Job ID = 16432230 SRX = SRX15407772 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T00:31:55 prefetch.2.10.7: 1) Downloading 'SRR19348978'... 2022-08-02T00:31:55 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T00:33:01 prefetch.2.10.7: HTTPS download succeed 2022-08-02T00:33:01 prefetch.2.10.7: 1) 'SRR19348978' was downloaded successfully 2022-08-02T00:33:01 prefetch.2.10.7: 'SRR19348978' has 0 unresolved dependencies Read 31442701 spots for SRR19348978/SRR19348978.sra Written 31442701 spots for SRR19348978/SRR19348978.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434125 ("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: 00:08:53 31442701 reads; of these: 31442701 (100.00%) were unpaired; of these: 1502439 (4.78%) aligned 0 times 26119352 (83.07%) aligned exactly 1 time 3820910 (12.15%) aligned >1 times 95.22% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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 16 files... [bam_rmdupse_core] 7232217 / 29940262 = 0.2416 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 09:50:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.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, 02 Aug 2022 09:50:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:50:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:50:31: 1000000 INFO @ Tue, 02 Aug 2022 09:50:37: 2000000 INFO @ Tue, 02 Aug 2022 09:50:43: 3000000 INFO @ Tue, 02 Aug 2022 09:50:49: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 09:50:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.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, 02 Aug 2022 09:50:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:50:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:50:55: 5000000 INFO @ Tue, 02 Aug 2022 09:51:01: 6000000 INFO @ Tue, 02 Aug 2022 09:51:01: 1000000 INFO @ Tue, 02 Aug 2022 09:51:08: 7000000 INFO @ Tue, 02 Aug 2022 09:51:08: 2000000 INFO @ Tue, 02 Aug 2022 09:51:14: 8000000 INFO @ Tue, 02 Aug 2022 09:51:14: 3000000 INFO @ Tue, 02 Aug 2022 09:51:20: 9000000 INFO @ Tue, 02 Aug 2022 09:51:21: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 09:51:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.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, 02 Aug 2022 09:51:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:51:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:51:26: 10000000 INFO @ Tue, 02 Aug 2022 09:51:27: 5000000 INFO @ Tue, 02 Aug 2022 09:51:31: 1000000 INFO @ Tue, 02 Aug 2022 09:51:33: 11000000 INFO @ Tue, 02 Aug 2022 09:51:34: 6000000 INFO @ Tue, 02 Aug 2022 09:51:38: 2000000 INFO @ Tue, 02 Aug 2022 09:51:39: 12000000 INFO @ Tue, 02 Aug 2022 09:51:40: 7000000 INFO @ Tue, 02 Aug 2022 09:51:44: 3000000 INFO @ Tue, 02 Aug 2022 09:51:45: 13000000 INFO @ Tue, 02 Aug 2022 09:51:46: 8000000 INFO @ Tue, 02 Aug 2022 09:51:50: 4000000 INFO @ Tue, 02 Aug 2022 09:51:51: 14000000 INFO @ Tue, 02 Aug 2022 09:51:52: 9000000 INFO @ Tue, 02 Aug 2022 09:51:57: 5000000 INFO @ Tue, 02 Aug 2022 09:51:57: 15000000 INFO @ Tue, 02 Aug 2022 09:51:59: 10000000 INFO @ Tue, 02 Aug 2022 09:52:03: 6000000 INFO @ Tue, 02 Aug 2022 09:52:03: 16000000 INFO @ Tue, 02 Aug 2022 09:52:05: 11000000 INFO @ Tue, 02 Aug 2022 09:52:09: 7000000 INFO @ Tue, 02 Aug 2022 09:52:09: 17000000 INFO @ Tue, 02 Aug 2022 09:52:11: 12000000 INFO @ Tue, 02 Aug 2022 09:52:15: 8000000 INFO @ Tue, 02 Aug 2022 09:52:15: 18000000 INFO @ Tue, 02 Aug 2022 09:52:17: 13000000 INFO @ Tue, 02 Aug 2022 09:52:21: 19000000 INFO @ Tue, 02 Aug 2022 09:52:21: 9000000 INFO @ Tue, 02 Aug 2022 09:52:23: 14000000 INFO @ Tue, 02 Aug 2022 09:52:28: 20000000 INFO @ Tue, 02 Aug 2022 09:52:28: 10000000 INFO @ Tue, 02 Aug 2022 09:52:30: 15000000 INFO @ Tue, 02 Aug 2022 09:52:34: 21000000 INFO @ Tue, 02 Aug 2022 09:52:34: 11000000 INFO @ Tue, 02 Aug 2022 09:52:36: 16000000 INFO @ Tue, 02 Aug 2022 09:52:40: 22000000 INFO @ Tue, 02 Aug 2022 09:52:41: 12000000 INFO @ Tue, 02 Aug 2022 09:52:42: 17000000 INFO @ Tue, 02 Aug 2022 09:52:44: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:52:44: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:52:44: #1 total tags in treatment: 22708045 INFO @ Tue, 02 Aug 2022 09:52:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:52:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 09:52:45: #1 tags after filtering in treatment: 22708045 INFO @ Tue, 02 Aug 2022 09:52:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:52:45: #1 finished! INFO @ Tue, 02 Aug 2022 09:52:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:52:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:52:46: #2 number of paired peaks: 448 WARNING @ Tue, 02 Aug 2022 09:52:46: Fewer paired peaks (448) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 448 pairs to build model! INFO @ Tue, 02 Aug 2022 09:52:46: start model_add_line... INFO @ Tue, 02 Aug 2022 09:52:46: start X-correlation... INFO @ Tue, 02 Aug 2022 09:52:46: end of X-cor INFO @ Tue, 02 Aug 2022 09:52:46: #2 finished! INFO @ Tue, 02 Aug 2022 09:52:46: #2 predicted fragment length is 160 bps INFO @ Tue, 02 Aug 2022 09:52:46: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 02 Aug 2022 09:52:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.05_model.r INFO @ Tue, 02 Aug 2022 09:52:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:52:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:52:47: 13000000 INFO @ Tue, 02 Aug 2022 09:52:48: 18000000 INFO @ Tue, 02 Aug 2022 09:52:53: 14000000 INFO @ Tue, 02 Aug 2022 09:52:54: 19000000 INFO @ Tue, 02 Aug 2022 09:52:59: 15000000 INFO @ Tue, 02 Aug 2022 09:53:01: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:53:05: 16000000 INFO @ Tue, 02 Aug 2022 09:53:07: 21000000 INFO @ Tue, 02 Aug 2022 09:53:12: 17000000 INFO @ Tue, 02 Aug 2022 09:53:13: 22000000 INFO @ Tue, 02 Aug 2022 09:53:18: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:53:18: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:53:18: #1 total tags in treatment: 22708045 INFO @ Tue, 02 Aug 2022 09:53:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:53:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 09:53:18: 18000000 INFO @ Tue, 02 Aug 2022 09:53:18: #1 tags after filtering in treatment: 22708045 INFO @ Tue, 02 Aug 2022 09:53:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:53:18: #1 finished! INFO @ Tue, 02 Aug 2022 09:53:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:53:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:53:19: #2 number of paired peaks: 448 WARNING @ Tue, 02 Aug 2022 09:53:19: Fewer paired peaks (448) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 448 pairs to build model! INFO @ Tue, 02 Aug 2022 09:53:19: start model_add_line... INFO @ Tue, 02 Aug 2022 09:53:20: start X-correlation... INFO @ Tue, 02 Aug 2022 09:53:20: end of X-cor INFO @ Tue, 02 Aug 2022 09:53:20: #2 finished! INFO @ Tue, 02 Aug 2022 09:53:20: #2 predicted fragment length is 160 bps INFO @ Tue, 02 Aug 2022 09:53:20: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 02 Aug 2022 09:53:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.10_model.r INFO @ Tue, 02 Aug 2022 09:53:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:53:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:53:24: 19000000 INFO @ Tue, 02 Aug 2022 09:53:29: 20000000 INFO @ Tue, 02 Aug 2022 09:53:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:53:34: 21000000 INFO @ Tue, 02 Aug 2022 09:53:40: 22000000 INFO @ Tue, 02 Aug 2022 09:53:44: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:53:44: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:53:44: #1 total tags in treatment: 22708045 INFO @ Tue, 02 Aug 2022 09:53:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:53:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 09:53:44: #1 tags after filtering in treatment: 22708045 INFO @ Tue, 02 Aug 2022 09:53:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:53:44: #1 finished! INFO @ Tue, 02 Aug 2022 09:53:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:53:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:53:45: #2 number of paired peaks: 448 WARNING @ Tue, 02 Aug 2022 09:53:45: Fewer paired peaks (448) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 448 pairs to build model! INFO @ Tue, 02 Aug 2022 09:53:45: start model_add_line... INFO @ Tue, 02 Aug 2022 09:53:45: start X-correlation... INFO @ Tue, 02 Aug 2022 09:53:45: end of X-cor INFO @ Tue, 02 Aug 2022 09:53:45: #2 finished! INFO @ Tue, 02 Aug 2022 09:53:45: #2 predicted fragment length is 160 bps INFO @ Tue, 02 Aug 2022 09:53:45: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 02 Aug 2022 09:53:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.20_model.r INFO @ Tue, 02 Aug 2022 09:53:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:53:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:53:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:53:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:53:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.05_summits.bed INFO @ Tue, 02 Aug 2022 09:53:49: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (12483 records, 4 fields): 63 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:54:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:54:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:54:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:54:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.10_summits.bed INFO @ Tue, 02 Aug 2022 09:54:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (9331 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:54:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:54:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:54:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:54:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407772/SRX15407772.20_summits.bed INFO @ Tue, 02 Aug 2022 09:54:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6078 records, 4 fields): 21 millis CompletedMACS2peakCalling