Job ID = 10165897 SRX = SRX6799184 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: 00:08:29 37933523 reads; of these: 37933523 (100.00%) were unpaired; of these: 2476163 (6.53%) aligned 0 times 28320651 (74.66%) aligned exactly 1 time 7136709 (18.81%) aligned >1 times 93.47% overall alignment rate Time searching: 00:08:29 Overall time: 00:08:29 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] 10796035 / 35457360 = 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:22:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 @ Thu, 08 Oct 2020 20:22:32: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:22:32: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:22:38: 1000000 INFO @ Thu, 08 Oct 2020 20:22:44: 2000000 INFO @ Thu, 08 Oct 2020 20:22:51: 3000000 INFO @ Thu, 08 Oct 2020 20:22:57: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:23:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 @ Thu, 08 Oct 2020 20:23:02: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:23:02: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:23:03: 5000000 INFO @ Thu, 08 Oct 2020 20:23:09: 1000000 INFO @ Thu, 08 Oct 2020 20:23:09: 6000000 INFO @ Thu, 08 Oct 2020 20:23:15: 2000000 INFO @ Thu, 08 Oct 2020 20:23:16: 7000000 INFO @ Thu, 08 Oct 2020 20:23:22: 3000000 INFO @ Thu, 08 Oct 2020 20:23:23: 8000000 INFO @ Thu, 08 Oct 2020 20:23:29: 4000000 INFO @ Thu, 08 Oct 2020 20:23:30: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:23:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 @ Thu, 08 Oct 2020 20:23:32: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:23:32: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:23:36: 5000000 INFO @ Thu, 08 Oct 2020 20:23:37: 10000000 INFO @ Thu, 08 Oct 2020 20:23:39: 1000000 INFO @ Thu, 08 Oct 2020 20:23:43: 6000000 INFO @ Thu, 08 Oct 2020 20:23:43: 11000000 INFO @ Thu, 08 Oct 2020 20:23:45: 2000000 INFO @ Thu, 08 Oct 2020 20:23:49: 7000000 INFO @ Thu, 08 Oct 2020 20:23:50: 12000000 INFO @ Thu, 08 Oct 2020 20:23:52: 3000000 INFO @ Thu, 08 Oct 2020 20:23:56: 8000000 INFO @ Thu, 08 Oct 2020 20:23:57: 13000000 INFO @ Thu, 08 Oct 2020 20:23:59: 4000000 INFO @ Thu, 08 Oct 2020 20:24:03: 9000000 INFO @ Thu, 08 Oct 2020 20:24:04: 14000000 INFO @ Thu, 08 Oct 2020 20:24:05: 5000000 INFO @ Thu, 08 Oct 2020 20:24:10: 10000000 INFO @ Thu, 08 Oct 2020 20:24:11: 15000000 INFO @ Thu, 08 Oct 2020 20:24:12: 6000000 INFO @ Thu, 08 Oct 2020 20:24:16: 11000000 INFO @ Thu, 08 Oct 2020 20:24:17: 16000000 INFO @ Thu, 08 Oct 2020 20:24:19: 7000000 INFO @ Thu, 08 Oct 2020 20:24:23: 12000000 INFO @ Thu, 08 Oct 2020 20:24:24: 17000000 INFO @ Thu, 08 Oct 2020 20:24:25: 8000000 INFO @ Thu, 08 Oct 2020 20:24:30: 13000000 INFO @ Thu, 08 Oct 2020 20:24:31: 18000000 INFO @ Thu, 08 Oct 2020 20:24:32: 9000000 INFO @ Thu, 08 Oct 2020 20:24:37: 14000000 INFO @ Thu, 08 Oct 2020 20:24:38: 19000000 INFO @ Thu, 08 Oct 2020 20:24:39: 10000000 INFO @ Thu, 08 Oct 2020 20:24:43: 15000000 INFO @ Thu, 08 Oct 2020 20:24:44: 20000000 INFO @ Thu, 08 Oct 2020 20:24:46: 11000000 INFO @ Thu, 08 Oct 2020 20:24:50: 16000000 INFO @ Thu, 08 Oct 2020 20:24:51: 21000000 INFO @ Thu, 08 Oct 2020 20:24:53: 12000000 INFO @ Thu, 08 Oct 2020 20:24:57: 17000000 INFO @ Thu, 08 Oct 2020 20:24:58: 22000000 INFO @ Thu, 08 Oct 2020 20:24:59: 13000000 INFO @ Thu, 08 Oct 2020 20:25:04: 18000000 INFO @ Thu, 08 Oct 2020 20:25:05: 23000000 INFO @ Thu, 08 Oct 2020 20:25:06: 14000000 INFO @ Thu, 08 Oct 2020 20:25:10: 19000000 INFO @ Thu, 08 Oct 2020 20:25:12: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:25:13: 15000000 INFO @ Thu, 08 Oct 2020 20:25:16: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 20:25:16: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 20:25:16: #1 total tags in treatment: 24661325 INFO @ Thu, 08 Oct 2020 20:25:16: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:25:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:25:16: #1 tags after filtering in treatment: 24661325 INFO @ Thu, 08 Oct 2020 20:25:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:25:16: #1 finished! INFO @ Thu, 08 Oct 2020 20:25:16: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:25:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:25:17: 20000000 INFO @ Thu, 08 Oct 2020 20:25:18: #2 number of paired peaks: 224 WARNING @ Thu, 08 Oct 2020 20:25:18: 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 @ Thu, 08 Oct 2020 20:25:18: start model_add_line... INFO @ Thu, 08 Oct 2020 20:25:18: start X-correlation... INFO @ Thu, 08 Oct 2020 20:25:18: end of X-cor INFO @ Thu, 08 Oct 2020 20:25:18: #2 finished! INFO @ Thu, 08 Oct 2020 20:25:18: #2 predicted fragment length is 296 bps INFO @ Thu, 08 Oct 2020 20:25:18: #2 alternative fragment length(s) may be 4,278,296 bps INFO @ Thu, 08 Oct 2020 20:25:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.05_model.r INFO @ Thu, 08 Oct 2020 20:25:18: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:25:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:25:19: 16000000 INFO @ Thu, 08 Oct 2020 20:25:24: 21000000 INFO @ Thu, 08 Oct 2020 20:25:26: 17000000 INFO @ Thu, 08 Oct 2020 20:25:31: 22000000 INFO @ Thu, 08 Oct 2020 20:25:33: 18000000 INFO @ Thu, 08 Oct 2020 20:25:38: 23000000 INFO @ Thu, 08 Oct 2020 20:25:39: 19000000 INFO @ Thu, 08 Oct 2020 20:25:44: 24000000 INFO @ Thu, 08 Oct 2020 20:25:46: 20000000 INFO @ Thu, 08 Oct 2020 20:25:49: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 20:25:49: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 20:25:49: #1 total tags in treatment: 24661325 INFO @ Thu, 08 Oct 2020 20:25:49: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:25:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:25:49: #1 tags after filtering in treatment: 24661325 INFO @ Thu, 08 Oct 2020 20:25:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:25:49: #1 finished! INFO @ Thu, 08 Oct 2020 20:25:49: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:25:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:25:51: #2 number of paired peaks: 224 WARNING @ Thu, 08 Oct 2020 20:25:51: 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 @ Thu, 08 Oct 2020 20:25:51: start model_add_line... INFO @ Thu, 08 Oct 2020 20:25:51: start X-correlation... INFO @ Thu, 08 Oct 2020 20:25:51: end of X-cor INFO @ Thu, 08 Oct 2020 20:25:51: #2 finished! INFO @ Thu, 08 Oct 2020 20:25:51: #2 predicted fragment length is 296 bps INFO @ Thu, 08 Oct 2020 20:25:51: #2 alternative fragment length(s) may be 4,278,296 bps INFO @ Thu, 08 Oct 2020 20:25:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.10_model.r INFO @ Thu, 08 Oct 2020 20:25:51: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:25:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:25:52: 21000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:25:58: 22000000 INFO @ Thu, 08 Oct 2020 20:26:04: 23000000 INFO @ Thu, 08 Oct 2020 20:26:10: 24000000 INFO @ Thu, 08 Oct 2020 20:26:14: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 20:26:14: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 20:26:14: #1 total tags in treatment: 24661325 INFO @ Thu, 08 Oct 2020 20:26:14: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:26:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:26:14: #1 tags after filtering in treatment: 24661325 INFO @ Thu, 08 Oct 2020 20:26:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:26:14: #1 finished! INFO @ Thu, 08 Oct 2020 20:26:14: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:26:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:26:16: #2 number of paired peaks: 224 WARNING @ Thu, 08 Oct 2020 20:26:16: 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 @ Thu, 08 Oct 2020 20:26:16: start model_add_line... INFO @ Thu, 08 Oct 2020 20:26:16: start X-correlation... INFO @ Thu, 08 Oct 2020 20:26:16: end of X-cor INFO @ Thu, 08 Oct 2020 20:26:16: #2 finished! INFO @ Thu, 08 Oct 2020 20:26:16: #2 predicted fragment length is 296 bps INFO @ Thu, 08 Oct 2020 20:26:16: #2 alternative fragment length(s) may be 4,278,296 bps INFO @ Thu, 08 Oct 2020 20:26:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.20_model.r INFO @ Thu, 08 Oct 2020 20:26:16: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:26:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:26:22: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:26:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:26:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:26:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.05_summits.bed INFO @ Thu, 08 Oct 2020 20:26:49: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (14720 records, 4 fields): 120 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:26:53: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:27:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:27:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:27:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.10_summits.bed INFO @ Thu, 08 Oct 2020 20:27:18: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (10909 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:27:19: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:27:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:27:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:27:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.20_summits.bed INFO @ Thu, 08 Oct 2020 20:27:45: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6229 records, 4 fields): 8 millis CompletedMACS2peakCalling