Job ID = 16435310 SRX = SRX13110342 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:42:15 prefetch.2.10.7: 1) Downloading 'SRR16918012'... 2022-08-02T01:42:15 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:42:43 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:42:44 prefetch.2.10.7: 'SRR16918012' is valid 2022-08-02T01:42:44 prefetch.2.10.7: 1) 'SRR16918012' was downloaded successfully 2022-08-02T01:42:44 prefetch.2.10.7: 'SRR16918012' has 0 unresolved dependencies Read 17870653 spots for SRR16918012/SRR16918012.sra Written 17870653 spots for SRR16918012/SRR16918012.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435599 ("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: 00:05:00 17870653 reads; of these: 17870653 (100.00%) were unpaired; of these: 4231954 (23.68%) aligned 0 times 11667383 (65.29%) aligned exactly 1 time 1971316 (11.03%) aligned >1 times 76.32% overall alignment rate Time searching: 00:05:00 Overall time: 00:05:00 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] 1977573 / 13638699 = 0.1450 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 10:52:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.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 10:52:06: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:52:06: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:52:12: 1000000 INFO @ Tue, 02 Aug 2022 10:52:18: 2000000 INFO @ Tue, 02 Aug 2022 10:52:24: 3000000 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 10:52:34: 4000000 INFO @ Tue, 02 Aug 2022 10:52:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.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 10:52:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:52:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:52:40: 5000000 INFO @ Tue, 02 Aug 2022 10:52:42: 1000000 INFO @ Tue, 02 Aug 2022 10:52:46: 6000000 INFO @ Tue, 02 Aug 2022 10:52:48: 2000000 INFO @ Tue, 02 Aug 2022 10:52:52: 7000000 INFO @ Tue, 02 Aug 2022 10:52:54: 3000000 INFO @ Tue, 02 Aug 2022 10:52:58: 8000000 INFO @ Tue, 02 Aug 2022 10:53:00: 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 10:53:04: 9000000 INFO @ Tue, 02 Aug 2022 10:53:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.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 10:53:06: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:53:06: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:53:06: 5000000 INFO @ Tue, 02 Aug 2022 10:53:10: 10000000 INFO @ Tue, 02 Aug 2022 10:53:11: 1000000 INFO @ Tue, 02 Aug 2022 10:53:11: 6000000 INFO @ Tue, 02 Aug 2022 10:53:16: 11000000 INFO @ Tue, 02 Aug 2022 10:53:17: 2000000 INFO @ Tue, 02 Aug 2022 10:53:17: 7000000 INFO @ Tue, 02 Aug 2022 10:53:20: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:53:20: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:53:20: #1 total tags in treatment: 11661126 INFO @ Tue, 02 Aug 2022 10:53:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:53:20: #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 10:53:20: #1 tags after filtering in treatment: 11661126 INFO @ Tue, 02 Aug 2022 10:53:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:53:20: #1 finished! INFO @ Tue, 02 Aug 2022 10:53:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:53:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:53:21: #2 number of paired peaks: 776 WARNING @ Tue, 02 Aug 2022 10:53:21: Fewer paired peaks (776) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 776 pairs to build model! INFO @ Tue, 02 Aug 2022 10:53:21: start model_add_line... INFO @ Tue, 02 Aug 2022 10:53:21: start X-correlation... INFO @ Tue, 02 Aug 2022 10:53:21: end of X-cor INFO @ Tue, 02 Aug 2022 10:53:21: #2 finished! INFO @ Tue, 02 Aug 2022 10:53:21: #2 predicted fragment length is 193 bps INFO @ Tue, 02 Aug 2022 10:53:21: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 02 Aug 2022 10:53:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.05_model.r INFO @ Tue, 02 Aug 2022 10:53:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:53:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:53:22: 3000000 INFO @ Tue, 02 Aug 2022 10:53:23: 8000000 INFO @ Tue, 02 Aug 2022 10:53:28: 4000000 INFO @ Tue, 02 Aug 2022 10:53:28: 9000000 INFO @ Tue, 02 Aug 2022 10:53:33: 5000000 INFO @ Tue, 02 Aug 2022 10:53:34: 10000000 INFO @ Tue, 02 Aug 2022 10:53:39: 6000000 INFO @ Tue, 02 Aug 2022 10:53:40: 11000000 INFO @ Tue, 02 Aug 2022 10:53:43: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:53:43: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:53:43: #1 total tags in treatment: 11661126 INFO @ Tue, 02 Aug 2022 10:53:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:53:43: #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 10:53:44: #1 tags after filtering in treatment: 11661126 INFO @ Tue, 02 Aug 2022 10:53:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:53:44: #1 finished! INFO @ Tue, 02 Aug 2022 10:53:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:53:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:53:44: 7000000 INFO @ Tue, 02 Aug 2022 10:53:44: #2 number of paired peaks: 776 WARNING @ Tue, 02 Aug 2022 10:53:44: Fewer paired peaks (776) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 776 pairs to build model! INFO @ Tue, 02 Aug 2022 10:53:44: start model_add_line... INFO @ Tue, 02 Aug 2022 10:53:45: start X-correlation... INFO @ Tue, 02 Aug 2022 10:53:45: end of X-cor INFO @ Tue, 02 Aug 2022 10:53:45: #2 finished! INFO @ Tue, 02 Aug 2022 10:53:45: #2 predicted fragment length is 193 bps INFO @ Tue, 02 Aug 2022 10:53:45: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 02 Aug 2022 10:53:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.10_model.r INFO @ Tue, 02 Aug 2022 10:53:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:53:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:53:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:53:50: 8000000 INFO @ Tue, 02 Aug 2022 10:53:55: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:54:01: 10000000 INFO @ Tue, 02 Aug 2022 10:54:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:54:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:54:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.05_summits.bed INFO @ Tue, 02 Aug 2022 10:54:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6266 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:54:06: 11000000 INFO @ Tue, 02 Aug 2022 10:54:10: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:54:10: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:54:10: #1 total tags in treatment: 11661126 INFO @ Tue, 02 Aug 2022 10:54:10: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:54:10: #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 10:54:10: #1 tags after filtering in treatment: 11661126 INFO @ Tue, 02 Aug 2022 10:54:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:54:10: #1 finished! INFO @ Tue, 02 Aug 2022 10:54:10: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:54:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:54:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:54:11: #2 number of paired peaks: 776 WARNING @ Tue, 02 Aug 2022 10:54:11: Fewer paired peaks (776) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 776 pairs to build model! INFO @ Tue, 02 Aug 2022 10:54:11: start model_add_line... INFO @ Tue, 02 Aug 2022 10:54:11: start X-correlation... INFO @ Tue, 02 Aug 2022 10:54:11: end of X-cor INFO @ Tue, 02 Aug 2022 10:54:11: #2 finished! INFO @ Tue, 02 Aug 2022 10:54:11: #2 predicted fragment length is 193 bps INFO @ Tue, 02 Aug 2022 10:54:11: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 02 Aug 2022 10:54:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.20_model.r INFO @ Tue, 02 Aug 2022 10:54:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:54:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:54:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:54:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:54:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.10_summits.bed INFO @ Tue, 02 Aug 2022 10:54:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4470 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:54:38: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:54:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:54:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:54:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110342/SRX13110342.20_summits.bed INFO @ Tue, 02 Aug 2022 10:54:51: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2833 records, 4 fields): 21 millis CompletedMACS2peakCalling