Job ID = 16432292 SRX = SRX15407776 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T00:32:10 prefetch.2.10.7: 1) Downloading 'SRR19348975'... 2022-08-02T00:32:10 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T00:33:00 prefetch.2.10.7: HTTPS download succeed 2022-08-02T00:33:01 prefetch.2.10.7: 'SRR19348975' is valid 2022-08-02T00:33:01 prefetch.2.10.7: 1) 'SRR19348975' was downloaded successfully 2022-08-02T00:33:01 prefetch.2.10.7: 'SRR19348975' has 0 unresolved dependencies Read 18679526 spots for SRR19348975/SRR19348975.sra Written 18679526 spots for SRR19348975/SRR19348975.sra fastq に変換しました。 bowtie でマッピング中... Your job 16433605 ("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: 00:05:04 18679526 reads; of these: 18679526 (100.00%) were unpaired; of these: 3697255 (19.79%) aligned 0 times 12815507 (68.61%) aligned exactly 1 time 2166764 (11.60%) aligned >1 times 80.21% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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] 3225364 / 14982271 = 0.2153 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 09:42:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.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 09:42:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:42:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:43:05: 1000000 INFO @ Tue, 02 Aug 2022 09:43:11: 2000000 INFO @ Tue, 02 Aug 2022 09:43:17: 3000000 INFO @ Tue, 02 Aug 2022 09:43:24: 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 09:43:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.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 09:43:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:43:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:43:30: 5000000 INFO @ Tue, 02 Aug 2022 09:43:34: 1000000 INFO @ Tue, 02 Aug 2022 09:43:37: 6000000 INFO @ Tue, 02 Aug 2022 09:43:41: 2000000 INFO @ Tue, 02 Aug 2022 09:43:43: 7000000 INFO @ Tue, 02 Aug 2022 09:43:47: 3000000 INFO @ Tue, 02 Aug 2022 09:43:50: 8000000 INFO @ Tue, 02 Aug 2022 09:43:53: 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 09:43:57: 9000000 INFO @ Tue, 02 Aug 2022 09:43:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.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 09:43:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:43:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:43:59: 5000000 INFO @ Tue, 02 Aug 2022 09:44:04: 10000000 INFO @ Tue, 02 Aug 2022 09:44:05: 1000000 INFO @ Tue, 02 Aug 2022 09:44:05: 6000000 INFO @ Tue, 02 Aug 2022 09:44:10: 11000000 INFO @ Tue, 02 Aug 2022 09:44:11: 7000000 INFO @ Tue, 02 Aug 2022 09:44:12: 2000000 INFO @ Tue, 02 Aug 2022 09:44:15: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:44:15: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:44:15: #1 total tags in treatment: 11756907 INFO @ Tue, 02 Aug 2022 09:44:15: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:44:15: #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 09:44:16: #1 tags after filtering in treatment: 11756907 INFO @ Tue, 02 Aug 2022 09:44:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:44:16: #1 finished! INFO @ Tue, 02 Aug 2022 09:44:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:44:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:44:16: #2 number of paired peaks: 800 WARNING @ Tue, 02 Aug 2022 09:44:16: Fewer paired peaks (800) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 800 pairs to build model! INFO @ Tue, 02 Aug 2022 09:44:16: start model_add_line... INFO @ Tue, 02 Aug 2022 09:44:16: start X-correlation... INFO @ Tue, 02 Aug 2022 09:44:16: end of X-cor INFO @ Tue, 02 Aug 2022 09:44:16: #2 finished! INFO @ Tue, 02 Aug 2022 09:44:16: #2 predicted fragment length is 165 bps INFO @ Tue, 02 Aug 2022 09:44:16: #2 alternative fragment length(s) may be 165 bps INFO @ Tue, 02 Aug 2022 09:44:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.05_model.r INFO @ Tue, 02 Aug 2022 09:44:16: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:44:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:44:17: 8000000 INFO @ Tue, 02 Aug 2022 09:44:19: 3000000 INFO @ Tue, 02 Aug 2022 09:44:23: 9000000 INFO @ Tue, 02 Aug 2022 09:44:25: 4000000 INFO @ Tue, 02 Aug 2022 09:44:29: 10000000 INFO @ Tue, 02 Aug 2022 09:44:32: 5000000 INFO @ Tue, 02 Aug 2022 09:44:35: 11000000 INFO @ Tue, 02 Aug 2022 09:44:39: 6000000 INFO @ Tue, 02 Aug 2022 09:44:40: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:44:40: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:44:40: #1 total tags in treatment: 11756907 INFO @ Tue, 02 Aug 2022 09:44:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:44:40: #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 09:44:40: #1 tags after filtering in treatment: 11756907 INFO @ Tue, 02 Aug 2022 09:44:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:44:40: #1 finished! INFO @ Tue, 02 Aug 2022 09:44:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:44:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:44:41: #2 number of paired peaks: 800 WARNING @ Tue, 02 Aug 2022 09:44:41: Fewer paired peaks (800) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 800 pairs to build model! INFO @ Tue, 02 Aug 2022 09:44:41: start model_add_line... INFO @ Tue, 02 Aug 2022 09:44:41: start X-correlation... INFO @ Tue, 02 Aug 2022 09:44:41: end of X-cor INFO @ Tue, 02 Aug 2022 09:44:41: #2 finished! INFO @ Tue, 02 Aug 2022 09:44:41: #2 predicted fragment length is 165 bps INFO @ Tue, 02 Aug 2022 09:44:41: #2 alternative fragment length(s) may be 165 bps INFO @ Tue, 02 Aug 2022 09:44:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.10_model.r INFO @ Tue, 02 Aug 2022 09:44:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:44:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:44:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:44:45: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:44:52: 8000000 INFO @ Tue, 02 Aug 2022 09:44:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:44:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:44:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.05_summits.bed INFO @ Tue, 02 Aug 2022 09:44:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1874 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:44:58: 9000000 INFO @ Tue, 02 Aug 2022 09:45:04: 10000000 INFO @ Tue, 02 Aug 2022 09:45:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:45:10: 11000000 INFO @ Tue, 02 Aug 2022 09:45:15: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:45:15: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:45:15: #1 total tags in treatment: 11756907 INFO @ Tue, 02 Aug 2022 09:45:15: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:45:15: #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 09:45:15: #1 tags after filtering in treatment: 11756907 INFO @ Tue, 02 Aug 2022 09:45:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:45:15: #1 finished! INFO @ Tue, 02 Aug 2022 09:45:15: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:45:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:45:16: #2 number of paired peaks: 800 WARNING @ Tue, 02 Aug 2022 09:45:16: Fewer paired peaks (800) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 800 pairs to build model! INFO @ Tue, 02 Aug 2022 09:45:16: start model_add_line... INFO @ Tue, 02 Aug 2022 09:45:16: start X-correlation... INFO @ Tue, 02 Aug 2022 09:45:16: end of X-cor INFO @ Tue, 02 Aug 2022 09:45:16: #2 finished! INFO @ Tue, 02 Aug 2022 09:45:16: #2 predicted fragment length is 165 bps INFO @ Tue, 02 Aug 2022 09:45:16: #2 alternative fragment length(s) may be 165 bps INFO @ Tue, 02 Aug 2022 09:45:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.20_model.r INFO @ Tue, 02 Aug 2022 09:45:16: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:45:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:45:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:45:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:45:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.10_summits.bed INFO @ Tue, 02 Aug 2022 09:45:19: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1302 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:45:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:45:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:45:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:45:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407776/SRX15407776.20_summits.bed INFO @ Tue, 02 Aug 2022 09:45:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (865 records, 4 fields): 17 millis CompletedMACS2peakCalling