Job ID = 14158282 SRX = SRX7665444 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15470898 spots for SRR11004628/SRR11004628.sra Written 15470898 spots for SRR11004628/SRR11004628.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158799 ("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: 00:02:38 15470898 reads; of these: 15470898 (100.00%) were unpaired; of these: 804844 (5.20%) aligned 0 times 12063229 (77.97%) aligned exactly 1 time 2602825 (16.82%) aligned >1 times 94.80% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 2194033 / 14666054 = 0.1496 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 15:49:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.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 @ Wed, 08 Dec 2021 15:49:41: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:49:41: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:49:46: 1000000 INFO @ Wed, 08 Dec 2021 15:49:51: 2000000 INFO @ Wed, 08 Dec 2021 15:49:55: 3000000 INFO @ Wed, 08 Dec 2021 15:50:00: 4000000 INFO @ Wed, 08 Dec 2021 15:50:05: 5000000 INFO @ Wed, 08 Dec 2021 15:50:09: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 15:50:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.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 @ Wed, 08 Dec 2021 15:50:11: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:50:11: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:50:14: 7000000 INFO @ Wed, 08 Dec 2021 15:50:17: 1000000 INFO @ Wed, 08 Dec 2021 15:50:19: 8000000 INFO @ Wed, 08 Dec 2021 15:50:22: 2000000 INFO @ Wed, 08 Dec 2021 15:50:24: 9000000 INFO @ Wed, 08 Dec 2021 15:50:27: 3000000 INFO @ Wed, 08 Dec 2021 15:50:29: 10000000 INFO @ Wed, 08 Dec 2021 15:50:32: 4000000 INFO @ Wed, 08 Dec 2021 15:50:34: 11000000 INFO @ Wed, 08 Dec 2021 15:50:37: 5000000 INFO @ Wed, 08 Dec 2021 15:50:39: 12000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 15:50:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.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 @ Wed, 08 Dec 2021 15:50:41: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:50:41: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:50:42: #1 tag size is determined as 36 bps INFO @ Wed, 08 Dec 2021 15:50:42: #1 tag size = 36 INFO @ Wed, 08 Dec 2021 15:50:42: #1 total tags in treatment: 12472021 INFO @ Wed, 08 Dec 2021 15:50:42: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:50:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 15:50:42: 6000000 INFO @ Wed, 08 Dec 2021 15:50:42: #1 tags after filtering in treatment: 12472021 INFO @ Wed, 08 Dec 2021 15:50:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 15:50:42: #1 finished! INFO @ Wed, 08 Dec 2021 15:50:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:50:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:50:43: #2 number of paired peaks: 716 WARNING @ Wed, 08 Dec 2021 15:50:43: Fewer paired peaks (716) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 716 pairs to build model! INFO @ Wed, 08 Dec 2021 15:50:43: start model_add_line... INFO @ Wed, 08 Dec 2021 15:50:43: start X-correlation... INFO @ Wed, 08 Dec 2021 15:50:43: end of X-cor INFO @ Wed, 08 Dec 2021 15:50:43: #2 finished! INFO @ Wed, 08 Dec 2021 15:50:43: #2 predicted fragment length is 104 bps INFO @ Wed, 08 Dec 2021 15:50:43: #2 alternative fragment length(s) may be 104 bps INFO @ Wed, 08 Dec 2021 15:50:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.05_model.r INFO @ Wed, 08 Dec 2021 15:50:43: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:50:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:50:47: 7000000 INFO @ Wed, 08 Dec 2021 15:50:47: 1000000 INFO @ Wed, 08 Dec 2021 15:50:52: 8000000 INFO @ Wed, 08 Dec 2021 15:50:53: 2000000 INFO @ Wed, 08 Dec 2021 15:50:58: 9000000 INFO @ Wed, 08 Dec 2021 15:50:59: 3000000 INFO @ Wed, 08 Dec 2021 15:51:03: 10000000 INFO @ Wed, 08 Dec 2021 15:51:05: 4000000 INFO @ Wed, 08 Dec 2021 15:51:07: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:51:08: 11000000 INFO @ Wed, 08 Dec 2021 15:51:11: 5000000 INFO @ Wed, 08 Dec 2021 15:51:13: 12000000 INFO @ Wed, 08 Dec 2021 15:51:16: #1 tag size is determined as 36 bps INFO @ Wed, 08 Dec 2021 15:51:16: #1 tag size = 36 INFO @ Wed, 08 Dec 2021 15:51:16: #1 total tags in treatment: 12472021 INFO @ Wed, 08 Dec 2021 15:51:16: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:51:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 15:51:16: #1 tags after filtering in treatment: 12472021 INFO @ Wed, 08 Dec 2021 15:51:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 15:51:16: #1 finished! INFO @ Wed, 08 Dec 2021 15:51:16: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:51:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:51:17: 6000000 INFO @ Wed, 08 Dec 2021 15:51:17: #2 number of paired peaks: 716 WARNING @ Wed, 08 Dec 2021 15:51:17: Fewer paired peaks (716) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 716 pairs to build model! INFO @ Wed, 08 Dec 2021 15:51:17: start model_add_line... INFO @ Wed, 08 Dec 2021 15:51:17: start X-correlation... INFO @ Wed, 08 Dec 2021 15:51:17: end of X-cor INFO @ Wed, 08 Dec 2021 15:51:17: #2 finished! INFO @ Wed, 08 Dec 2021 15:51:17: #2 predicted fragment length is 104 bps INFO @ Wed, 08 Dec 2021 15:51:17: #2 alternative fragment length(s) may be 104 bps INFO @ Wed, 08 Dec 2021 15:51:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.10_model.r INFO @ Wed, 08 Dec 2021 15:51:17: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:51:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:51:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.05_peaks.xls INFO @ Wed, 08 Dec 2021 15:51:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:51:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.05_summits.bed INFO @ Wed, 08 Dec 2021 15:51:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6089 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:51:22: 7000000 INFO @ Wed, 08 Dec 2021 15:51:28: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 15:51:34: 9000000 INFO @ Wed, 08 Dec 2021 15:51:39: 10000000 INFO @ Wed, 08 Dec 2021 15:51:40: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:51:45: 11000000 INFO @ Wed, 08 Dec 2021 15:51:50: 12000000 INFO @ Wed, 08 Dec 2021 15:51:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.10_peaks.xls INFO @ Wed, 08 Dec 2021 15:51:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:51:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.10_summits.bed INFO @ Wed, 08 Dec 2021 15:51:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3616 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:51:53: #1 tag size is determined as 36 bps INFO @ Wed, 08 Dec 2021 15:51:53: #1 tag size = 36 INFO @ Wed, 08 Dec 2021 15:51:53: #1 total tags in treatment: 12472021 INFO @ Wed, 08 Dec 2021 15:51:53: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:51:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 15:51:53: #1 tags after filtering in treatment: 12472021 INFO @ Wed, 08 Dec 2021 15:51:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 15:51:53: #1 finished! INFO @ Wed, 08 Dec 2021 15:51:53: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:51:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:51:54: #2 number of paired peaks: 716 WARNING @ Wed, 08 Dec 2021 15:51:54: Fewer paired peaks (716) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 716 pairs to build model! INFO @ Wed, 08 Dec 2021 15:51:54: start model_add_line... INFO @ Wed, 08 Dec 2021 15:51:54: start X-correlation... INFO @ Wed, 08 Dec 2021 15:51:54: end of X-cor INFO @ Wed, 08 Dec 2021 15:51:54: #2 finished! INFO @ Wed, 08 Dec 2021 15:51:54: #2 predicted fragment length is 104 bps INFO @ Wed, 08 Dec 2021 15:51:54: #2 alternative fragment length(s) may be 104 bps INFO @ Wed, 08 Dec 2021 15:51:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.20_model.r INFO @ Wed, 08 Dec 2021 15:51:54: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:51:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 15:52:17: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:52:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.20_peaks.xls INFO @ Wed, 08 Dec 2021 15:52:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:52:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7665444/SRX7665444.20_summits.bed INFO @ Wed, 08 Dec 2021 15:52:29: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2008 records, 4 fields): 4 millis CompletedMACS2peakCalling