Job ID = 16434874 SRX = SRX10435528 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15770325 spots for SRR14060928/SRR14060928.sra Written 15770325 spots for SRR14060928/SRR14060928.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434942 ("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: 00:05:02 15770325 reads; of these: 15770325 (100.00%) were unpaired; of these: 2982183 (18.91%) aligned 0 times 10981272 (69.63%) aligned exactly 1 time 1806870 (11.46%) aligned >1 times 81.09% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 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] 2034169 / 12788142 = 0.1591 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 10:17:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.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 10:17:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:17:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:17:23: 1000000 INFO @ Tue, 02 Aug 2022 10:17:28: 2000000 INFO @ Tue, 02 Aug 2022 10:17:33: 3000000 INFO @ Tue, 02 Aug 2022 10:17:38: 4000000 INFO @ Tue, 02 Aug 2022 10:17:43: 5000000 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 10:17:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.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 10:17:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:17:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:17:48: 6000000 INFO @ Tue, 02 Aug 2022 10:17:52: 7000000 INFO @ Tue, 02 Aug 2022 10:17:53: 1000000 INFO @ Tue, 02 Aug 2022 10:17:57: 8000000 INFO @ Tue, 02 Aug 2022 10:17:59: 2000000 INFO @ Tue, 02 Aug 2022 10:18:02: 9000000 INFO @ Tue, 02 Aug 2022 10:18:05: 3000000 INFO @ Tue, 02 Aug 2022 10:18:07: 10000000 INFO @ Tue, 02 Aug 2022 10:18:11: 4000000 INFO @ Tue, 02 Aug 2022 10:18:11: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:18:11: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:18:11: #1 total tags in treatment: 10753973 INFO @ Tue, 02 Aug 2022 10:18:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:18:11: #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 10:18:11: #1 tags after filtering in treatment: 10753973 INFO @ Tue, 02 Aug 2022 10:18:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:18:11: #1 finished! INFO @ Tue, 02 Aug 2022 10:18:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:18:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:18:12: #2 number of paired peaks: 930 WARNING @ Tue, 02 Aug 2022 10:18:12: Fewer paired peaks (930) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 930 pairs to build model! INFO @ Tue, 02 Aug 2022 10:18:12: start model_add_line... INFO @ Tue, 02 Aug 2022 10:18:12: start X-correlation... INFO @ Tue, 02 Aug 2022 10:18:12: end of X-cor INFO @ Tue, 02 Aug 2022 10:18:12: #2 finished! INFO @ Tue, 02 Aug 2022 10:18:12: #2 predicted fragment length is 176 bps INFO @ Tue, 02 Aug 2022 10:18:12: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 02 Aug 2022 10:18:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.05_model.r INFO @ Tue, 02 Aug 2022 10:18:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:18:12: #3 Pre-compute pvalue-qvalue table... 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 10:18:16: 5000000 INFO @ Tue, 02 Aug 2022 10:18:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.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 10:18:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:18:17: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:18:21: 6000000 INFO @ Tue, 02 Aug 2022 10:18:22: 1000000 INFO @ Tue, 02 Aug 2022 10:18:26: 7000000 INFO @ Tue, 02 Aug 2022 10:18:28: 2000000 INFO @ Tue, 02 Aug 2022 10:18:31: 8000000 INFO @ Tue, 02 Aug 2022 10:18:33: 3000000 INFO @ Tue, 02 Aug 2022 10:18:35: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:18:36: 9000000 INFO @ Tue, 02 Aug 2022 10:18:38: 4000000 INFO @ Tue, 02 Aug 2022 10:18:41: 10000000 INFO @ Tue, 02 Aug 2022 10:18:43: 5000000 INFO @ Tue, 02 Aug 2022 10:18:44: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:18:44: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:18:44: #1 total tags in treatment: 10753973 INFO @ Tue, 02 Aug 2022 10:18:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:18:44: #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 10:18:45: #1 tags after filtering in treatment: 10753973 INFO @ Tue, 02 Aug 2022 10:18:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:18:45: #1 finished! INFO @ Tue, 02 Aug 2022 10:18:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:18:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:18:45: #2 number of paired peaks: 930 WARNING @ Tue, 02 Aug 2022 10:18:45: Fewer paired peaks (930) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 930 pairs to build model! INFO @ Tue, 02 Aug 2022 10:18:45: start model_add_line... INFO @ Tue, 02 Aug 2022 10:18:45: start X-correlation... INFO @ Tue, 02 Aug 2022 10:18:45: end of X-cor INFO @ Tue, 02 Aug 2022 10:18:45: #2 finished! INFO @ Tue, 02 Aug 2022 10:18:45: #2 predicted fragment length is 176 bps INFO @ Tue, 02 Aug 2022 10:18:45: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 02 Aug 2022 10:18:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.10_model.r INFO @ Tue, 02 Aug 2022 10:18:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:18:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:18:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:18:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:18:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.05_summits.bed INFO @ Tue, 02 Aug 2022 10:18:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4010 records, 4 fields): 45 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:18:48: 6000000 INFO @ Tue, 02 Aug 2022 10:18:52: 7000000 INFO @ Tue, 02 Aug 2022 10:18:57: 8000000 INFO @ Tue, 02 Aug 2022 10:19:02: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:19:07: 10000000 INFO @ Tue, 02 Aug 2022 10:19:08: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:19:10: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:19:10: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:19:10: #1 total tags in treatment: 10753973 INFO @ Tue, 02 Aug 2022 10:19:10: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:19:10: #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 10:19:11: #1 tags after filtering in treatment: 10753973 INFO @ Tue, 02 Aug 2022 10:19:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:19:11: #1 finished! INFO @ Tue, 02 Aug 2022 10:19:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:19:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:19:11: #2 number of paired peaks: 930 WARNING @ Tue, 02 Aug 2022 10:19:11: Fewer paired peaks (930) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 930 pairs to build model! INFO @ Tue, 02 Aug 2022 10:19:11: start model_add_line... INFO @ Tue, 02 Aug 2022 10:19:11: start X-correlation... INFO @ Tue, 02 Aug 2022 10:19:11: end of X-cor INFO @ Tue, 02 Aug 2022 10:19:11: #2 finished! INFO @ Tue, 02 Aug 2022 10:19:11: #2 predicted fragment length is 176 bps INFO @ Tue, 02 Aug 2022 10:19:11: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 02 Aug 2022 10:19:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.20_model.r INFO @ Tue, 02 Aug 2022 10:19:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:19:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:19:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:19:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:19:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.10_summits.bed INFO @ Tue, 02 Aug 2022 10:19:20: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2484 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:19:35: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:19:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:19:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:19:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435528/SRX10435528.20_summits.bed INFO @ Tue, 02 Aug 2022 10:19:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1438 records, 4 fields): 18 millis CompletedMACS2peakCalling