Job ID = 10165699 SRX = SRX8832069 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14729232 spots for SRR12332011/SRR12332011.sra Written 14729232 spots for SRR12332011/SRR12332011.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165834 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:57 14729232 reads; of these: 14729232 (100.00%) were unpaired; of these: 689125 (4.68%) aligned 0 times 11959769 (81.20%) aligned exactly 1 time 2080338 (14.12%) aligned >1 times 95.32% overall alignment rate Time searching: 00:02:57 Overall time: 00:02:57 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] 1740732 / 14040107 = 0.1240 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 @ Thu, 08 Oct 2020 19:42:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.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 @ Thu, 08 Oct 2020 19:42:41: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:42:41: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:42:46: 1000000 INFO @ Thu, 08 Oct 2020 19:42:51: 2000000 INFO @ Thu, 08 Oct 2020 19:42:57: 3000000 INFO @ Thu, 08 Oct 2020 19:43:02: 4000000 INFO @ Thu, 08 Oct 2020 19:43:07: 5000000 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 @ Thu, 08 Oct 2020 19:43:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.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 @ Thu, 08 Oct 2020 19:43:10: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:43:10: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:43:13: 6000000 INFO @ Thu, 08 Oct 2020 19:43:16: 1000000 INFO @ Thu, 08 Oct 2020 19:43:19: 7000000 INFO @ Thu, 08 Oct 2020 19:43:22: 2000000 INFO @ Thu, 08 Oct 2020 19:43:24: 8000000 INFO @ Thu, 08 Oct 2020 19:43:28: 3000000 INFO @ Thu, 08 Oct 2020 19:43:30: 9000000 INFO @ Thu, 08 Oct 2020 19:43:34: 4000000 INFO @ Thu, 08 Oct 2020 19:43:36: 10000000 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 @ Thu, 08 Oct 2020 19:43:40: 5000000 INFO @ Thu, 08 Oct 2020 19:43:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.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 @ Thu, 08 Oct 2020 19:43:41: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:43:41: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:43:41: 11000000 INFO @ Thu, 08 Oct 2020 19:43:46: 6000000 INFO @ Thu, 08 Oct 2020 19:43:48: 1000000 INFO @ Thu, 08 Oct 2020 19:43:48: 12000000 INFO @ Thu, 08 Oct 2020 19:43:49: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:43:49: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:43:49: #1 total tags in treatment: 12299375 INFO @ Thu, 08 Oct 2020 19:43:49: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:43:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:43:50: #1 tags after filtering in treatment: 12299375 INFO @ Thu, 08 Oct 2020 19:43:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:43:50: #1 finished! INFO @ Thu, 08 Oct 2020 19:43:50: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:43:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:43:51: #2 number of paired peaks: 889 WARNING @ Thu, 08 Oct 2020 19:43:51: Fewer paired peaks (889) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 889 pairs to build model! INFO @ Thu, 08 Oct 2020 19:43:51: start model_add_line... INFO @ Thu, 08 Oct 2020 19:43:51: start X-correlation... INFO @ Thu, 08 Oct 2020 19:43:51: end of X-cor INFO @ Thu, 08 Oct 2020 19:43:51: #2 finished! INFO @ Thu, 08 Oct 2020 19:43:51: #2 predicted fragment length is 163 bps INFO @ Thu, 08 Oct 2020 19:43:51: #2 alternative fragment length(s) may be 163 bps INFO @ Thu, 08 Oct 2020 19:43:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.05_model.r INFO @ Thu, 08 Oct 2020 19:43:51: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:43:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:43:52: 7000000 INFO @ Thu, 08 Oct 2020 19:43:54: 2000000 INFO @ Thu, 08 Oct 2020 19:43:58: 8000000 INFO @ Thu, 08 Oct 2020 19:43:59: 3000000 INFO @ Thu, 08 Oct 2020 19:44:03: 9000000 INFO @ Thu, 08 Oct 2020 19:44:05: 4000000 INFO @ Thu, 08 Oct 2020 19:44:09: 10000000 INFO @ Thu, 08 Oct 2020 19:44:11: 5000000 INFO @ Thu, 08 Oct 2020 19:44:15: 11000000 INFO @ Thu, 08 Oct 2020 19:44:17: 6000000 INFO @ Thu, 08 Oct 2020 19:44:18: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:44:21: 12000000 INFO @ Thu, 08 Oct 2020 19:44:23: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:44:23: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:44:23: #1 total tags in treatment: 12299375 INFO @ Thu, 08 Oct 2020 19:44:23: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:44:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:44:23: #1 tags after filtering in treatment: 12299375 INFO @ Thu, 08 Oct 2020 19:44:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:44:23: #1 finished! INFO @ Thu, 08 Oct 2020 19:44:23: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:44:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:44:23: 7000000 INFO @ Thu, 08 Oct 2020 19:44:24: #2 number of paired peaks: 889 WARNING @ Thu, 08 Oct 2020 19:44:24: Fewer paired peaks (889) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 889 pairs to build model! INFO @ Thu, 08 Oct 2020 19:44:24: start model_add_line... INFO @ Thu, 08 Oct 2020 19:44:24: start X-correlation... INFO @ Thu, 08 Oct 2020 19:44:24: end of X-cor INFO @ Thu, 08 Oct 2020 19:44:24: #2 finished! INFO @ Thu, 08 Oct 2020 19:44:24: #2 predicted fragment length is 163 bps INFO @ Thu, 08 Oct 2020 19:44:24: #2 alternative fragment length(s) may be 163 bps INFO @ Thu, 08 Oct 2020 19:44:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.10_model.r INFO @ Thu, 08 Oct 2020 19:44:24: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:44:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:44:28: 8000000 INFO @ Thu, 08 Oct 2020 19:44:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:44:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:44:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.05_summits.bed INFO @ Thu, 08 Oct 2020 19:44:32: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7391 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:44:34: 9000000 INFO @ Thu, 08 Oct 2020 19:44:39: 10000000 INFO @ Thu, 08 Oct 2020 19:44:45: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:44:50: 12000000 INFO @ Thu, 08 Oct 2020 19:44:51: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:44:52: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:44:52: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:44:52: #1 total tags in treatment: 12299375 INFO @ Thu, 08 Oct 2020 19:44:52: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:44:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:44:52: #1 tags after filtering in treatment: 12299375 INFO @ Thu, 08 Oct 2020 19:44:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:44:52: #1 finished! INFO @ Thu, 08 Oct 2020 19:44:52: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:44:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:44:53: #2 number of paired peaks: 889 WARNING @ Thu, 08 Oct 2020 19:44:53: Fewer paired peaks (889) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 889 pairs to build model! INFO @ Thu, 08 Oct 2020 19:44:53: start model_add_line... INFO @ Thu, 08 Oct 2020 19:44:53: start X-correlation... INFO @ Thu, 08 Oct 2020 19:44:53: end of X-cor INFO @ Thu, 08 Oct 2020 19:44:53: #2 finished! INFO @ Thu, 08 Oct 2020 19:44:53: #2 predicted fragment length is 163 bps INFO @ Thu, 08 Oct 2020 19:44:53: #2 alternative fragment length(s) may be 163 bps INFO @ Thu, 08 Oct 2020 19:44:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.20_model.r INFO @ Thu, 08 Oct 2020 19:44:53: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:44:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:45:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:45:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:45:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.10_summits.bed INFO @ Thu, 08 Oct 2020 19:45:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4922 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:45:20: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:45:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:45:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:45:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.20_summits.bed INFO @ Thu, 08 Oct 2020 19:45:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2380 records, 4 fields): 4 millis CompletedMACS2peakCalling