Job ID = 16434922 SRX = SRX10435527 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:42 16193821 reads; of these: 16193821 (100.00%) were unpaired; of these: 2091707 (12.92%) aligned 0 times 12115197 (74.81%) aligned exactly 1 time 1986917 (12.27%) aligned >1 times 87.08% overall alignment rate Time searching: 00:04:43 Overall time: 00:04:43 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] 2198142 / 14102114 = 0.1559 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 10:23:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.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 10:23:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:23:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:23:14: 1000000 INFO @ Tue, 02 Aug 2022 10:23:22: 2000000 INFO @ Tue, 02 Aug 2022 10:23:30: 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 10:23:37: 4000000 INFO @ Tue, 02 Aug 2022 10:23:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.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 10:23:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:23:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:23:44: 1000000 INFO @ Tue, 02 Aug 2022 10:23:45: 5000000 INFO @ Tue, 02 Aug 2022 10:23:51: 2000000 INFO @ Tue, 02 Aug 2022 10:23:53: 6000000 INFO @ Tue, 02 Aug 2022 10:23:58: 3000000 INFO @ Tue, 02 Aug 2022 10:24:01: 7000000 BedGraph に変換中... INFO @ Tue, 02 Aug 2022 10:24:05: 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 10:24:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.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 10:24:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:24:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:24:09: 8000000 INFO @ Tue, 02 Aug 2022 10:24:12: 5000000 INFO @ Tue, 02 Aug 2022 10:24:15: 1000000 INFO @ Tue, 02 Aug 2022 10:24:17: 9000000 INFO @ Tue, 02 Aug 2022 10:24:19: 6000000 INFO @ Tue, 02 Aug 2022 10:24:23: 2000000 INFO @ Tue, 02 Aug 2022 10:24:25: 10000000 INFO @ Tue, 02 Aug 2022 10:24:26: 7000000 INFO @ Tue, 02 Aug 2022 10:24:31: 3000000 INFO @ Tue, 02 Aug 2022 10:24:33: 11000000 INFO @ Tue, 02 Aug 2022 10:24:34: 8000000 INFO @ Tue, 02 Aug 2022 10:24:38: 4000000 INFO @ Tue, 02 Aug 2022 10:24:40: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:24:40: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:24:40: #1 total tags in treatment: 11903972 INFO @ Tue, 02 Aug 2022 10:24:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:24:40: #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 10:24:40: #1 tags after filtering in treatment: 11903972 INFO @ Tue, 02 Aug 2022 10:24:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:24:40: #1 finished! INFO @ Tue, 02 Aug 2022 10:24:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:24:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:24:41: 9000000 INFO @ Tue, 02 Aug 2022 10:24:41: #2 number of paired peaks: 810 WARNING @ Tue, 02 Aug 2022 10:24:41: Fewer paired peaks (810) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 810 pairs to build model! INFO @ Tue, 02 Aug 2022 10:24:41: start model_add_line... INFO @ Tue, 02 Aug 2022 10:24:41: start X-correlation... INFO @ Tue, 02 Aug 2022 10:24:41: end of X-cor INFO @ Tue, 02 Aug 2022 10:24:41: #2 finished! INFO @ Tue, 02 Aug 2022 10:24:41: #2 predicted fragment length is 165 bps INFO @ Tue, 02 Aug 2022 10:24:41: #2 alternative fragment length(s) may be 165 bps INFO @ Tue, 02 Aug 2022 10:24:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.05_model.r INFO @ Tue, 02 Aug 2022 10:24:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:24:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:24:47: 5000000 INFO @ Tue, 02 Aug 2022 10:24:47: 10000000 INFO @ Tue, 02 Aug 2022 10:24:55: 11000000 INFO @ Tue, 02 Aug 2022 10:24:55: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:25:01: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:25:01: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:25:01: #1 total tags in treatment: 11903972 INFO @ Tue, 02 Aug 2022 10:25:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:25:01: #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 10:25:01: #1 tags after filtering in treatment: 11903972 INFO @ Tue, 02 Aug 2022 10:25:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:25:01: #1 finished! INFO @ Tue, 02 Aug 2022 10:25:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:25:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:25:02: #2 number of paired peaks: 810 WARNING @ Tue, 02 Aug 2022 10:25:02: Fewer paired peaks (810) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 810 pairs to build model! INFO @ Tue, 02 Aug 2022 10:25:02: start model_add_line... INFO @ Tue, 02 Aug 2022 10:25:02: start X-correlation... INFO @ Tue, 02 Aug 2022 10:25:02: end of X-cor INFO @ Tue, 02 Aug 2022 10:25:02: #2 finished! INFO @ Tue, 02 Aug 2022 10:25:02: #2 predicted fragment length is 165 bps INFO @ Tue, 02 Aug 2022 10:25:02: #2 alternative fragment length(s) may be 165 bps INFO @ Tue, 02 Aug 2022 10:25:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.10_model.r INFO @ Tue, 02 Aug 2022 10:25:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:25:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:25:03: 7000000 INFO @ Tue, 02 Aug 2022 10:25:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:25:11: 8000000 INFO @ Tue, 02 Aug 2022 10:25:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:25:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:25:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.05_summits.bed INFO @ Tue, 02 Aug 2022 10:25:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2630 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:25:18: 9000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:25:25: 10000000 INFO @ Tue, 02 Aug 2022 10:25:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:25:32: 11000000 INFO @ Tue, 02 Aug 2022 10:25:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:25:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:25:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.10_summits.bed INFO @ Tue, 02 Aug 2022 10:25:38: Done! pass1 - making usageList (7 chroms): 1 millis INFO @ Tue, 02 Aug 2022 10:25:39: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:25:39: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:25:39: #1 total tags in treatment: 11903972 INFO @ Tue, 02 Aug 2022 10:25:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:25:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass2 - checking and writing primary data (1773 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:25:39: #1 tags after filtering in treatment: 11903972 INFO @ Tue, 02 Aug 2022 10:25:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:25:39: #1 finished! INFO @ Tue, 02 Aug 2022 10:25:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:25:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:25:40: #2 number of paired peaks: 810 WARNING @ Tue, 02 Aug 2022 10:25:40: Fewer paired peaks (810) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 810 pairs to build model! INFO @ Tue, 02 Aug 2022 10:25:40: start model_add_line... INFO @ Tue, 02 Aug 2022 10:25:40: start X-correlation... INFO @ Tue, 02 Aug 2022 10:25:40: end of X-cor INFO @ Tue, 02 Aug 2022 10:25:40: #2 finished! INFO @ Tue, 02 Aug 2022 10:25:40: #2 predicted fragment length is 165 bps INFO @ Tue, 02 Aug 2022 10:25:40: #2 alternative fragment length(s) may be 165 bps INFO @ Tue, 02 Aug 2022 10:25:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.20_model.r INFO @ Tue, 02 Aug 2022 10:25:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:25:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:26:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:26:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:26:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:26:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435527/SRX10435527.20_summits.bed INFO @ Tue, 02 Aug 2022 10:26:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1096 records, 4 fields): 98 millis CompletedMACS2peakCalling