Job ID = 16434125 SRX = SRX15407772 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: 00:11:05 31442701 reads; of these: 31442701 (100.00%) were unpaired; of these: 1502212 (4.78%) aligned 0 times 26119499 (83.07%) aligned exactly 1 time 3820990 (12.15%) aligned >1 times 95.22% overall alignment rate Time searching: 00:11:05 Overall time: 00:11:05 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 16 files... [bam_rmdupse_core] 7232225 / 29940489 = 0.2416 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 10:07:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.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 10:07:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:07:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:08:00: 1000000 INFO @ Tue, 02 Aug 2022 10:08:08: 2000000 INFO @ Tue, 02 Aug 2022 10:08:17: 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 10:08:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.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 10:08:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:08:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:08:25: 4000000 INFO @ Tue, 02 Aug 2022 10:08:29: 1000000 INFO @ Tue, 02 Aug 2022 10:08:33: 5000000 INFO @ Tue, 02 Aug 2022 10:08:38: 2000000 INFO @ Tue, 02 Aug 2022 10:08:42: 6000000 INFO @ Tue, 02 Aug 2022 10:08:46: 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 10:08:50: 7000000 INFO @ Tue, 02 Aug 2022 10:08:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.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 10:08:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:08:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:08:55: 4000000 INFO @ Tue, 02 Aug 2022 10:08:59: 8000000 INFO @ Tue, 02 Aug 2022 10:08:59: 1000000 INFO @ Tue, 02 Aug 2022 10:09:04: 5000000 INFO @ Tue, 02 Aug 2022 10:09:08: 9000000 INFO @ Tue, 02 Aug 2022 10:09:08: 2000000 INFO @ Tue, 02 Aug 2022 10:09:13: 6000000 INFO @ Tue, 02 Aug 2022 10:09:16: 10000000 INFO @ Tue, 02 Aug 2022 10:09:17: 3000000 INFO @ Tue, 02 Aug 2022 10:09:22: 7000000 INFO @ Tue, 02 Aug 2022 10:09:25: 11000000 INFO @ Tue, 02 Aug 2022 10:09:26: 4000000 INFO @ Tue, 02 Aug 2022 10:09:32: 8000000 INFO @ Tue, 02 Aug 2022 10:09:34: 12000000 INFO @ Tue, 02 Aug 2022 10:09:34: 5000000 INFO @ Tue, 02 Aug 2022 10:09:41: 9000000 INFO @ Tue, 02 Aug 2022 10:09:43: 13000000 INFO @ Tue, 02 Aug 2022 10:09:44: 6000000 INFO @ Tue, 02 Aug 2022 10:09:50: 10000000 INFO @ Tue, 02 Aug 2022 10:09:52: 14000000 INFO @ Tue, 02 Aug 2022 10:09:53: 7000000 INFO @ Tue, 02 Aug 2022 10:10:00: 11000000 INFO @ Tue, 02 Aug 2022 10:10:02: 15000000 INFO @ Tue, 02 Aug 2022 10:10:02: 8000000 INFO @ Tue, 02 Aug 2022 10:10:09: 12000000 INFO @ Tue, 02 Aug 2022 10:10:11: 16000000 INFO @ Tue, 02 Aug 2022 10:10:11: 9000000 INFO @ Tue, 02 Aug 2022 10:10:19: 13000000 INFO @ Tue, 02 Aug 2022 10:10:20: 17000000 INFO @ Tue, 02 Aug 2022 10:10:21: 10000000 INFO @ Tue, 02 Aug 2022 10:10:28: 14000000 INFO @ Tue, 02 Aug 2022 10:10:29: 18000000 INFO @ Tue, 02 Aug 2022 10:10:30: 11000000 INFO @ Tue, 02 Aug 2022 10:10:38: 15000000 INFO @ Tue, 02 Aug 2022 10:10:38: 19000000 INFO @ Tue, 02 Aug 2022 10:10:39: 12000000 INFO @ Tue, 02 Aug 2022 10:10:47: 20000000 INFO @ Tue, 02 Aug 2022 10:10:47: 16000000 INFO @ Tue, 02 Aug 2022 10:10:48: 13000000 INFO @ Tue, 02 Aug 2022 10:10:56: 21000000 INFO @ Tue, 02 Aug 2022 10:10:56: 17000000 INFO @ Tue, 02 Aug 2022 10:10:56: 14000000 INFO @ Tue, 02 Aug 2022 10:11:05: 22000000 INFO @ Tue, 02 Aug 2022 10:11:05: 15000000 INFO @ Tue, 02 Aug 2022 10:11:05: 18000000 INFO @ Tue, 02 Aug 2022 10:11:11: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:11:11: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:11:11: #1 total tags in treatment: 22708264 INFO @ Tue, 02 Aug 2022 10:11:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:11:11: #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 10:11:12: #1 tags after filtering in treatment: 22708264 INFO @ Tue, 02 Aug 2022 10:11:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:11:12: #1 finished! INFO @ Tue, 02 Aug 2022 10:11:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:11:12: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:11:13: #2 number of paired peaks: 451 WARNING @ Tue, 02 Aug 2022 10:11:13: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Tue, 02 Aug 2022 10:11:13: start model_add_line... INFO @ Tue, 02 Aug 2022 10:11:13: start X-correlation... INFO @ Tue, 02 Aug 2022 10:11:14: end of X-cor INFO @ Tue, 02 Aug 2022 10:11:14: #2 finished! INFO @ Tue, 02 Aug 2022 10:11:14: #2 predicted fragment length is 161 bps INFO @ Tue, 02 Aug 2022 10:11:14: #2 alternative fragment length(s) may be 161 bps INFO @ Tue, 02 Aug 2022 10:11:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.05_model.r INFO @ Tue, 02 Aug 2022 10:11:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:11:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:11:14: 16000000 INFO @ Tue, 02 Aug 2022 10:11:15: 19000000 INFO @ Tue, 02 Aug 2022 10:11:23: 17000000 INFO @ Tue, 02 Aug 2022 10:11:24: 20000000 INFO @ Tue, 02 Aug 2022 10:11:31: 18000000 INFO @ Tue, 02 Aug 2022 10:11:33: 21000000 INFO @ Tue, 02 Aug 2022 10:11:40: 19000000 INFO @ Tue, 02 Aug 2022 10:11:42: 22000000 INFO @ Tue, 02 Aug 2022 10:11:48: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:11:48: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:11:48: #1 total tags in treatment: 22708264 INFO @ Tue, 02 Aug 2022 10:11:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:11:48: #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 10:11:49: #1 tags after filtering in treatment: 22708264 INFO @ Tue, 02 Aug 2022 10:11:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:11:49: #1 finished! INFO @ Tue, 02 Aug 2022 10:11:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:11:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:11:49: 20000000 INFO @ Tue, 02 Aug 2022 10:11:50: #2 number of paired peaks: 451 WARNING @ Tue, 02 Aug 2022 10:11:50: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Tue, 02 Aug 2022 10:11:50: start model_add_line... INFO @ Tue, 02 Aug 2022 10:11:51: start X-correlation... INFO @ Tue, 02 Aug 2022 10:11:51: end of X-cor INFO @ Tue, 02 Aug 2022 10:11:51: #2 finished! INFO @ Tue, 02 Aug 2022 10:11:51: #2 predicted fragment length is 161 bps INFO @ Tue, 02 Aug 2022 10:11:51: #2 alternative fragment length(s) may be 161 bps INFO @ Tue, 02 Aug 2022 10:11:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.10_model.r INFO @ Tue, 02 Aug 2022 10:11:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:11:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:11:58: 21000000 INFO @ Tue, 02 Aug 2022 10:12:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:12:07: 22000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:12:14: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:12:14: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:12:14: #1 total tags in treatment: 22708264 INFO @ Tue, 02 Aug 2022 10:12:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:12:14: #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 10:12:14: #1 tags after filtering in treatment: 22708264 INFO @ Tue, 02 Aug 2022 10:12:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:12:14: #1 finished! INFO @ Tue, 02 Aug 2022 10:12:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:12:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:12:16: #2 number of paired peaks: 451 WARNING @ Tue, 02 Aug 2022 10:12:16: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Tue, 02 Aug 2022 10:12:16: start model_add_line... INFO @ Tue, 02 Aug 2022 10:12:16: start X-correlation... INFO @ Tue, 02 Aug 2022 10:12:16: end of X-cor INFO @ Tue, 02 Aug 2022 10:12:16: #2 finished! INFO @ Tue, 02 Aug 2022 10:12:16: #2 predicted fragment length is 161 bps INFO @ Tue, 02 Aug 2022 10:12:16: #2 alternative fragment length(s) may be 161 bps INFO @ Tue, 02 Aug 2022 10:12:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.20_model.r INFO @ Tue, 02 Aug 2022 10:12:16: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:12:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:12:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:12:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:12:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.05_summits.bed INFO @ Tue, 02 Aug 2022 10:12:22: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (12535 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:12:39: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:12:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:12:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:12:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.10_summits.bed INFO @ Tue, 02 Aug 2022 10:13:00: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9349 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:13:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:13:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:13:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:13:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407772/SRX15407772.20_summits.bed INFO @ Tue, 02 Aug 2022 10:13:25: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6094 records, 4 fields): 81 millis CompletedMACS2peakCalling