Job ID = 16434282 SRX = SRX10925641 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: 00:06:24 20770353 reads; of these: 20770353 (100.00%) were unpaired; of these: 5848519 (28.16%) aligned 0 times 10772809 (51.87%) aligned exactly 1 time 4149025 (19.98%) aligned >1 times 71.84% overall alignment rate Time searching: 00:06:24 Overall time: 00:06:24 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] 4004795 / 14921834 = 0.2684 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 10:00:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.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 10:00:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:00:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:00:13: 1000000 INFO @ Tue, 02 Aug 2022 10:00:20: 2000000 INFO @ Tue, 02 Aug 2022 10:00:28: 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 10:00:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.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 10:00:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:00:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:00:35: 4000000 INFO @ Tue, 02 Aug 2022 10:00:43: 1000000 INFO @ Tue, 02 Aug 2022 10:00:44: 5000000 INFO @ Tue, 02 Aug 2022 10:00:51: 2000000 INFO @ Tue, 02 Aug 2022 10:00:53: 6000000 INFO @ Tue, 02 Aug 2022 10:00:59: 3000000 INFO @ Tue, 02 Aug 2022 10:01:01: 7000000 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 10:01:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.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 10:01:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:01:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:01:08: 4000000 INFO @ Tue, 02 Aug 2022 10:01:10: 8000000 INFO @ Tue, 02 Aug 2022 10:01:13: 1000000 INFO @ Tue, 02 Aug 2022 10:01:17: 5000000 INFO @ Tue, 02 Aug 2022 10:01:19: 9000000 INFO @ Tue, 02 Aug 2022 10:01:22: 2000000 INFO @ Tue, 02 Aug 2022 10:01:26: 6000000 INFO @ Tue, 02 Aug 2022 10:01:29: 10000000 INFO @ Tue, 02 Aug 2022 10:01:31: 3000000 INFO @ Tue, 02 Aug 2022 10:01:34: 7000000 INFO @ Tue, 02 Aug 2022 10:01:37: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:01:37: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:01:37: #1 total tags in treatment: 10917039 INFO @ Tue, 02 Aug 2022 10:01:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:01:37: #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 10:01:37: #1 tags after filtering in treatment: 10917039 INFO @ Tue, 02 Aug 2022 10:01:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:01:37: #1 finished! INFO @ Tue, 02 Aug 2022 10:01:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:01:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:01:38: #2 number of paired peaks: 3424 INFO @ Tue, 02 Aug 2022 10:01:38: start model_add_line... INFO @ Tue, 02 Aug 2022 10:01:38: start X-correlation... INFO @ Tue, 02 Aug 2022 10:01:38: end of X-cor INFO @ Tue, 02 Aug 2022 10:01:38: #2 finished! INFO @ Tue, 02 Aug 2022 10:01:38: #2 predicted fragment length is 202 bps INFO @ Tue, 02 Aug 2022 10:01:38: #2 alternative fragment length(s) may be 4,202 bps INFO @ Tue, 02 Aug 2022 10:01:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.05_model.r INFO @ Tue, 02 Aug 2022 10:01:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:01:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:01:39: 4000000 INFO @ Tue, 02 Aug 2022 10:01:43: 8000000 INFO @ Tue, 02 Aug 2022 10:01:49: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:01:52: 9000000 INFO @ Tue, 02 Aug 2022 10:01:58: 6000000 INFO @ Tue, 02 Aug 2022 10:02:01: 10000000 INFO @ Tue, 02 Aug 2022 10:02:07: 7000000 INFO @ Tue, 02 Aug 2022 10:02:07: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:02:09: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:02:09: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:02:09: #1 total tags in treatment: 10917039 INFO @ Tue, 02 Aug 2022 10:02:09: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:02:09: #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 10:02:09: #1 tags after filtering in treatment: 10917039 INFO @ Tue, 02 Aug 2022 10:02:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:02:09: #1 finished! INFO @ Tue, 02 Aug 2022 10:02:09: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:02:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:02:10: #2 number of paired peaks: 3424 INFO @ Tue, 02 Aug 2022 10:02:10: start model_add_line... INFO @ Tue, 02 Aug 2022 10:02:10: start X-correlation... INFO @ Tue, 02 Aug 2022 10:02:10: end of X-cor INFO @ Tue, 02 Aug 2022 10:02:10: #2 finished! INFO @ Tue, 02 Aug 2022 10:02:10: #2 predicted fragment length is 202 bps INFO @ Tue, 02 Aug 2022 10:02:10: #2 alternative fragment length(s) may be 4,202 bps INFO @ Tue, 02 Aug 2022 10:02:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.10_model.r INFO @ Tue, 02 Aug 2022 10:02:10: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:02:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:02:16: 8000000 INFO @ Tue, 02 Aug 2022 10:02:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:02:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:02:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.05_summits.bed INFO @ Tue, 02 Aug 2022 10:02:20: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (21349 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:02:24: 9000000 INFO @ Tue, 02 Aug 2022 10:02:32: 10000000 INFO @ Tue, 02 Aug 2022 10:02:38: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:02:38: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:02:38: #1 total tags in treatment: 10917039 INFO @ Tue, 02 Aug 2022 10:02:38: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:02:38: #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 10:02:39: #1 tags after filtering in treatment: 10917039 INFO @ Tue, 02 Aug 2022 10:02:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:02:39: #1 finished! INFO @ Tue, 02 Aug 2022 10:02:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:02:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:02:40: #2 number of paired peaks: 3424 INFO @ Tue, 02 Aug 2022 10:02:40: start model_add_line... INFO @ Tue, 02 Aug 2022 10:02:40: start X-correlation... INFO @ Tue, 02 Aug 2022 10:02:40: end of X-cor INFO @ Tue, 02 Aug 2022 10:02:40: #2 finished! INFO @ Tue, 02 Aug 2022 10:02:40: #2 predicted fragment length is 202 bps INFO @ Tue, 02 Aug 2022 10:02:40: #2 alternative fragment length(s) may be 4,202 bps INFO @ Tue, 02 Aug 2022 10:02:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.20_model.r INFO @ Tue, 02 Aug 2022 10:02:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:02:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:02:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:02:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:02:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:02:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.10_summits.bed INFO @ Tue, 02 Aug 2022 10:02:53: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (13932 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:03:08: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:03:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:03:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:03:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10925641/SRX10925641.20_summits.bed INFO @ Tue, 02 Aug 2022 10:03:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6359 records, 4 fields): 39 millis CompletedMACS2peakCalling