Job ID = 14160703 SRX = SRX10399028 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:34 11513557 reads; of these: 11513557 (100.00%) were unpaired; of these: 1758544 (15.27%) aligned 0 times 8258844 (71.73%) aligned exactly 1 time 1496169 (12.99%) aligned >1 times 84.73% overall alignment rate Time searching: 00:03:34 Overall time: 00:03:34 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_rmdupse_core] 1153323 / 9755013 = 0.1182 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:54:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.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 @ Thu, 09 Dec 2021 03:54:56: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:54:56: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:55:01: 1000000 INFO @ Thu, 09 Dec 2021 03:55:07: 2000000 INFO @ Thu, 09 Dec 2021 03:55:13: 3000000 INFO @ Thu, 09 Dec 2021 03:55:19: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:55:25: 5000000 INFO @ Thu, 09 Dec 2021 03:55:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.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 @ Thu, 09 Dec 2021 03:55:26: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:55:26: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:55:32: 6000000 INFO @ Thu, 09 Dec 2021 03:55:33: 1000000 INFO @ Thu, 09 Dec 2021 03:55:39: 7000000 INFO @ Thu, 09 Dec 2021 03:55:39: 2000000 INFO @ Thu, 09 Dec 2021 03:55:45: 8000000 INFO @ Thu, 09 Dec 2021 03:55:46: 3000000 INFO @ Thu, 09 Dec 2021 03:55:49: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:55:49: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:55:49: #1 total tags in treatment: 8601690 INFO @ Thu, 09 Dec 2021 03:55:49: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:55:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:55:49: #1 tags after filtering in treatment: 8601690 INFO @ Thu, 09 Dec 2021 03:55:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:55:49: #1 finished! INFO @ Thu, 09 Dec 2021 03:55:49: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:55:50: #2 number of paired peaks: 840 WARNING @ Thu, 09 Dec 2021 03:55:50: Fewer paired peaks (840) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 840 pairs to build model! INFO @ Thu, 09 Dec 2021 03:55:50: start model_add_line... INFO @ Thu, 09 Dec 2021 03:55:50: start X-correlation... INFO @ Thu, 09 Dec 2021 03:55:50: end of X-cor INFO @ Thu, 09 Dec 2021 03:55:50: #2 finished! INFO @ Thu, 09 Dec 2021 03:55:50: #2 predicted fragment length is 175 bps INFO @ Thu, 09 Dec 2021 03:55:50: #2 alternative fragment length(s) may be 175 bps INFO @ Thu, 09 Dec 2021 03:55:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.05_model.r INFO @ Thu, 09 Dec 2021 03:55:50: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:55:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:55:53: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:55:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.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 @ Thu, 09 Dec 2021 03:55:55: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:55:55: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:56:00: 5000000 INFO @ Thu, 09 Dec 2021 03:56:03: 1000000 INFO @ Thu, 09 Dec 2021 03:56:07: 6000000 INFO @ Thu, 09 Dec 2021 03:56:10: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:56:11: 2000000 INFO @ Thu, 09 Dec 2021 03:56:14: 7000000 INFO @ Thu, 09 Dec 2021 03:56:19: 3000000 INFO @ Thu, 09 Dec 2021 03:56:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:56:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:56:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.05_summits.bed INFO @ Thu, 09 Dec 2021 03:56:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2184 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:56:21: 8000000 INFO @ Thu, 09 Dec 2021 03:56:25: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:56:25: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:56:25: #1 total tags in treatment: 8601690 INFO @ Thu, 09 Dec 2021 03:56:25: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:56:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:56:26: #1 tags after filtering in treatment: 8601690 INFO @ Thu, 09 Dec 2021 03:56:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:56:26: #1 finished! INFO @ Thu, 09 Dec 2021 03:56:26: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:56:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:56:26: #2 number of paired peaks: 840 WARNING @ Thu, 09 Dec 2021 03:56:26: Fewer paired peaks (840) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 840 pairs to build model! INFO @ Thu, 09 Dec 2021 03:56:26: start model_add_line... INFO @ Thu, 09 Dec 2021 03:56:26: start X-correlation... INFO @ Thu, 09 Dec 2021 03:56:26: end of X-cor INFO @ Thu, 09 Dec 2021 03:56:26: #2 finished! INFO @ Thu, 09 Dec 2021 03:56:26: #2 predicted fragment length is 175 bps INFO @ Thu, 09 Dec 2021 03:56:26: #2 alternative fragment length(s) may be 175 bps INFO @ Thu, 09 Dec 2021 03:56:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.10_model.r INFO @ Thu, 09 Dec 2021 03:56:26: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:56:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:56:27: 4000000 INFO @ Thu, 09 Dec 2021 03:56:34: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:56:42: 6000000 INFO @ Thu, 09 Dec 2021 03:56:46: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:56:49: 7000000 INFO @ Thu, 09 Dec 2021 03:56:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:56:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:56:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.10_summits.bed INFO @ Thu, 09 Dec 2021 03:56:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1419 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:56:56: 8000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:57:01: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:57:01: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:57:01: #1 total tags in treatment: 8601690 INFO @ Thu, 09 Dec 2021 03:57:01: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:57:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:57:01: #1 tags after filtering in treatment: 8601690 INFO @ Thu, 09 Dec 2021 03:57:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:57:01: #1 finished! INFO @ Thu, 09 Dec 2021 03:57:01: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:57:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:57:01: #2 number of paired peaks: 840 WARNING @ Thu, 09 Dec 2021 03:57:01: Fewer paired peaks (840) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 840 pairs to build model! INFO @ Thu, 09 Dec 2021 03:57:01: start model_add_line... INFO @ Thu, 09 Dec 2021 03:57:01: start X-correlation... INFO @ Thu, 09 Dec 2021 03:57:01: end of X-cor INFO @ Thu, 09 Dec 2021 03:57:01: #2 finished! INFO @ Thu, 09 Dec 2021 03:57:01: #2 predicted fragment length is 175 bps INFO @ Thu, 09 Dec 2021 03:57:01: #2 alternative fragment length(s) may be 175 bps INFO @ Thu, 09 Dec 2021 03:57:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.20_model.r INFO @ Thu, 09 Dec 2021 03:57:01: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:57:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:57:21: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:57:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:57:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:57:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399028/SRX10399028.20_summits.bed INFO @ Thu, 09 Dec 2021 03:57:30: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (900 records, 4 fields): 3 millis CompletedMACS2peakCalling