Job ID = 16434492 SRX = SRX10925679 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: 00:04:27 21745646 reads; of these: 21745646 (100.00%) were unpaired; of these: 15415537 (70.89%) aligned 0 times 5163083 (23.74%) aligned exactly 1 time 1167026 (5.37%) aligned >1 times 29.11% overall alignment rate Time searching: 00:04:27 Overall time: 00:04:27 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] 1057684 / 6330109 = 0.1671 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 09:58:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.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 09:58:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:58:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:58:29: 1000000 INFO @ Tue, 02 Aug 2022 09:58:36: 2000000 INFO @ Tue, 02 Aug 2022 09:58:42: 3000000 INFO @ Tue, 02 Aug 2022 09:58:48: 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 09:58:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.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 09:58:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:58:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:58:55: 5000000 INFO @ Tue, 02 Aug 2022 09:58:57: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:58:57: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:58:57: #1 total tags in treatment: 5272425 INFO @ Tue, 02 Aug 2022 09:58:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:58:57: #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 09:58:57: #1 tags after filtering in treatment: 5272425 INFO @ Tue, 02 Aug 2022 09:58:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:58:57: #1 finished! INFO @ Tue, 02 Aug 2022 09:58:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:58:58: #2 number of paired peaks: 5842 INFO @ Tue, 02 Aug 2022 09:58:58: start model_add_line... INFO @ Tue, 02 Aug 2022 09:58:58: start X-correlation... INFO @ Tue, 02 Aug 2022 09:58:58: end of X-cor INFO @ Tue, 02 Aug 2022 09:58:58: #2 finished! INFO @ Tue, 02 Aug 2022 09:58:58: #2 predicted fragment length is 236 bps INFO @ Tue, 02 Aug 2022 09:58:58: #2 alternative fragment length(s) may be 236 bps INFO @ Tue, 02 Aug 2022 09:58:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.05_model.r INFO @ Tue, 02 Aug 2022 09:58:58: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:58:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:58:58: 1000000 INFO @ Tue, 02 Aug 2022 09:59:04: 2000000 INFO @ Tue, 02 Aug 2022 09:59:10: 3000000 INFO @ Tue, 02 Aug 2022 09:59:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:59:16: 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 09:59:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.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 09:59:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:59:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:59:22: 5000000 INFO @ Tue, 02 Aug 2022 09:59:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:59:24: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:59:24: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:59:24: #1 total tags in treatment: 5272425 INFO @ Tue, 02 Aug 2022 09:59:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:59:24: #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 09:59:24: #1 tags after filtering in treatment: 5272425 INFO @ Tue, 02 Aug 2022 09:59:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:59:24: #1 finished! INFO @ Tue, 02 Aug 2022 09:59:24: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:59:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:59:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:59:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.05_summits.bed INFO @ Tue, 02 Aug 2022 09:59:24: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (10088 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:59:25: #2 number of paired peaks: 5842 INFO @ Tue, 02 Aug 2022 09:59:25: start model_add_line... INFO @ Tue, 02 Aug 2022 09:59:25: start X-correlation... INFO @ Tue, 02 Aug 2022 09:59:25: end of X-cor INFO @ Tue, 02 Aug 2022 09:59:25: #2 finished! INFO @ Tue, 02 Aug 2022 09:59:25: #2 predicted fragment length is 236 bps INFO @ Tue, 02 Aug 2022 09:59:25: #2 alternative fragment length(s) may be 236 bps INFO @ Tue, 02 Aug 2022 09:59:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.10_model.r INFO @ Tue, 02 Aug 2022 09:59:25: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:59:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:59:28: 1000000 INFO @ Tue, 02 Aug 2022 09:59:34: 2000000 INFO @ Tue, 02 Aug 2022 09:59:41: 3000000 INFO @ Tue, 02 Aug 2022 09:59:42: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:59:47: 4000000 INFO @ Tue, 02 Aug 2022 09:59:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:59:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:59:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.10_summits.bed INFO @ Tue, 02 Aug 2022 09:59:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5858 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:59:54: 5000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:59:56: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:59:56: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:59:56: #1 total tags in treatment: 5272425 INFO @ Tue, 02 Aug 2022 09:59:56: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:59:56: #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 09:59:56: #1 tags after filtering in treatment: 5272425 INFO @ Tue, 02 Aug 2022 09:59:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:59:56: #1 finished! INFO @ Tue, 02 Aug 2022 09:59:56: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:59:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:59:57: #2 number of paired peaks: 5842 INFO @ Tue, 02 Aug 2022 09:59:57: start model_add_line... INFO @ Tue, 02 Aug 2022 09:59:57: start X-correlation... INFO @ Tue, 02 Aug 2022 09:59:57: end of X-cor INFO @ Tue, 02 Aug 2022 09:59:57: #2 finished! INFO @ Tue, 02 Aug 2022 09:59:57: #2 predicted fragment length is 236 bps INFO @ Tue, 02 Aug 2022 09:59:57: #2 alternative fragment length(s) may be 236 bps INFO @ Tue, 02 Aug 2022 09:59:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.20_model.r INFO @ Tue, 02 Aug 2022 09:59:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:59:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:00:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:00:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:00:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:00:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10925679/SRX10925679.20_summits.bed INFO @ Tue, 02 Aug 2022 10:00:24: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2508 records, 4 fields): 20 millis CompletedMACS2peakCalling