFO @ Tue, 16 Jun 2020 09:16:08: #2 alternative fragment length(s) may be 3,224,240,268 bps INFO @ Tue, 16 Jun 2020 09:16:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.10_model.r INFO @ Tue, 16 Jun 2020 09:16:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:14: 3000000 INFO @ Tue, 16 Jun 2020 09:16:21: 4000000 INFO @ Tue, 16 Jun 2020 09:16:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:28: 5000000 INFO @ Tue, 16 Jun 2020 09:16:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.10_summits.bed INFO @ Tue, 16 Jun 2020 09:16:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (243 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:16:35: 6000000 INFO @ Tue, 16 Jun 2020 09:16:37: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:16:37: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:16:37: #1 total tags in treatment: 6372372 INFO @ Tue, 16 Jun 2020 09:16:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:37: #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 09:16:37: #1 tags after filtering in treatment: 6372372 INFO @ Tue, 16 Jun 2020 09:16:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:16:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:38: #2 number of paired peaks: 282 WARNING @ Tue, 16 Jun 2020 09:16:38: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:38: #2 predicted fragment length is 224 bps INFO @ Tue, 16 Jun 2020 09:16:38: #2 alternative fragment length(s) may be 3,224,240,268 bps INFO @ Tue, 16 Jun 2020 09:16:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.20_model.r INFO @ Tue, 16 Jun 2020 09:16:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:38: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:16:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX341786/SRX341786.20_summits.bed INFO @ Tue, 16 Jun 2020 09:17:00: Done! BigWig に変換しました。 pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (89 records, 4 fields): 1 millis CompletedMACS2peakCalling