Job ID = 10165694 SRX = SRX8832065 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20163291 spots for SRR12332007/SRR12332007.sra Written 20163291 spots for SRR12332007/SRR12332007.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165881 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:20 20163291 reads; of these: 20163291 (100.00%) were unpaired; of these: 303262 (1.50%) aligned 0 times 16862384 (83.63%) aligned exactly 1 time 2997645 (14.87%) aligned >1 times 98.50% overall alignment rate Time searching: 00:04:21 Overall time: 00:04:21 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 12 files... [bam_rmdupse_core] 3144640 / 19860029 = 0.1583 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 19:46:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.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 19:46:20: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:46:20: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:46:27: 1000000 INFO @ Thu, 08 Oct 2020 19:46:34: 2000000 INFO @ Thu, 08 Oct 2020 19:46:42: 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 @ Thu, 08 Oct 2020 19:46:49: 4000000 INFO @ Thu, 08 Oct 2020 19:46:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.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 19:46:50: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:46:50: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:46:57: 5000000 INFO @ Thu, 08 Oct 2020 19:46:58: 1000000 INFO @ Thu, 08 Oct 2020 19:47:04: 6000000 INFO @ Thu, 08 Oct 2020 19:47:06: 2000000 INFO @ Thu, 08 Oct 2020 19:47:12: 7000000 INFO @ Thu, 08 Oct 2020 19:47:13: 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 @ Thu, 08 Oct 2020 19:47:19: 8000000 INFO @ Thu, 08 Oct 2020 19:47:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.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 19:47:20: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:47:20: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:47:21: 4000000 INFO @ Thu, 08 Oct 2020 19:47:27: 9000000 INFO @ Thu, 08 Oct 2020 19:47:28: 1000000 INFO @ Thu, 08 Oct 2020 19:47:29: 5000000 INFO @ Thu, 08 Oct 2020 19:47:35: 10000000 INFO @ Thu, 08 Oct 2020 19:47:35: 2000000 INFO @ Thu, 08 Oct 2020 19:47:36: 6000000 INFO @ Thu, 08 Oct 2020 19:47:42: 11000000 INFO @ Thu, 08 Oct 2020 19:47:43: 3000000 INFO @ Thu, 08 Oct 2020 19:47:44: 7000000 INFO @ Thu, 08 Oct 2020 19:47:50: 12000000 INFO @ Thu, 08 Oct 2020 19:47:51: 4000000 INFO @ Thu, 08 Oct 2020 19:47:52: 8000000 INFO @ Thu, 08 Oct 2020 19:47:58: 13000000 INFO @ Thu, 08 Oct 2020 19:47:59: 5000000 INFO @ Thu, 08 Oct 2020 19:48:00: 9000000 INFO @ Thu, 08 Oct 2020 19:48:05: 14000000 INFO @ Thu, 08 Oct 2020 19:48:06: 6000000 INFO @ Thu, 08 Oct 2020 19:48:07: 10000000 INFO @ Thu, 08 Oct 2020 19:48:12: 15000000 INFO @ Thu, 08 Oct 2020 19:48:13: 7000000 INFO @ Thu, 08 Oct 2020 19:48:14: 11000000 INFO @ Thu, 08 Oct 2020 19:48:19: 16000000 INFO @ Thu, 08 Oct 2020 19:48:21: 8000000 INFO @ Thu, 08 Oct 2020 19:48:22: 12000000 INFO @ Thu, 08 Oct 2020 19:48:25: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 19:48:25: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 19:48:25: #1 total tags in treatment: 16715389 INFO @ Thu, 08 Oct 2020 19:48:25: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:48:25: #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 19:48:25: #1 tags after filtering in treatment: 16715389 INFO @ Thu, 08 Oct 2020 19:48:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:48:25: #1 finished! INFO @ Thu, 08 Oct 2020 19:48:25: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:48:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:48:26: #2 number of paired peaks: 199 WARNING @ Thu, 08 Oct 2020 19:48:26: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Thu, 08 Oct 2020 19:48:26: start model_add_line... INFO @ Thu, 08 Oct 2020 19:48:26: start X-correlation... INFO @ Thu, 08 Oct 2020 19:48:26: end of X-cor INFO @ Thu, 08 Oct 2020 19:48:26: #2 finished! INFO @ Thu, 08 Oct 2020 19:48:26: #2 predicted fragment length is 122 bps INFO @ Thu, 08 Oct 2020 19:48:26: #2 alternative fragment length(s) may be 3,67,88,122 bps INFO @ Thu, 08 Oct 2020 19:48:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.05_model.r INFO @ Thu, 08 Oct 2020 19:48:26: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:48:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:48:28: 9000000 INFO @ Thu, 08 Oct 2020 19:48:29: 13000000 INFO @ Thu, 08 Oct 2020 19:48:35: 10000000 INFO @ Thu, 08 Oct 2020 19:48:36: 14000000 INFO @ Thu, 08 Oct 2020 19:48:41: 11000000 INFO @ Thu, 08 Oct 2020 19:48:42: 15000000 INFO @ Thu, 08 Oct 2020 19:48:48: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:48:49: 16000000 INFO @ Thu, 08 Oct 2020 19:48:53: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 19:48:53: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 19:48:53: #1 total tags in treatment: 16715389 INFO @ Thu, 08 Oct 2020 19:48:53: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:48:53: #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 19:48:54: #1 tags after filtering in treatment: 16715389 INFO @ Thu, 08 Oct 2020 19:48:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:48:54: #1 finished! INFO @ Thu, 08 Oct 2020 19:48:54: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:48:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:48:54: 13000000 INFO @ Thu, 08 Oct 2020 19:48:55: #2 number of paired peaks: 199 WARNING @ Thu, 08 Oct 2020 19:48:55: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Thu, 08 Oct 2020 19:48:55: start model_add_line... INFO @ Thu, 08 Oct 2020 19:48:55: start X-correlation... INFO @ Thu, 08 Oct 2020 19:48:55: end of X-cor INFO @ Thu, 08 Oct 2020 19:48:55: #2 finished! INFO @ Thu, 08 Oct 2020 19:48:55: #2 predicted fragment length is 122 bps INFO @ Thu, 08 Oct 2020 19:48:55: #2 alternative fragment length(s) may be 3,67,88,122 bps INFO @ Thu, 08 Oct 2020 19:48:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.10_model.r INFO @ Thu, 08 Oct 2020 19:48:55: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:48:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:48:59: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:49:00: 14000000 INFO @ Thu, 08 Oct 2020 19:49:06: 15000000 INFO @ Thu, 08 Oct 2020 19:49:12: 16000000 INFO @ Thu, 08 Oct 2020 19:49:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:49:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:49:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.05_summits.bed INFO @ Thu, 08 Oct 2020 19:49:16: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7499 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:49:17: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 19:49:17: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 19:49:17: #1 total tags in treatment: 16715389 INFO @ Thu, 08 Oct 2020 19:49:17: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:49:17: #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 19:49:17: #1 tags after filtering in treatment: 16715389 INFO @ Thu, 08 Oct 2020 19:49:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:49:17: #1 finished! INFO @ Thu, 08 Oct 2020 19:49:17: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:49:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:49:18: #2 number of paired peaks: 199 WARNING @ Thu, 08 Oct 2020 19:49:18: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Thu, 08 Oct 2020 19:49:18: start model_add_line... INFO @ Thu, 08 Oct 2020 19:49:18: start X-correlation... INFO @ Thu, 08 Oct 2020 19:49:18: end of X-cor INFO @ Thu, 08 Oct 2020 19:49:18: #2 finished! INFO @ Thu, 08 Oct 2020 19:49:18: #2 predicted fragment length is 122 bps INFO @ Thu, 08 Oct 2020 19:49:18: #2 alternative fragment length(s) may be 3,67,88,122 bps INFO @ Thu, 08 Oct 2020 19:49:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.20_model.r INFO @ Thu, 08 Oct 2020 19:49:18: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:49:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:49:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:49:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:49:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:49:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.10_summits.bed INFO @ Thu, 08 Oct 2020 19:49:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4226 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:49:50: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:50:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:50:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:50:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832065/SRX8832065.20_summits.bed INFO @ Thu, 08 Oct 2020 19:50:06: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1390 records, 4 fields): 3 millis CompletedMACS2peakCalling