Job ID = 16435531 SRX = SRX13110341 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:47 16667868 reads; of these: 16667868 (100.00%) were unpaired; of these: 2655557 (15.93%) aligned 0 times 12121074 (72.72%) aligned exactly 1 time 1891237 (11.35%) aligned >1 times 84.07% overall alignment rate Time searching: 00:04:48 Overall time: 00:04:48 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] 2495853 / 14012311 = 0.1781 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 10:55:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.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 10:55:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:55:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:55:14: 1000000 INFO @ Tue, 02 Aug 2022 10:55:20: 2000000 INFO @ Tue, 02 Aug 2022 10:55:26: 3000000 INFO @ Tue, 02 Aug 2022 10:55:32: 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 10:55:37: 5000000 INFO @ Tue, 02 Aug 2022 10:55:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.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 10:55:38: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:55:38: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:55:43: 6000000 INFO @ Tue, 02 Aug 2022 10:55:44: 1000000 INFO @ Tue, 02 Aug 2022 10:55:50: 7000000 INFO @ Tue, 02 Aug 2022 10:55:51: 2000000 INFO @ Tue, 02 Aug 2022 10:55:56: 8000000 INFO @ Tue, 02 Aug 2022 10:55:57: 3000000 INFO @ Tue, 02 Aug 2022 10:56:03: 9000000 INFO @ Tue, 02 Aug 2022 10:56:03: 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 10:56:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.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 10:56:08: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:56:08: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:56:10: 10000000 INFO @ Tue, 02 Aug 2022 10:56:10: 5000000 INFO @ Tue, 02 Aug 2022 10:56:15: 1000000 INFO @ Tue, 02 Aug 2022 10:56:17: 11000000 INFO @ Tue, 02 Aug 2022 10:56:17: 6000000 INFO @ Tue, 02 Aug 2022 10:56:20: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:56:20: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:56:20: #1 total tags in treatment: 11516458 INFO @ Tue, 02 Aug 2022 10:56:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:56:20: #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 10:56:21: #1 tags after filtering in treatment: 11516458 INFO @ Tue, 02 Aug 2022 10:56:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:56:21: #1 finished! INFO @ Tue, 02 Aug 2022 10:56:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:56:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:56:22: #2 number of paired peaks: 1365 INFO @ Tue, 02 Aug 2022 10:56:22: start model_add_line... INFO @ Tue, 02 Aug 2022 10:56:22: 2000000 INFO @ Tue, 02 Aug 2022 10:56:22: start X-correlation... INFO @ Tue, 02 Aug 2022 10:56:22: end of X-cor INFO @ Tue, 02 Aug 2022 10:56:22: #2 finished! INFO @ Tue, 02 Aug 2022 10:56:22: #2 predicted fragment length is 208 bps INFO @ Tue, 02 Aug 2022 10:56:22: #2 alternative fragment length(s) may be 208 bps INFO @ Tue, 02 Aug 2022 10:56:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.05_model.r INFO @ Tue, 02 Aug 2022 10:56:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:56:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:56:23: 7000000 INFO @ Tue, 02 Aug 2022 10:56:28: 3000000 INFO @ Tue, 02 Aug 2022 10:56:30: 8000000 INFO @ Tue, 02 Aug 2022 10:56:34: 4000000 INFO @ Tue, 02 Aug 2022 10:56:36: 9000000 INFO @ Tue, 02 Aug 2022 10:56:41: 5000000 INFO @ Tue, 02 Aug 2022 10:56:43: 10000000 INFO @ Tue, 02 Aug 2022 10:56:47: 6000000 INFO @ Tue, 02 Aug 2022 10:56:49: 11000000 INFO @ Tue, 02 Aug 2022 10:56:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:56:53: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:56:53: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:56:53: #1 total tags in treatment: 11516458 INFO @ Tue, 02 Aug 2022 10:56:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:56:53: #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 10:56:53: #1 tags after filtering in treatment: 11516458 INFO @ Tue, 02 Aug 2022 10:56:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:56:53: #1 finished! INFO @ Tue, 02 Aug 2022 10:56:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:56:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:56:54: 7000000 INFO @ Tue, 02 Aug 2022 10:56:54: #2 number of paired peaks: 1365 INFO @ Tue, 02 Aug 2022 10:56:54: start model_add_line... INFO @ Tue, 02 Aug 2022 10:56:54: start X-correlation... INFO @ Tue, 02 Aug 2022 10:56:54: end of X-cor INFO @ Tue, 02 Aug 2022 10:56:54: #2 finished! INFO @ Tue, 02 Aug 2022 10:56:54: #2 predicted fragment length is 208 bps INFO @ Tue, 02 Aug 2022 10:56:54: #2 alternative fragment length(s) may be 208 bps INFO @ Tue, 02 Aug 2022 10:56:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.10_model.r INFO @ Tue, 02 Aug 2022 10:56:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:56:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:57:00: 8000000 INFO @ Tue, 02 Aug 2022 10:57:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:57:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:57:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.05_summits.bed INFO @ Tue, 02 Aug 2022 10:57:04: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8948 records, 4 fields): 68 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:57:06: 9000000 INFO @ Tue, 02 Aug 2022 10:57:12: 10000000 INFO @ Tue, 02 Aug 2022 10:57:17: 11000000 INFO @ Tue, 02 Aug 2022 10:57:20: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:57:20: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:57:20: #1 total tags in treatment: 11516458 INFO @ Tue, 02 Aug 2022 10:57:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:57:20: #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 10:57:21: #1 tags after filtering in treatment: 11516458 INFO @ Tue, 02 Aug 2022 10:57:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:57:21: #1 finished! INFO @ Tue, 02 Aug 2022 10:57:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:57:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:57:22: #2 number of paired peaks: 1365 INFO @ Tue, 02 Aug 2022 10:57:22: start model_add_line... INFO @ Tue, 02 Aug 2022 10:57:22: start X-correlation... INFO @ Tue, 02 Aug 2022 10:57:22: end of X-cor INFO @ Tue, 02 Aug 2022 10:57:22: #2 finished! INFO @ Tue, 02 Aug 2022 10:57:22: #2 predicted fragment length is 208 bps INFO @ Tue, 02 Aug 2022 10:57:22: #2 alternative fragment length(s) may be 208 bps INFO @ Tue, 02 Aug 2022 10:57:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.20_model.r INFO @ Tue, 02 Aug 2022 10:57:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:57:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:57:22: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:57:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:57:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:57:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.10_summits.bed INFO @ Tue, 02 Aug 2022 10:57:34: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6672 records, 4 fields): 95 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:57:49: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:58:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:58:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:58:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110341/SRX13110341.20_summits.bed INFO @ Tue, 02 Aug 2022 10:58:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4502 records, 4 fields): 20 millis CompletedMACS2peakCalling