Job ID = 16435509 SRX = SRX13110324 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: 00:03:55 16808427 reads; of these: 16808427 (100.00%) were unpaired; of these: 7714518 (45.90%) aligned 0 times 7884974 (46.91%) aligned exactly 1 time 1208935 (7.19%) aligned >1 times 54.10% overall alignment rate Time searching: 00:03:55 Overall time: 00:03:55 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] 2310071 / 9093909 = 0.2540 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 10:50:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.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 10:50:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:50:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:50:59: 1000000 INFO @ Tue, 02 Aug 2022 10:51:05: 2000000 INFO @ Tue, 02 Aug 2022 10:51:10: 3000000 INFO @ Tue, 02 Aug 2022 10:51:16: 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 10:51:21: 5000000 INFO @ Tue, 02 Aug 2022 10:51:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.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 10:51:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:51:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:51:26: 6000000 INFO @ Tue, 02 Aug 2022 10:51:29: 1000000 INFO @ Tue, 02 Aug 2022 10:51:30: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:51:30: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:51:30: #1 total tags in treatment: 6783838 INFO @ Tue, 02 Aug 2022 10:51:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:51:30: #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 10:51:30: #1 tags after filtering in treatment: 6783838 INFO @ Tue, 02 Aug 2022 10:51:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:51:30: #1 finished! INFO @ Tue, 02 Aug 2022 10:51:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:51:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:51:31: #2 number of paired peaks: 1389 INFO @ Tue, 02 Aug 2022 10:51:31: start model_add_line... INFO @ Tue, 02 Aug 2022 10:51:31: start X-correlation... INFO @ Tue, 02 Aug 2022 10:51:31: end of X-cor INFO @ Tue, 02 Aug 2022 10:51:31: #2 finished! INFO @ Tue, 02 Aug 2022 10:51:31: #2 predicted fragment length is 181 bps INFO @ Tue, 02 Aug 2022 10:51:31: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 02 Aug 2022 10:51:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.05_model.r INFO @ Tue, 02 Aug 2022 10:51:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:51:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:51:34: 2000000 INFO @ Tue, 02 Aug 2022 10:51:39: 3000000 INFO @ Tue, 02 Aug 2022 10:51:45: 4000000 INFO @ Tue, 02 Aug 2022 10:51:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:51:50: 5000000 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 10:51:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.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 10:51:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:51:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:51:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:51:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:51:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.05_summits.bed INFO @ Tue, 02 Aug 2022 10:51:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2226 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:51:55: 6000000 INFO @ Tue, 02 Aug 2022 10:51:58: 1000000 INFO @ Tue, 02 Aug 2022 10:52:00: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:52:00: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:52:00: #1 total tags in treatment: 6783838 INFO @ Tue, 02 Aug 2022 10:52:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:52:00: #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 10:52:00: #1 tags after filtering in treatment: 6783838 INFO @ Tue, 02 Aug 2022 10:52:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:52:00: #1 finished! INFO @ Tue, 02 Aug 2022 10:52:00: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:52:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:52:00: #2 number of paired peaks: 1389 INFO @ Tue, 02 Aug 2022 10:52:00: start model_add_line... INFO @ Tue, 02 Aug 2022 10:52:00: start X-correlation... INFO @ Tue, 02 Aug 2022 10:52:00: end of X-cor INFO @ Tue, 02 Aug 2022 10:52:00: #2 finished! INFO @ Tue, 02 Aug 2022 10:52:00: #2 predicted fragment length is 181 bps INFO @ Tue, 02 Aug 2022 10:52:00: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 02 Aug 2022 10:52:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.10_model.r INFO @ Tue, 02 Aug 2022 10:52:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:52:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:52:04: 2000000 INFO @ Tue, 02 Aug 2022 10:52:09: 3000000 INFO @ Tue, 02 Aug 2022 10:52:14: 4000000 INFO @ Tue, 02 Aug 2022 10:52:16: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:52:19: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:52:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:52:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:52:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.10_summits.bed INFO @ Tue, 02 Aug 2022 10:52:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1492 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:52:25: 6000000 INFO @ Tue, 02 Aug 2022 10:52:29: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:52:29: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:52:29: #1 total tags in treatment: 6783838 INFO @ Tue, 02 Aug 2022 10:52:29: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:52:29: #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 10:52:29: #1 tags after filtering in treatment: 6783838 INFO @ Tue, 02 Aug 2022 10:52:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:52:29: #1 finished! INFO @ Tue, 02 Aug 2022 10:52:29: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:52:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:52:29: #2 number of paired peaks: 1389 INFO @ Tue, 02 Aug 2022 10:52:29: start model_add_line... INFO @ Tue, 02 Aug 2022 10:52:29: start X-correlation... INFO @ Tue, 02 Aug 2022 10:52:29: end of X-cor INFO @ Tue, 02 Aug 2022 10:52:29: #2 finished! INFO @ Tue, 02 Aug 2022 10:52:29: #2 predicted fragment length is 181 bps INFO @ Tue, 02 Aug 2022 10:52:29: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 02 Aug 2022 10:52:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.20_model.r INFO @ Tue, 02 Aug 2022 10:52:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:52:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:52:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:52:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:52:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:52:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110324/SRX13110324.20_summits.bed INFO @ Tue, 02 Aug 2022 10:52:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (950 records, 4 fields): 19 millis CompletedMACS2peakCalling