Job ID = 14157866 SRX = SRX6799184 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 37933523 spots for SRR10065391/SRR10065391.sra Written 37933523 spots for SRR10065391/SRR10065391.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158046 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:27 37933523 reads; of these: 37933523 (100.00%) were unpaired; of these: 2476764 (6.53%) aligned 0 times 28320241 (74.66%) aligned exactly 1 time 7136518 (18.81%) aligned >1 times 93.47% overall alignment rate Time searching: 00:09:27 Overall time: 00:09:27 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_sort_core] merging from 16 files... [bam_rmdupse_core] 10795830 / 35456759 = 0.3045 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 12:09:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.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 @ Wed, 08 Dec 2021 12:09:45: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:09:45: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:09:54: 1000000 INFO @ Wed, 08 Dec 2021 12:10:01: 2000000 INFO @ Wed, 08 Dec 2021 12:10:10: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 12:10:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.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 @ Wed, 08 Dec 2021 12:10:14: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:10:14: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:10:19: 4000000 INFO @ Wed, 08 Dec 2021 12:10:23: 1000000 INFO @ Wed, 08 Dec 2021 12:10:27: 5000000 INFO @ Wed, 08 Dec 2021 12:10:31: 2000000 INFO @ Wed, 08 Dec 2021 12:10:36: 6000000 INFO @ Wed, 08 Dec 2021 12:10:40: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 12:10:44: 7000000 INFO @ Wed, 08 Dec 2021 12:10:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.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 @ Wed, 08 Dec 2021 12:10:44: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:10:44: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:10:49: 4000000 INFO @ Wed, 08 Dec 2021 12:10:52: 8000000 INFO @ Wed, 08 Dec 2021 12:10:54: 1000000 INFO @ Wed, 08 Dec 2021 12:10:59: 5000000 INFO @ Wed, 08 Dec 2021 12:11:01: 9000000 INFO @ Wed, 08 Dec 2021 12:11:03: 2000000 INFO @ Wed, 08 Dec 2021 12:11:08: 6000000 INFO @ Wed, 08 Dec 2021 12:11:10: 10000000 INFO @ Wed, 08 Dec 2021 12:11:12: 3000000 INFO @ Wed, 08 Dec 2021 12:11:18: 7000000 INFO @ Wed, 08 Dec 2021 12:11:20: 11000000 INFO @ Wed, 08 Dec 2021 12:11:22: 4000000 INFO @ Wed, 08 Dec 2021 12:11:28: 8000000 INFO @ Wed, 08 Dec 2021 12:11:30: 12000000 INFO @ Wed, 08 Dec 2021 12:11:31: 5000000 INFO @ Wed, 08 Dec 2021 12:11:37: 9000000 INFO @ Wed, 08 Dec 2021 12:11:40: 13000000 INFO @ Wed, 08 Dec 2021 12:11:41: 6000000 INFO @ Wed, 08 Dec 2021 12:11:46: 10000000 INFO @ Wed, 08 Dec 2021 12:11:50: 14000000 INFO @ Wed, 08 Dec 2021 12:11:50: 7000000 INFO @ Wed, 08 Dec 2021 12:11:55: 11000000 INFO @ Wed, 08 Dec 2021 12:11:59: 15000000 INFO @ Wed, 08 Dec 2021 12:12:00: 8000000 INFO @ Wed, 08 Dec 2021 12:12:05: 12000000 INFO @ Wed, 08 Dec 2021 12:12:08: 16000000 INFO @ Wed, 08 Dec 2021 12:12:10: 9000000 INFO @ Wed, 08 Dec 2021 12:12:14: 13000000 INFO @ Wed, 08 Dec 2021 12:12:17: 17000000 INFO @ Wed, 08 Dec 2021 12:12:19: 10000000 INFO @ Wed, 08 Dec 2021 12:12:24: 14000000 INFO @ Wed, 08 Dec 2021 12:12:27: 18000000 INFO @ Wed, 08 Dec 2021 12:12:27: 11000000 INFO @ Wed, 08 Dec 2021 12:12:34: 15000000 INFO @ Wed, 08 Dec 2021 12:12:36: 12000000 INFO @ Wed, 08 Dec 2021 12:12:37: 19000000 INFO @ Wed, 08 Dec 2021 12:12:44: 16000000 INFO @ Wed, 08 Dec 2021 12:12:44: 13000000 INFO @ Wed, 08 Dec 2021 12:12:48: 20000000 INFO @ Wed, 08 Dec 2021 12:12:53: 14000000 INFO @ Wed, 08 Dec 2021 12:12:53: 17000000 INFO @ Wed, 08 Dec 2021 12:12:58: 21000000 INFO @ Wed, 08 Dec 2021 12:13:02: 15000000 INFO @ Wed, 08 Dec 2021 12:13:03: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 12:13:08: 22000000 INFO @ Wed, 08 Dec 2021 12:13:10: 16000000 INFO @ Wed, 08 Dec 2021 12:13:13: 19000000 INFO @ Wed, 08 Dec 2021 12:13:18: 23000000 INFO @ Wed, 08 Dec 2021 12:13:19: 17000000 INFO @ Wed, 08 Dec 2021 12:13:24: 20000000 INFO @ Wed, 08 Dec 2021 12:13:27: 24000000 INFO @ Wed, 08 Dec 2021 12:13:27: 18000000 INFO @ Wed, 08 Dec 2021 12:13:33: #1 tag size is determined as 49 bps INFO @ Wed, 08 Dec 2021 12:13:33: #1 tag size = 49 INFO @ Wed, 08 Dec 2021 12:13:33: #1 total tags in treatment: 24660929 INFO @ Wed, 08 Dec 2021 12:13:33: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:13:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 12:13:33: #1 tags after filtering in treatment: 24660929 INFO @ Wed, 08 Dec 2021 12:13:33: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:13:33: #1 finished! INFO @ Wed, 08 Dec 2021 12:13:33: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:13:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:13:34: 21000000 INFO @ Wed, 08 Dec 2021 12:13:35: #2 number of paired peaks: 224 WARNING @ Wed, 08 Dec 2021 12:13:35: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Wed, 08 Dec 2021 12:13:35: start model_add_line... INFO @ Wed, 08 Dec 2021 12:13:35: start X-correlation... INFO @ Wed, 08 Dec 2021 12:13:36: end of X-cor INFO @ Wed, 08 Dec 2021 12:13:36: #2 finished! INFO @ Wed, 08 Dec 2021 12:13:36: #2 predicted fragment length is 295 bps INFO @ Wed, 08 Dec 2021 12:13:36: #2 alternative fragment length(s) may be 4,280,295 bps INFO @ Wed, 08 Dec 2021 12:13:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.05_model.r INFO @ Wed, 08 Dec 2021 12:13:36: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:13:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:13:37: 19000000 INFO @ Wed, 08 Dec 2021 12:13:42: 22000000 INFO @ Wed, 08 Dec 2021 12:13:47: 20000000 INFO @ Wed, 08 Dec 2021 12:13:51: 23000000 INFO @ Wed, 08 Dec 2021 12:13:57: 21000000 INFO @ Wed, 08 Dec 2021 12:14:00: 24000000 INFO @ Wed, 08 Dec 2021 12:14:06: #1 tag size is determined as 49 bps INFO @ Wed, 08 Dec 2021 12:14:06: #1 tag size = 49 INFO @ Wed, 08 Dec 2021 12:14:06: #1 total tags in treatment: 24660929 INFO @ Wed, 08 Dec 2021 12:14:06: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:14:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 12:14:06: 22000000 INFO @ Wed, 08 Dec 2021 12:14:06: #1 tags after filtering in treatment: 24660929 INFO @ Wed, 08 Dec 2021 12:14:06: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:14:06: #1 finished! INFO @ Wed, 08 Dec 2021 12:14:06: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:14:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:14:08: #2 number of paired peaks: 224 WARNING @ Wed, 08 Dec 2021 12:14:08: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Wed, 08 Dec 2021 12:14:08: start model_add_line... INFO @ Wed, 08 Dec 2021 12:14:09: start X-correlation... INFO @ Wed, 08 Dec 2021 12:14:09: end of X-cor INFO @ Wed, 08 Dec 2021 12:14:09: #2 finished! INFO @ Wed, 08 Dec 2021 12:14:09: #2 predicted fragment length is 295 bps INFO @ Wed, 08 Dec 2021 12:14:09: #2 alternative fragment length(s) may be 4,280,295 bps INFO @ Wed, 08 Dec 2021 12:14:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.10_model.r INFO @ Wed, 08 Dec 2021 12:14:09: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:14:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 12:14:14: 23000000 INFO @ Wed, 08 Dec 2021 12:14:21: 24000000 INFO @ Wed, 08 Dec 2021 12:14:27: #1 tag size is determined as 49 bps INFO @ Wed, 08 Dec 2021 12:14:27: #1 tag size = 49 INFO @ Wed, 08 Dec 2021 12:14:27: #1 total tags in treatment: 24660929 INFO @ Wed, 08 Dec 2021 12:14:27: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:14:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 12:14:27: #1 tags after filtering in treatment: 24660929 INFO @ Wed, 08 Dec 2021 12:14:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:14:27: #1 finished! INFO @ Wed, 08 Dec 2021 12:14:27: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:14:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:14:29: #2 number of paired peaks: 224 WARNING @ Wed, 08 Dec 2021 12:14:29: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Wed, 08 Dec 2021 12:14:29: start model_add_line... INFO @ Wed, 08 Dec 2021 12:14:29: start X-correlation... INFO @ Wed, 08 Dec 2021 12:14:29: end of X-cor INFO @ Wed, 08 Dec 2021 12:14:29: #2 finished! INFO @ Wed, 08 Dec 2021 12:14:29: #2 predicted fragment length is 295 bps INFO @ Wed, 08 Dec 2021 12:14:29: #2 alternative fragment length(s) may be 4,280,295 bps INFO @ Wed, 08 Dec 2021 12:14:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.20_model.r INFO @ Wed, 08 Dec 2021 12:14:29: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:14:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:14:55: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:15:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.05_peaks.xls INFO @ Wed, 08 Dec 2021 12:15:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:15:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.05_summits.bed INFO @ Wed, 08 Dec 2021 12:15:25: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (14706 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:15:28: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:15:49: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:15:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.10_peaks.xls INFO @ Wed, 08 Dec 2021 12:15:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:15:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.10_summits.bed INFO @ Wed, 08 Dec 2021 12:15:57: Done! pass1 - making usageList (7 chroms): 5 millis pass2 - checking and writing primary data (10906 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:16:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.20_peaks.xls INFO @ Wed, 08 Dec 2021 12:16:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:16:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.20_summits.bed INFO @ Wed, 08 Dec 2021 12:16:17: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (6261 records, 4 fields): 9 millis CompletedMACS2peakCalling