Job ID = 14158046 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: 00:07:42 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: 00:07:42 Overall time: 00:07:42 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 14:15:25: # 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 @ Wed, 08 Dec 2021 14:15:25: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:15:25: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:15:32: 1000000 INFO @ Wed, 08 Dec 2021 14:15:38: 2000000 INFO @ Wed, 08 Dec 2021 14:15:45: 3000000 INFO @ Wed, 08 Dec 2021 14:15:51: 4000000 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 14:15:55: # 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 @ Wed, 08 Dec 2021 14:15:55: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:15:55: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:15:58: 5000000 INFO @ Wed, 08 Dec 2021 14:16:02: 1000000 INFO @ Wed, 08 Dec 2021 14:16:05: 6000000 INFO @ Wed, 08 Dec 2021 14:16:08: 2000000 INFO @ Wed, 08 Dec 2021 14:16:12: 7000000 INFO @ Wed, 08 Dec 2021 14:16:14: 3000000 INFO @ Wed, 08 Dec 2021 14:16:20: 8000000 INFO @ Wed, 08 Dec 2021 14:16:21: 4000000 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 14:16:25: # 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 @ Wed, 08 Dec 2021 14:16:25: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:16:25: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:16:27: 9000000 INFO @ Wed, 08 Dec 2021 14:16:27: 5000000 INFO @ Wed, 08 Dec 2021 14:16:32: 1000000 INFO @ Wed, 08 Dec 2021 14:16:34: 6000000 INFO @ Wed, 08 Dec 2021 14:16:34: 10000000 INFO @ Wed, 08 Dec 2021 14:16:38: 2000000 INFO @ Wed, 08 Dec 2021 14:16:41: 7000000 INFO @ Wed, 08 Dec 2021 14:16:41: 11000000 INFO @ Wed, 08 Dec 2021 14:16:45: 3000000 INFO @ Wed, 08 Dec 2021 14:16:47: 8000000 INFO @ Wed, 08 Dec 2021 14:16:48: 12000000 INFO @ Wed, 08 Dec 2021 14:16:52: 4000000 INFO @ Wed, 08 Dec 2021 14:16:54: 9000000 INFO @ Wed, 08 Dec 2021 14:16:56: 13000000 INFO @ Wed, 08 Dec 2021 14:16:58: 5000000 INFO @ Wed, 08 Dec 2021 14:17:01: 10000000 INFO @ Wed, 08 Dec 2021 14:17:03: 14000000 INFO @ Wed, 08 Dec 2021 14:17:05: 6000000 INFO @ Wed, 08 Dec 2021 14:17:07: 11000000 INFO @ Wed, 08 Dec 2021 14:17:10: 15000000 INFO @ Wed, 08 Dec 2021 14:17:12: 7000000 INFO @ Wed, 08 Dec 2021 14:17:14: 12000000 INFO @ Wed, 08 Dec 2021 14:17:17: 16000000 INFO @ Wed, 08 Dec 2021 14:17:18: 8000000 INFO @ Wed, 08 Dec 2021 14:17:20: 13000000 INFO @ Wed, 08 Dec 2021 14:17:24: 17000000 INFO @ Wed, 08 Dec 2021 14:17:25: 9000000 INFO @ Wed, 08 Dec 2021 14:17:27: 14000000 INFO @ Wed, 08 Dec 2021 14:17:31: 10000000 INFO @ Wed, 08 Dec 2021 14:17:31: 18000000 INFO @ Wed, 08 Dec 2021 14:17:34: 15000000 INFO @ Wed, 08 Dec 2021 14:17:38: 11000000 INFO @ Wed, 08 Dec 2021 14:17:39: 19000000 INFO @ Wed, 08 Dec 2021 14:17:40: 16000000 INFO @ Wed, 08 Dec 2021 14:17:44: 12000000 INFO @ Wed, 08 Dec 2021 14:17:46: 20000000 INFO @ Wed, 08 Dec 2021 14:17:47: 17000000 INFO @ Wed, 08 Dec 2021 14:17:51: 13000000 INFO @ Wed, 08 Dec 2021 14:17:53: 21000000 INFO @ Wed, 08 Dec 2021 14:17:54: 18000000 INFO @ Wed, 08 Dec 2021 14:17:58: 14000000 INFO @ Wed, 08 Dec 2021 14:18:00: 22000000 INFO @ Wed, 08 Dec 2021 14:18:01: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:18:05: 15000000 INFO @ Wed, 08 Dec 2021 14:18:07: 23000000 INFO @ Wed, 08 Dec 2021 14:18:07: 20000000 INFO @ Wed, 08 Dec 2021 14:18:11: 16000000 INFO @ Wed, 08 Dec 2021 14:18:14: 21000000 INFO @ Wed, 08 Dec 2021 14:18:14: 24000000 INFO @ Wed, 08 Dec 2021 14:18:18: 17000000 INFO @ Wed, 08 Dec 2021 14:18:19: #1 tag size is determined as 49 bps INFO @ Wed, 08 Dec 2021 14:18:19: #1 tag size = 49 INFO @ Wed, 08 Dec 2021 14:18:19: #1 total tags in treatment: 24661325 INFO @ Wed, 08 Dec 2021 14:18:19: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:18:19: #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 14:18:19: #1 tags after filtering in treatment: 24661325 INFO @ Wed, 08 Dec 2021 14:18:19: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:18:19: #1 finished! INFO @ Wed, 08 Dec 2021 14:18:19: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:18:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:18:21: 22000000 INFO @ Wed, 08 Dec 2021 14:18:21: #2 number of paired peaks: 224 WARNING @ Wed, 08 Dec 2021 14:18:21: 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 14:18:21: start model_add_line... INFO @ Wed, 08 Dec 2021 14:18:21: start X-correlation... INFO @ Wed, 08 Dec 2021 14:18:21: end of X-cor INFO @ Wed, 08 Dec 2021 14:18:21: #2 finished! INFO @ Wed, 08 Dec 2021 14:18:21: #2 predicted fragment length is 296 bps INFO @ Wed, 08 Dec 2021 14:18:21: #2 alternative fragment length(s) may be 4,278,296 bps INFO @ Wed, 08 Dec 2021 14:18:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.05_model.r INFO @ Wed, 08 Dec 2021 14:18:21: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:18:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:18:24: 18000000 INFO @ Wed, 08 Dec 2021 14:18:27: 23000000 INFO @ Wed, 08 Dec 2021 14:18:30: 19000000 INFO @ Wed, 08 Dec 2021 14:18:33: 24000000 INFO @ Wed, 08 Dec 2021 14:18:37: 20000000 INFO @ Wed, 08 Dec 2021 14:18:37: #1 tag size is determined as 49 bps INFO @ Wed, 08 Dec 2021 14:18:37: #1 tag size = 49 INFO @ Wed, 08 Dec 2021 14:18:37: #1 total tags in treatment: 24661325 INFO @ Wed, 08 Dec 2021 14:18:37: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:18:37: #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 14:18:37: #1 tags after filtering in treatment: 24661325 INFO @ Wed, 08 Dec 2021 14:18:37: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:18:37: #1 finished! INFO @ Wed, 08 Dec 2021 14:18:37: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:18:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:18:39: #2 number of paired peaks: 224 WARNING @ Wed, 08 Dec 2021 14:18:39: 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 14:18:39: start model_add_line... INFO @ Wed, 08 Dec 2021 14:18:39: start X-correlation... INFO @ Wed, 08 Dec 2021 14:18:39: end of X-cor INFO @ Wed, 08 Dec 2021 14:18:39: #2 finished! INFO @ Wed, 08 Dec 2021 14:18:39: #2 predicted fragment length is 296 bps INFO @ Wed, 08 Dec 2021 14:18:39: #2 alternative fragment length(s) may be 4,278,296 bps INFO @ Wed, 08 Dec 2021 14:18:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.10_model.r INFO @ Wed, 08 Dec 2021 14:18:39: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:18:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:18:42: 21000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:18:47: 22000000 INFO @ Wed, 08 Dec 2021 14:18:53: 23000000 INFO @ Wed, 08 Dec 2021 14:18:58: 24000000 INFO @ Wed, 08 Dec 2021 14:19:01: #1 tag size is determined as 49 bps INFO @ Wed, 08 Dec 2021 14:19:01: #1 tag size = 49 INFO @ Wed, 08 Dec 2021 14:19:01: #1 total tags in treatment: 24661325 INFO @ Wed, 08 Dec 2021 14:19:01: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:19:01: #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 14:19:02: #1 tags after filtering in treatment: 24661325 INFO @ Wed, 08 Dec 2021 14:19:02: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:19:02: #1 finished! INFO @ Wed, 08 Dec 2021 14:19:02: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:19:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:19:03: #2 number of paired peaks: 224 WARNING @ Wed, 08 Dec 2021 14:19:03: 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 14:19:03: start model_add_line... INFO @ Wed, 08 Dec 2021 14:19:03: start X-correlation... INFO @ Wed, 08 Dec 2021 14:19:03: end of X-cor INFO @ Wed, 08 Dec 2021 14:19:03: #2 finished! INFO @ Wed, 08 Dec 2021 14:19:03: #2 predicted fragment length is 296 bps INFO @ Wed, 08 Dec 2021 14:19:03: #2 alternative fragment length(s) may be 4,278,296 bps INFO @ Wed, 08 Dec 2021 14:19:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.20_model.r INFO @ Wed, 08 Dec 2021 14:19:03: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:19:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:19:20: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:19:39: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:19:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:19:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:19:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.05_summits.bed INFO @ Wed, 08 Dec 2021 14:19:42: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (14720 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:20:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:20:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:20:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.10_summits.bed INFO @ Wed, 08 Dec 2021 14:20:03: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (10909 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:20:04: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:20:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:20:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:20:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799184/SRX6799184.20_summits.bed INFO @ Wed, 08 Dec 2021 14:20:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6229 records, 4 fields): 7 millis CompletedMACS2peakCalling