Job ID = 16434809 SRX = SRX10925681 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: 00:04:58 22685309 reads; of these: 22685309 (100.00%) were unpaired; of these: 16969404 (74.80%) aligned 0 times 4661692 (20.55%) aligned exactly 1 time 1054213 (4.65%) aligned >1 times 25.20% overall alignment rate Time searching: 00:04:58 Overall time: 00:04:58 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] 821169 / 5715905 = 0.1437 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 10:02:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.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 10:02:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:02:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:03:02: 1000000 INFO @ Tue, 02 Aug 2022 10:03:10: 2000000 INFO @ Tue, 02 Aug 2022 10:03:18: 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 10:03:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.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 10:03:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:03:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:03:26: 4000000 INFO @ Tue, 02 Aug 2022 10:03:31: 1000000 INFO @ Tue, 02 Aug 2022 10:03:34: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:03:34: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:03:34: #1 total tags in treatment: 4894736 INFO @ Tue, 02 Aug 2022 10:03:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:03:34: #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 10:03:34: #1 tags after filtering in treatment: 4894736 INFO @ Tue, 02 Aug 2022 10:03:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:03:34: #1 finished! INFO @ Tue, 02 Aug 2022 10:03:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:03:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:03:35: #2 number of paired peaks: 5168 INFO @ Tue, 02 Aug 2022 10:03:35: start model_add_line... INFO @ Tue, 02 Aug 2022 10:03:35: start X-correlation... INFO @ Tue, 02 Aug 2022 10:03:35: end of X-cor INFO @ Tue, 02 Aug 2022 10:03:35: #2 finished! INFO @ Tue, 02 Aug 2022 10:03:35: #2 predicted fragment length is 234 bps INFO @ Tue, 02 Aug 2022 10:03:35: #2 alternative fragment length(s) may be 234 bps INFO @ Tue, 02 Aug 2022 10:03:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.05_model.r INFO @ Tue, 02 Aug 2022 10:03:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:03:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:03:40: 2000000 INFO @ Tue, 02 Aug 2022 10:03:48: 3000000 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 10:03:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:03:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.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 10:03:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:03:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:03:56: 4000000 INFO @ Tue, 02 Aug 2022 10:03:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:03:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:03:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.05_summits.bed INFO @ Tue, 02 Aug 2022 10:03:59: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (9007 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:04:01: 1000000 INFO @ Tue, 02 Aug 2022 10:04:04: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:04:04: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:04:04: #1 total tags in treatment: 4894736 INFO @ Tue, 02 Aug 2022 10:04:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:04:04: #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 10:04:05: #1 tags after filtering in treatment: 4894736 INFO @ Tue, 02 Aug 2022 10:04:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:04:05: #1 finished! INFO @ Tue, 02 Aug 2022 10:04:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:04:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:04:05: #2 number of paired peaks: 5168 INFO @ Tue, 02 Aug 2022 10:04:05: start model_add_line... INFO @ Tue, 02 Aug 2022 10:04:05: start X-correlation... INFO @ Tue, 02 Aug 2022 10:04:05: end of X-cor INFO @ Tue, 02 Aug 2022 10:04:05: #2 finished! INFO @ Tue, 02 Aug 2022 10:04:05: #2 predicted fragment length is 234 bps INFO @ Tue, 02 Aug 2022 10:04:05: #2 alternative fragment length(s) may be 234 bps INFO @ Tue, 02 Aug 2022 10:04:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.10_model.r INFO @ Tue, 02 Aug 2022 10:04:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:04:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:04:10: 2000000 INFO @ Tue, 02 Aug 2022 10:04:18: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:04:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:04:26: 4000000 INFO @ Tue, 02 Aug 2022 10:04:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:04:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:04:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.10_summits.bed INFO @ Tue, 02 Aug 2022 10:04:29: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4826 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:04:34: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:04:34: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:04:34: #1 total tags in treatment: 4894736 INFO @ Tue, 02 Aug 2022 10:04:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:04:34: #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 10:04:34: #1 tags after filtering in treatment: 4894736 INFO @ Tue, 02 Aug 2022 10:04:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:04:34: #1 finished! INFO @ Tue, 02 Aug 2022 10:04:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:04:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:04:34: #2 number of paired peaks: 5168 INFO @ Tue, 02 Aug 2022 10:04:34: start model_add_line... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:04:34: start X-correlation... INFO @ Tue, 02 Aug 2022 10:04:34: end of X-cor INFO @ Tue, 02 Aug 2022 10:04:34: #2 finished! INFO @ Tue, 02 Aug 2022 10:04:34: #2 predicted fragment length is 234 bps INFO @ Tue, 02 Aug 2022 10:04:34: #2 alternative fragment length(s) may be 234 bps INFO @ Tue, 02 Aug 2022 10:04:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.20_model.r INFO @ Tue, 02 Aug 2022 10:04:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:04:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:04:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:04:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:04:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:04:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10925681/SRX10925681.20_summits.bed INFO @ Tue, 02 Aug 2022 10:04:58: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1828 records, 4 fields): 30 millis CompletedMACS2peakCalling